Canonical structures for the hypervariable regions of immunoglobulins
Abstract
We have analysed the atomic structures of Fab and VL fragments of immunoglobulins to determine the relationship between their amino acid sequences and the three-dimensional structures of their antigen binding sites. We identify the relatively few residues that, through their packing, hydrogen bonding or the ability to assume unusual phi, psi or omega conformations, are primarily responsible for the main-chain conformations of the hypervariable regions. These residues are found to occur at sites within the hypervariable regions and in the conserved beta-sheet framework. Examination of the sequences of immunoglobulins of unknown structure shows that many have hypervariable regions that are similar in size to one of the known structures and contain identical residues at the sites responsible for the observed conformation. This implies that these hypervariable regions have conformations close to those in the known structures. For five of the hypervariable regions, the repertoire of conformations appears to be limited to a relatively small number of discrete structural classes. We call the commonly occurring main-chain conformations of the hypervariable regions "canonical structures". The accuracy of the analysis is being tested and refined by the prediction of immunoglobulin structures prior to their experimental determination.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
Despite the intrinsic sequence diversity in the CDRs, all hypervariable loops with the exception of CDRH3 adopt a constrained set of conformations termed canonical classes.
“Despite the intrinsic sequence diversity in the CDRs, all hypervariable loops with the exception of CDRH3 adopt a constrained set of conformations termed canonical classes [32].”
From Computational approaches to therapeutic antibody design: established methods and emerging trends (2020) · cites this paper as [32]
Kabat and IMGT definitions are based on sequence alignments identifying conserved positions in the variable region whereas Chothia takes into account the 3D structure of the CDR loops.
“Kabat and IMGT definitions are based on sequence alignments identifying conserved positions in the variable region [152, 153] whereas Chothia takes into account the 3D structure of the CDR loops.”
From Computational approaches to therapeutic antibody design: established methods and emerging trends (2020) · cites this paper as [32]
Since the seminal work to define a standard numbering scheme for antibodies was carried out by Kabat in 1970, the Chothia and IMGT schemes have been adopted as the main alternatives.
“Since the seminal work to define a standard numbering scheme for antibodies was carried out by Kabat in 1970 [152], the Chothia [32] and IMGT [153] schemes have been adopted as the main alternatives.”
From Computational approaches to therapeutic antibody design: established methods and emerging trends (2020) · cites this paper as [32]
Cites
The protein data bank: A computer-based archival file for macromolecular structures
Bernstein, F. C., Koetzle, T. F., Williams, G. J. B., Meyer, E. F., Brice, M. D., Rodgers, J. R., Kennard, O., Shimanouchi, T., & Tasumi, M. (1977) · Journal of Molecular Biology · doi:10.1016/s0022-2836(77)80200-3 · Cited by 8,582 · see citing works
The interpretation of protein structures: Estimation of static accessibility
Lee, B., & Richards, F. M. (1971) · Journal of Molecular Biology · doi:10.1016/0022-2836(71)90324-x · Cited by 5,884 · see citing works
Somatic generation of antibody diversity
Tonegawa, S. (1983) · Nature · doi:10.1038/302575a0 · Cited by 4,005 · see citing works
Sequences of proteins of immunological interest
Kabat, B. E. A. (1984) · Analytical Biochemistry · doi:10.1016/0003-2697(84)90805-4 · Cited by 3,387 · see citing works
Somatic generation of antibody diversity.
Matthyssens, G., Hozumi, N., & Tonegawa, S. (1976) · PubMed · Cited by 3,237 · see citing works
Three-Dimensional Structure of an Antigen-Antibody Complex at 2.8 Å Resolution
Amit, A. G., Mariuzza, R. A., Phillips, S. E. V., & Poljak, R. J. (1986) · Science · doi:10.1126/science.2426778 · Cited by 1,183 · see citing works
Principles of protein–protein recognition
Chothia, C., & Janin, J. (1975) · Nature · doi:10.1038/256705a0 · Cited by 1,014 · see citing works
Self-citationRavetch, J. V., Siebenlist, U. K., Korsmeyer, S. J., et al. (1981) · Cell · doi:10.1016/0092-8674(81)90400-1 · Cited by 939 · see citing works
Sakano, H., Maki, R. A., Kurosawa, Y., et al. (1980) · Nature · doi:10.1038/286676a0 · Cited by 802 · see citing works
Three-Dimensional Structure of Immunoglobulins
Amzel, L. M., & Poljak, R. J. (1979) · Annual Review of Biochemistry · doi:10.1146/annurev.bi.48.070179.004525 · Cited by 697 · see citing works
β-Hairpin families in globular proteins
Sibanda, B. L., & Thornton, J. M. (1985) · Nature · doi:10.1038/316170a0 · Cited by 540 · see citing works
Marquart, M., Deisenhofer, J., Huber, R., & Palm, W. (1980) · Journal of Molecular Biology · doi:10.1016/0022-2836(80)90252-1 · Cited by 457 · see citing works
Domain association in immunoglobulin molecules
Chothia, C., Novotný, J., Bruccoleri, R. E., & Karplus, M. (1985) · Journal of Molecular Biology · doi:10.1016/0022-2836(85)90137-8 · Cited by 396 · see citing works
Self-citationStructural Basis of Antibody Function
Davies, D. R., & Metzger, H. (1983) · Annual Review of Immunology · doi:10.1146/annurev.iy.01.040183.000511 · Cited by 375 · see citing works
Structure of a λ-type Bence-Jones protein at 3.5-Å resolution
Schiffer, M., Girling, R. L., Ely, K. R., et al. (1973) · Biochemistry · doi:10.1021/bi00747a013 · Cited by 356 · see citing works
Saul, F. A., Amzel, L. M., & Poljak, R. J. (1978) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(17)38249-2 · Cited by 292 · see citing works
Evolution of proteins formed by β-sheets
Lesk, A. M., & Chothia, C. (1982) · Journal of Molecular Biology · doi:10.1016/0022-2836(82)90179-6 · Cited by 274 · see citing works
Self-citationEpp, O., Lattman, E. E., Schiffer, M., et al. (1975) · Biochemistry · doi:10.1021/bi00693a025 · Cited by 263 · see citing works
The Predicted Structure of Immunoglobulin D1.3 and Its Comparison with the Crystal Structure
Chothia, C., Lesk, A. M., Levitt, M., et al. (1986) · Science · doi:10.1126/science.3090684 · Cited by 204 · see citing works
Self-citationKabat, E. A., Wu, T. T., & Bilofsky, H. S. (1977) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(17)39891-5 · Cited by 199 · see citing works
The galactan‐binding immunoglobulin Fab J539: An x‐ray diffraction study at 2.6‐Å resolution
Suh, S. W., Bhat, T. N., Navia, M. A., et al. (1986) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.340010112 · Cited by 173 · see citing works
Structure of a novel bence-jones protein (Rhe) fragment at 1·6 Å resolution
Furey, W. S., Wang, B. C., Yoo, C. S., Sax, M., & Huber, R. (1983) · Journal of Molecular Biology · doi:10.1016/s0022-2836(83)80104-1 · Cited by 117 · see citing works
de la Paz, P., Sutton, B. J., Darsley, M. J., et al. (1986) · The EMBO Journal · doi:10.1002/j.1460-2075.1986.tb04227.x · Cited by 110 · see citing works
Antibodies in human diagnosis and therapy
Haber, E., & Krause, R. M. (1977) · Raven Press eBooks · Cited by 103 · see citing works
The response of protein structures to amino-acid sequence changes
Lesk, A. M., & Chothia, C. (1986) · Philosophical Transactions of the Royal Society of London Series A Mathematical and Physical Sciences · doi:10.1098/rsta.1986.0044 · Cited by 100 · see citing works
Self-citationThe Structural Basis for Antibody Complementary
Kabat, E. A. (1978) · Advances in protein chemistry · doi:10.1016/s0065-3233(08)60574-4 · Cited by 100 · see citing works
PADLAN, E. A. (1977) · Quarterly Reviews of Biophysics · doi:10.1017/s0033583500000135 · Cited by 96 · see citing works
The three-dimensional structure of antibodies
Marquart, M., & Deisenhofer, J. (1982) · Immunology Today · doi:10.1016/0167-5699(82)90107-4 · Cited by 74 · see citing works
Feldmann, R. J., POTTER, M., & Glaudemans, C. P. J. (1981) · Molecular Immunology · doi:10.1016/0161-5890(81)90060-2 · Cited by 57 · see citing works
The structure determination of the variable portion of the Bence-Jones protein Au
Fehlhammer, H., Schiffer, M., Epp, O., et al. (1975) · European Biophysics Journal · doi:10.1007/bf00539775 · Cited by 56 · see citing works
Crystal and molecular structure of the dimer of variable domains of the Bence-Jones protein ROY
Colman, P. M., Schramm, H. J., & Guss, J. M. (1977) · Journal of Molecular Biology · doi:10.1016/0022-2836(77)90119-x · Cited by 36 · see citing works
Stanford, J. M., & Wu, T. T. (1981) · Journal of Theoretical Biology · doi:10.1016/0022-5193(81)90275-7 · Cited by 28 · see citing works
Laver, W. G., Webster, R. G., & Colman, P. M. (1987) · Virology · doi:10.1016/0042-6822(87)90451-x · Cited by 25 · see citing works
Poljak, R. J., Amzel, L. M., Chen, B. L., et al. (1975) · Immunogenetics · doi:10.1007/bf01572309 · Cited by 24 · see citing works
Investigation and Exploitation of Antibody Combining Sites
Reid, E., Cook, G. M., & Morré, D. J. (1985) · Springer eBooks · doi:10.1007/978-1-4684-5006-4 · Cited by 19 · see citing works
Mariuzza, R. A., Boulot, G., Guillon, V., et al. (1985) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(17)39241-4 · Cited by 17 · see citing works
Stura, E. A., Feinstein, A., & Wilson, I. A. (1987) · Journal of Molecular Biology · doi:10.1016/0022-2836(87)90642-5 · Cited by 16 · see citing works
Evaluation of the structural variation among light chain variable domains
PADLAN, E. A. (1979) · Molecular Immunology · doi:10.1016/0161-5890(79)90128-7 · Cited by 11 · see citing works
Possible distortion of antibody binding site of the Mcg bence-jones protein by lattice forces
Schiffer, M. (1980) · Biophysical Journal · doi:10.1016/s0006-3495(80)84943-5 · Cited by 3 · see citing works
Flagged first, then by citations
Cited by
Sorted by citations
T-cell antigen receptor genes and T-cell recognition
Davis, M. M., & Bjorkman, P. J. (1988) · Nature · doi:10.1038/334395a0 · Cited by 3,202 · see citing works
Comparative Protein Structure Modeling of Genes and Genomes
Martí-Renom, M. A., Stuart, A. C., Fiser, A., Sánchez, R., Melo, F., & Šali, A. (2000) · Annual Review of Biophysics and Biomolecular Structure · doi:10.1146/annurev.biophys.29.1.291 · Cited by 3,169 · see citing works
Diversity in the CDR3 Region of VH Is Sufficient for Most Antibody Specificities
Xu, J. L., & Davis, M. M. (2000) · Immunity · doi:10.1016/s1074-7613(00)00006-6 · Cited by 779 · see citing works
Knappik, A., Ge, L., Honegger, A., Pack, P., Fischer, M., Wellnhofer, G., Hoess, A., Wölle, J., Plückthun, A., & Virnekäs, B. (2000) · Journal of Molecular Biology · doi:10.1006/jmbi.1999.3444 · Cited by 728 · see citing works
Comparative protein structure modeling using MODELLER
Webb, B., & Sali, A. (2016) · Current Protocols in Protein Science · doi:10.1002/cpps.20 · Cited by 730 · see citing works
“…search approaches that scan a database of all known protein structures to find segments fitting the anchor core regions (Jones and Thirup, 1986; Chothia and Lesk, 1987); (ii) conformational search approaches that rely on optimizing a scoring function (Moult and James, 1986; Bruccoleri and…”
BackgroundMethodSAbDab: the structural antibody database
Dunbar, J., Krawczyk, K., Leem, J., Baker, T., Fuchs, A., Georges, G., Shi, J., & Deane, C. M. (2014) · Nucleic Acids Research · doi:10.1093/nar/gkt1043 · Cited by 674 · see citing works
The structural basis of antibody–antigen recognition
Sela-Culang, I., Kunik, V., & Ofran, Y. (2013) · Frontiers in Immunology · doi:10.3389/fimmu.2013.00302 · Cited by 530 · see citing works
IEDB-AR: immune epitope database-analysis resource in 2019
Dhanda, S. K., Mahajan, S., Paul, S., Yan, Z., Kim, H., Jespersen, M. C., Jurtz, V., Andreatta, M., Greenbaum, J. A., Marcatili, P., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz452 · Cited by 427 · see citing works
A new clustering of antibody CDR loop conformations
North, B., Lehmann, A., & Dunbrack, R. L. (2011) · Journal of Molecular Biology · doi:10.1016/j.jmb.2010.10.030 · Cited by 380 · see citing works
Five computational developability guidelines for therapeutic antibody profiling
Raybould, M. I. J., Marks, C., Krawczyk, K., Taddese, B., Nowak, J., Lewis, A. P., Bujotzek, A., Shi, J., & Deane, C. M. (2019) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1810576116 · Cited by 357 · see citing works
ABodyBuilder: automated antibody structure prediction with data-driven accuracy estimation
Leem, J., Dunbar, J., Georges, G., Shi, J., & Deane, C. M. (2016) · mAbs · doi:10.1080/19420862.2016.1205773 · Cited by 238 · see citing works
RosettaAntibodyDesign (RAbD): a general framework for computational antibody design
Adolf-Bryfogle, J., Kalyuzhniy, O., Kubitz, M., Weitzner, B. D., Hu, X., Adachi, Y., Schief, W. R., & Dunbrack, R. L. (2018) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1006112 · Cited by 227 · see citing works
Computational approaches to therapeutic antibody design: established methods and emerging trends
Norman, R. A., Ambrosetti, F., Bonvin, A. M. J. J., Colwell, L. J., Kelm, S., Kumar, S., & Krawczyk, K. (2020) · Briefings in Bioinformatics · doi:10.1093/bib/bbz095 · Cited by 219 · see citing works
“Despite the intrinsic sequence diversity in the CDRs, all hypervariable loops with the exception of CDRH3 adopt a constrained set of conformations termed canonical classes [32].”
BackgroundMethodInfluentialAntibody structure prediction using interpretable deep learning
Ruffolo, J. A., Sulam, J., & Gray, J. J. (2022) · Patterns · doi:10.1016/j.patter.2021.100406 · Cited by 216 · see citing works
Prediction of aggregation prone regions of therapeutic proteins
Chennamsetty, N., Voynov, V., Kayser, V., Helk, B., & Trout, B. L. (2010) · The Journal of Physical Chemistry B · doi:10.1021/jp911706q · Cited by 200 · see citing works
<scp>AB</scp> ‐Bind: Antibody binding mutational database for computational affinity predictions
Sirin, S., Apgar, J. R., Bennett, E. M., & Keating, A. E. (2016) · Protein Science · doi:10.1002/pro.2829 · Cited by 179 · see citing works
Second antibody modeling assessment (AMA-II)
Almagro, J. C., Teplyakov, A., Luo, J., Sweet, R. W., Kodangattil, S., Hernandez‐Guzman, F., & Gilliland, G. L. (2014) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.24567 · Cited by 144 · see citing works
Kunik, V., Ashkenazi, S., & Ofran, Y. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks480 · Cited by 132 · see citing works
Almagro, J. C., Beavers, M. P., Hernandez‐Guzman, F., Maier, J., Shaulsky, J., Butenhof, K., Labute, P., Thorsteinson, N., Kelly, K., Teplyakov, A., et al. (2011) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.23130 · Cited by 131 · see citing works
ABangle: characterising the VH-VL orientation in antibodies
Dunbar, J., Fuchs, A., Shi, J., & Deane, C. M. (2013) · Protein Engineering Design and Selection · doi:10.1093/protein/gzt020 · Cited by 125 · see citing works
Structural consensus among antibodies defines the antigen binding site
Kunik, V., Peters, B., & Ofran, Y. (2012) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002388 · Cited by 117 · see citing works
Lapidoth, G. D., Baran, D., Pszolla, G. M., Norn, C., Alon, A., Tyka, M. D., & Fleishman, S. J. (2015) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.24779 · Cited by 107 · see citing works
Dondelinger, M., Filée, P., Sauvage, E., Quinting, B., Muyldermans, S., Galleni, M., & Vandevenne, M. S. (2018) · Frontiers in Immunology · doi:10.3389/fimmu.2018.02278 · Cited by 107 · see citing works
The H3 loop of antibodies shows unique structural characteristics
Regep, C., Georges, G., Shi, J., Popovic, B., & Deane, C. M. (2017) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.25291 · Cited by 99 · see citing works
Pantazes, R. J., & Maranas, C. D. (2010) · Protein Engineering Design and Selection · doi:10.1093/protein/gzq061 · Cited by 97 · see citing works
Kunik, V., & Ofran, Y. (2013) · Protein Engineering Design and Selection · doi:10.1093/protein/gzt027 · Cited by 96 · see citing works
Prediction of site-specific interactions in antibody–antigen complexes: the proABC method and server
Olimpieri, P. P., Chailyan, A., Tramontano, A., & Marcatili, P. (2013) · Bioinformatics · doi:10.1093/bioinformatics/btt369 · Cited by 90 · see citing works
Antibody interface prediction with 3D Zernike descriptors and SVM
Daberdaku, S., & Ferrari, C. (2019) · Bioinformatics · doi:10.1093/bioinformatics/bty918 · Cited by 88 · see citing works
Tsuchiya, Y., & Mizuguchi, K. (2016) · Protein Science · doi:10.1002/pro.2874 · Cited by 86 · see citing works
Antibody modeling assessment II. Structures and models
Teplyakov, A., Luo, J., Obmolova, G., Malia, T. J., Sweet, R., Stanfield, R. L., Kodangattil, S., Almagro, J. C., & Gilliland, G. L. (2014) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.24554 · Cited by 72 · see citing works
Antibody H3 structure prediction
Marks, C., & Deane, C. M. (2017) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2017.01.010 · Cited by 56 · see citing works
Prediction of VH-VL domain orientation for antibody variable domain modeling
Bujotzek, A., Dunbar, J., Lipsmeier, F., Schäfer, W., Antes, I., Deane, C. M., & Georges, G. (2015) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.24756 · Cited by 56 · see citing works
Sphinx: merging knowledge-based and<i>ab initio</i>approaches to improve protein loop prediction
Marks, C., Nowak, J., Klostermann, S., Georges, G., Dunbar, J., Shi, J., Kelm, S., & Deane, C. M. (2017) · Bioinformatics · doi:10.1093/bioinformatics/btw823 · Cited by 56 · see citing works
Shirai, H., Ikeda, K., Yamashita, K., Tsuchiya, Y., Sarmiento, J., Liang, S., Morokata, T., Mizuguchi, K., Higo, J., Standley, D. M., et al. (2014) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.24591 · Cited by 51 · see citing works
Structurally mapping antibody repertoires
Krawczyk, K., Kelm, S., Kovaltsuk, A., Galson, J. D., Kelly, D., Trück, J., Regep, C., Leem, J., Wong, W. K., Nowak, J., et al. (2018) · Frontiers in Immunology · doi:10.3389/fimmu.2018.01698 · Cited by 42 · see citing works
Molecular basis for the mechanism of action of an anti‐TACE antibody
Peng, L., Cook, K., Xu, L., Cheng, L., Damschroder, M., Gao, C., Wu, H., & Dall'Acqua, W. F. (2016) · mAbs · doi:10.1080/19420862.2016.1226716 · Cited by 30 · see citing works
“CDRs are shown in bold and underlined according to Chothia definition.(29) (B) Modeled 3-dimensional structure of MEDI3622 variable domains, with VH in orange and VL in beige.”
BackgroundAntibody affinity maturation by computational design
Kuroda, D., & Tsumoto, K. (2018) · Methods in molecular biology · doi:10.1007/978-1-4939-8648-4_2 · Cited by 26 · see citing works
Computational tools for aiding rational antibody design
Krawczyk, K., Dunbar, J., & Deane, C. M. (2017) · Methods in molecular biology · doi:10.1007/978-1-4939-6637-0_21 · Cited by 26 · see citing works
Antibody side chain conformations are position-dependent
Leem, J., Georges, G., Shi, J., & Deane, C. M. (2018) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.25453 · Cited by 22 · see citing works
- Authors
- Chothia, C., & Lesk, A. M.
- Affiliations
- MRC Laboratory of Molecular Biology (GB)
- ORCID
- Lesk, Arthur M.
- Venue
- Journal of Molecular Biology
- Publisher
- Elsevier BV
- Published
- 1987-08
- Volume
- 196
- Issue
- 4
- Pages
- 901-917
- ISSN
- 0022-2836 (ISSN-L)
- OpenAlex
- W1982679430
- Cited by
- 1,406
- References
- 39
- Citations by year
- 2026: 35 · 2025: 37 · 2024: 37 · 2023: 35 · 2022: 32 · 2021: 31 · 2020: 33 · 2019: 38 · 2018: 30 · 2017: 30 · 2016: 29 · 2015: 29 · 2014: 55 · 2013: 33 · 2012: 31
- FWCI
- 5.23
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Journal of Molecular Biology (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Institute of General Medical Sciences (GM25435)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
- Health Sciences › Medicine › Radiology, Nuclear Medicine and Imaging › Monoclonal and Polyclonal Antibodies Research
- Keywords
- canonical structure, Fab fragment, variable light chain, antibody binding sites, main-chain conformation, sequence-structure relationship
- MeSH terms
- Amino Acid Sequence, Binding Sites, Antibody, Immunoglobulin Variable Region, Models, Molecular, Protein Conformation, Surface Properties
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
