Crystal structure of rhodopsin: a template for cone visual pigments and other G protein-coupled receptors

Stenkamp, R.E.; Filipek, S.; Driessen, C.A.G.G.; Teller, D.C.; Palczewski, K.

doi:10.1016/s0005-2736(02)00567-9

Cited by 128Receptor Mechanisms and SignalingPhotoreceptor and optogenetics researchEnzyme Structure and Function

Crystal structure of rhodopsin: a template for cone visual pigments and other G protein-coupled receptors

Open access

Stenkamp, R.E., Filipek, S., Driessen, C.A.G.G., Teller, D.C., Palczewski, K.·2002·Biochimica et Biophysica Acta (BBA) - Biomembranes

DOI 10.1016/s0005-2736(02)00567-9

Open this paper in CoChat — free account Open PDF

Abstract

The crystal structure of rhodopsin has provided the first three-dimensional molecular model for a G-protein-coupled receptor (GPCR). Alignment of the molecular model from the crystallographic structure with the helical axes seen in cryo-electron microscopic (cryo-EM) studies provides an opportunity to investigate the properties of the molecule as a function of orientation and location within the membrane. In addition, the structure provides a starting point for modeling and rational experimental approaches of the cone pigments, the GPCRs in cone cells responsible for color vision. Homology models of the cone pigments provide a means of understanding the roles of amino acid sequence differences that shift the absorption maximum of the retinal chromophore in the environments of different opsins.

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

Integrity signals

Registry

Crossref · 10.1016/s0005-2736(02)00567-9

Cites

49 of 49 references verified0 citation errors · 0 not checkable

Statistics

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

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?

Key residues in the rhodopsin active site are Lys296, Glu113, and Glu181.
“Key residues in rhodopsin’s active site are Lys296, Glu113, and Glu181”
From Chemistry of the Retinoid (Visual) Cycle (2014) · cites this paper as [240]
Section 6, “Retinal binding site” (page unavailable), identifies Lys-296 at the retinal Schiff-base linkage and Glu-113 nearby as a possible counterion. The available text does not identify Glu-181 as a key residue in that site, so only two of the three named residues are supported. (LLM, conf=0.85)
Experimental — accuracy not yet measured

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

The Protein Data Bank
Berman, H. M. (2000) · Nucleic Acids Research · doi:10.1093/nar/28.1.235 · Cited by 40,196 · see citing works
MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures
Kraulis, P. J. (1991) · Journal of Applied Crystallography · doi:10.1107/s0021889891004399 · Cited by 14,011 · see citing works
Comparative Protein Modelling by Satisfaction of Spatial Restraints
Šali, A., & Blundell, T. L. (1993) · Journal of Molecular Biology · doi:10.1006/jmbi.1993.1626 · Cited by 12,977 · 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
Crystal Structure of Rhodopsin: A G Protein-Coupled Receptor
Palczewski, K., Kumasaka, T., Hori, T., Behnke, C. A., Motoshima, H., Fox, B. A., Trong, I. L., Teller, D. C., Okada, T., Stenkamp, R. E., et al. (2000) · Science · doi:10.1126/science.289.5480.739 · Cited by 5,637 · see citing works
Self-citation
[26] Raster3D: Photorealistic molecular graphics
Merritt, E. A., & Bacon, D. (1997) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/s0076-6879(97)77028-9 · Cited by 3,749 · see citing works
A Method to Identify Protein Sequences That Fold into a Known Three-Dimensional Structure
Bowie, J. U., Lüthy, R., & Eisenberg, D. (1991) · Science · doi:10.1126/science.1853201 · Cited by 2,851 · see citing works
MEMBRANE PROTEIN FOLDING AND STABILITY: Physical Principles
White, S. H., & Wimley, W. C. (1999) · Annual Review of Biophysics and Biomolecular Structure · doi:10.1146/annurev.biophys.28.1.319 · Cited by 1,767 · see citing works
Molecular Genetics of Human Color Vision: The Genes Encoding Blue, Green, and Red Pigments
Nathans, J., Thomas, D., & Hogness, D. S. (1986) · Science · doi:10.1126/science.2937147 · Cited by 1,732 · see citing works
Environment and exposure to solvent of protein atoms. Lysozyme and insulin
Shrake, A., & Rupley, J. A. (1973) · Journal of Molecular Biology · doi:10.1016/0022-2836(73)90011-9 · Cited by 1,387 · see citing works
G Protein-coupled Receptors
Ji, T. H., Grossmann, M., & Ji, I. (1998) · Journal of Biological Chemistry · doi:10.1074/jbc.273.28.17299 · Cited by 1,291 · see citing works
G Protein-coupled Receptors
Lefkowitz, R. J. (1998) · Journal of Biological Chemistry · doi:10.1074/jbc.273.30.18677 · Cited by 1,067 · see citing works
Hydrophobic bonding and accessible surface area in proteins
Chothia, C. (1974) · Nature · doi:10.1038/248338a0 · Cited by 897 · see citing works
Comparative protein modeling by satisfaction of spatial restraints
⩽ali, A. (1995) · Molecular Medicine Today · doi:10.1016/s1357-4310(95)91170-7 · Cited by 785 · see citing works
Molecular Genetics of Inherited Variation in Human Color Vision
Nathans, J., Piantanida, T. P., Eddy, R. L., Shows, T. B., & Hogness, D. S. (1986) · Science · doi:10.1126/science.3485310 · Cited by 783 · see citing works
Projection structure of rhodopsin
Schertler, G. F. X., Villa, C., & Henderson, R. A. (1993) · Nature · doi:10.1038/362770a0 · Cited by 766 · see citing works
An alpha-carbon template for the transmembrane helices in the rhodopsin family of G-protein-coupled receptors 1 1Edited by R. Huber
Baldwin, J. M., Schertler, G. F. X., & Unger, V. M. (1997) · Journal of Molecular Biology · doi:10.1006/jmbi.1997.1240 · Cited by 643 · see citing works
Advances in Determination of a High-Resolution Three-Dimensional Structure of Rhodopsin, a Model of G-Protein-Coupled Receptors (GPCRs),
Teller, D. C., Okada, T., Behnke, C. A., Palczewski, K., & Stenkamp, R. E. (2001) · Biochemistry · doi:10.1021/bi0155091 · Cited by 603 · see citing works
Self-citation
G Protein-coupled Receptors
Gether, U., & Kobilka, B. K. (1998) · Journal of Biological Chemistry · doi:10.1074/jbc.273.29.17979 · Cited by 585 · see citing works
Arrangement of rhodopsin transmembrane α-helices
Unger, V. M., Hargrave, P. A., Baldwin, J. M., & Schertler, G. F. X. (1997) · Nature · doi:10.1038/38316 · Cited by 454 · see citing works
Structural Mimicry in G Protein-Coupled Receptors: Implications of the High-Resolution Structure of Rhodopsin for Structure-Function Analysis of Rhodopsin-Like Receptors
Ballesteros, J. A., Shi, L., & Javitch, J. A. (2001) · Molecular Pharmacology · doi:10.1124/mol.60.1.1 · Cited by 440 · see citing works
Activation of rhodopsin: new insights from structural and biochemical studies
Okada, T., Ernst, O. P., Palczewski, K., & Hofmann, K. P. (2001) · Trends in Biochemical Sciences · doi:10.1016/s0968-0004(01)01799-6 · Cited by 413 · see citing works
Self-citation
Confronting Complexity: the Interlink of Phototransduction and Retinoid Metabolism in the Vertebrate Retina
McBee, J. K., Palczewski, K., Baehr, W., & Pepperberg, D. R. (2001) · Progress in Retinal and Eye Research · doi:10.1016/s1350-9462(01)00002-7 · Cited by 366 · see citing works
Self-citation
Rhodopsin and phototransduction: a model system for G protein‐linked receptors
Hargrave, P. A., & McDowell, J. H. (1992) · The FASEB Journal · doi:10.1096/fasebj.6.6.1544542 · Cited by 328 · see citing works
Rhodopsin: Structural Basis of Molecular Physiology
Menon, S. T., Han, M., & Sakmar, T. P. (2001) · Physiological Reviews · doi:10.1152/physrev.2001.81.4.1659 · Cited by 304 · see citing works
How Membranes Shape Protein Structure
White, S. H., Ladokhin, A. S., Jayasinghe, S. A., & Hristova, K. A. (2001) · Journal of Biological Chemistry · doi:10.1074/jbc.r100008200 · Cited by 299 · see citing works
Visual pigment: G-protein-coupled receptor for light signals
Shichida, Y., & Imai, H. (1998) · Cellular and Molecular Life Sciences (CMLS) · doi:10.1007/s000180050256 · Cited by 242 · see citing works
Determinants of visual pigment absorbance: role of charged amino acids in the putative transmembrane segments
Nathans, J. (1990) · Biochemistry · doi:10.1021/bi00456a013 · Cited by 228 · see citing works
How color visual pigments are tuned
Kochendoerfer, G. G., Lin, S. W., Sakmar, T. P., & Mathies, R. A. (1999) · Trends in Biochemical Sciences · doi:10.1016/s0968-0004(99)01432-2 · Cited by 212 · see citing works
How activated receptors couple to G proteins
Hamm, H. E. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.011099798 · Cited by 203 · see citing works
X-Ray Diffraction Analysis of Three-Dimensional Crystals of Bovine Rhodopsin Obtained from Mixed Micelles
Okada, T., Trong, I. L., Fox, B. A., Behnke, C. A., Stenkamp, R. E., & Palczewski, K. (2000) · Journal of Structural Biology · doi:10.1006/jsbi.1999.4209 · Cited by 194 · see citing works
Self-citation
An amphipathic α-helix at a membrane interface: a structural study using a novel X-ray diffraction method 1 1Edited by D. C. Rees
Hristova, K. A., Wimley, W. C., Mishra, V., Anantharamiah, G. M., Segrest, J. P., & White, S. H. (1999) · Journal of Molecular Biology · doi:10.1006/jmbi.1999.2840 · Cited by 194 · see citing works
MOLECULAR GENETICS OF HUMAN VISUAL PIGMENTS
Nathans, J., Merbs, S. L., Sung, C.-H., Weitz, C. J., & Wang, Y. (1992) · Annual Review of Genetics · doi:10.1146/annurev.ge.26.120192.002155 · Cited by 185 · see citing works
Identification of the chloride-binding site in the human red and green color vision pigments
Wang, Z., Asenjo, A. B., & Oprian, D. D. (1993) · Biochemistry · doi:10.1021/bi00060a001 · Cited by 148 · see citing works
Crystal structure of rhodopsin: implications for vision and beyond
Okada, T. (2001) · Current Opinion in Structural Biology · doi:10.1016/s0959-440x(00)00227-x · Cited by 121 · see citing works
Structural Features and Light-Dependent Changes in the Sequence 306−322 Extending from Helix VII to the Palmitoylation Sites in Rhodopsin: A Site-Directed Spin-Labeling Study,
Altenbach, C., Cai, K., Khorana, H. G., et al. (1999) · Biochemistry · doi:10.1021/bi9900121 · Cited by 100 · see citing works
Non-α-helical elements modulate polytopic membrane protein architecture11Edited by G. Von Heijne
Riek, R., Rigoutsos, I., Novotný, J., & Graham, R. M. (2001) · Journal of Molecular Biology · doi:10.1006/jmbi.2000.4402 · Cited by 99 · see citing works
Studies on the Structure of the G-Protein-Coupled Receptor Rhodopsin Including the Putative G-Protein Binding Site in Unactivated and Activated Forms
Yèagle, P. L., Choi, G., & Albert, A. D. (2001) · Biochemistry · doi:10.1021/bi015543f · Cited by 96 · see citing works
Structure and function in rhodopsin: Rhodopsin mutants with a neutral amino acid at E134 have a partially activated conformation in the dark state
Kim, J., Altenbach, C., Thurmond, R. L., Khorana, H. G., & Hubbell, W. L. (1997) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.94.26.14273 · Cited by 90 · see citing works
Highly Selective Separation of Rhodopsin from Bovine Rod Outer Segment Membranes Using Combination of Divalent Cation and Alkyl(thio)glucoside
Okada, T., Takeda, K., & Kouyama, T. (1998) · Photochemistry and Photobiology · doi:10.1111/j.1751-1097.1998.tb09084.x · Cited by 67 · see citing works
Rhodopsin Sees the Light
Bourne, H. R., & Meng, E. C. (2000) · Science · doi:10.1126/science.289.5480.733 · Cited by 65 · see citing works
Signaling States of Rhodopsin
Bartl, F. J., Ritter, E., & Hofmann, K. P. (2001) · Journal of Biological Chemistry · doi:10.1074/jbc.m101506200 · Cited by 53 · see citing works
Chapter 2 The primary photoreaction of rhodopsin
Mathies, R. A., & Lugtenburg, J. (2000) · Handbook of biological physics · doi:10.1016/s1383-8121(00)80005-6 · Cited by 48 · see citing works
Highly Selective Separation of Rhodopsin from Bovine Rod Outer Segment Membranes Using Combination of Divalent Cation and Alkyl(thio)glucoside
Okada, T., Takeda, K., & Kouyama, T. (1998) · Photochemistry and Photobiology · doi:10.1111/j.1751-1097.1998.tb09445.x · Cited by 48 · see citing works
Ultra-High-Field MAS NMR Assay of a Multispin Labeled Ligand Bound to Its G-Protein Receptor Target in the Natural Membrane Environment: Electronic Structure of the Retinylidene Chromophore in Rhodopsin
Verhoeven, M. A., Creemers, A. F. L., Bovée‐Geurts, P. H. M., DeGrip, W. J., Lugtenburg, J., & de Groot, H. J. M. (2001) · Biochemistry · doi:10.1021/bi0023798 · Cited by 46 · see citing works
Mechanism of Rhodopsin Activation as Examined with Ring-constrained Retinal Analogs and the Crystal Structure of the Ground State Protein
Jang, G.-F., Kuksa, V., Filipek, S., Bartl, F. J., Ritter, E., Gelb, M. H., Hofmann, K. P., & Palczewski, K. (2001) · Journal of Biological Chemistry · doi:10.1074/jbc.m102212200 · Cited by 45 · see citing works
Self-citation
Solution structure of the sixth transmembrane helix of the G-protein-coupled receptor, rhodopsin11This work was supported by National Institutes of Health Grant EY03328 and in part by CA16056.
Chopra, A., Yèagle, P. L., Alderfer, J. A., et al. (2000) · Biochimica et Biophysica Acta (BBA) - Biomembranes · doi:10.1016/s0005-2736(99)00212-6 · Cited by 33 · see citing works
A distance measurement between specific sites on the cytoplasmic surface of bovine rhodopsin in rod outer segment disk membranes
Albert, A. D., Watts, A. G., Spooner, P. J. R., et al. (1997) · Biochimica et Biophysica Acta (BBA) - Biomembranes · doi:10.1016/s0005-2736(97)00100-4 · Cited by 22 · see citing works
G Protein-coupled Receptors Minireview Series
Vaughan, M. M. (1998) · Journal of Biological Chemistry · doi:10.1074/jbc.273.28.17297 · Cited by 14 · see citing works

Flagged first, then by citations

Research works printed but not linked: 2

H.E. Hamm, Proc. Natl. Acad. Sci. U. S. A. 98 (2001) 4819 -4821.
J.M. Kim, C. Altenbach, R.L. Thurmond, H.G. Khorana, W.L. Hubbell, Proc. Natl. Acad. Sci. U. S. A. 94 (1997) 14273 -14278.

Sorted by citations

Chemistry of the Retinoid (Visual) Cycle
Kiser, P. D., Golczak, M., & Palczewski, K. (2014) · Chemical Reviews · doi:10.1021/cr400107q · Cited by 353 · see citing works
Self-citation
Structure of cone photoreceptors
Mustafi, D., Engel, A. H., & Palczewski, K. (2009) · Progress in Retinal and Eye Research · doi:10.1016/j.preteyeres.2009.05.003 · Cited by 275 · see citing works
Self-citation
G Protein-Coupled Receptor Rhodopsin: A Prospectus
Filipek, S., Stenkamp, R. E., Teller, D. C., & Palczewski, K. (2003) · Annual Review of Physiology · doi:10.1146/annurev.physiol.65.092101.142611 · Cited by 267 · see citing works
Self-citation
The Crystallographic Model of Rhodopsin and Its Use in Studies of Other G Protein–Coupled Receptors
Filipek, S., Teller, D. C., Palczewski, K., & Stenkamp, R. (2003) · Annual Review of Biophysics and Biomolecular Structure · doi:10.1146/annurev.biophys.32.110601.142520 · Cited by 137 · see citing works
Self-citation
Molecular Mechanism of Spectral Tuning by Chloride Binding in Monkey Green Sensitive Visual Pigment
Fujimoto, K. J., Minowa, F., Nishina, M., Nakamura, S., Ohashi, S., Katayama, K., Kandori, H., & Yanai, T. (2023) · The Journal of Physical Chemistry Letters · doi:10.1021/acs.jpclett.2c03619 · Cited by 5 · see citing works

Immunoreactivity of rhodopsin and opsin
Plantner, J. J., & Kean, E. L. (1984) · Biochimica et Biophysica Acta (BBA) - General Subjects · doi:10.1016/0304-4165(84)90037-0 · Cited by 4 · see citing works
THE RHODOPSIN SYSTEM OF THE SQUID
Hubbard, R., & George, R. C. C. S. (1958) · The Journal of General Physiology · doi:10.1085/jgp.41.3.501 · Cited by 313 · see citing works
Experimental autoimmune uveoretinitis in rats induced by rod visual pigment: Rhodopsin is more pathogenic than opsin
Schalken, J. J., van Vugt, A. H. M., Winkens, H. J., et al. (1988) · Graefe s Archive for Clinical and Experimental Ophthalmology · doi:10.1007/bf02181192 · Cited by 19 · see citing works
On the occurrence of vitamin A aldehydes in fish and frog ova
Pollard, C. J., & Bieri, J. G. (1959) · Biochimica et Biophysica Acta · doi:10.1016/0006-3002(59)90038-1 · Cited by 6 · see citing works
Effect of opsin on the thermal stability of rhodopsin in bovine rod outer segment disk membranes
Albert, A. D., Edrington, T. C., & Bennett, M. P. (2007) · The FASEB Journal · doi:10.1096/fasebj.21.5.a422

Authors: Stenkamp, R. E., Filipek, S., Driessen, C. A. G. G., Teller, D. C., & Palczewski, K.
Affiliations: University of Washington (US)
University of Warsaw (PL)
Radboud University Nijmegen (NL)
Corresponding author: Stenkamp, R.E.
ORCID: Stenkamp, R.E.
Filipek, S.
Palczewski, K.
Venue: Biochimica et Biophysica Acta (BBA) - Biomembranes
Publisher: Elsevier BV
Published: 2002-10
Volume: 1565
Issue: 2
Pages: 168-182
ISSN: 0005-2736 (ISSN-L)
DOI: 10.1016/s0005-2736(02)00567-9
OpenAlex: W2110129016
Cited by: 128
References: 49
Citations by year: 2026: 3 · 2025: 2 · 2024: 2 · 2023: 3 · 2022: 1 · 2021: 3 · 2019: 17 · 2018: 3 · 2017: 3 · 2016: 3 · 2015: 3 · 2014: 5 · 2013: 6 · 2012: 5
FWCI: 3.48
Type: journal article
Language: en
Open access: bronze
doi.org
Licence: www.elsevier.com/tdm/userlicense/1.0/ (tdm)
www.elsevier.com/legal/tdmrep-license (tdm)
www.elsevier.com/open-access/userlicense/1.0/ (vor, 3943 d)
doi.org/10.15223/policy-017 (stm-asf)
doi.org/10.15223/policy-037 (stm-asf)
doi.org/10.15223/policy-012 (stm-asf)
doi.org/10.15223/policy-029 (stm-asf)
doi.org/10.15223/policy-004 (stm-asf)
Locations: Biochimica et Biophysica Acta (BBA) - Biomembranes (publishedVersion)
PubMed (publishedVersion)
Radboud Repository (Radboud University) (submittedVersion)
Funders: Alcon Research Institute
National Institutes of Health (EY08061, GM63020)
Research to Prevent Blindness
University of Washington
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Receptor Mechanisms and Signaling
Life Sciences › Neuroscience › Cellular and Molecular Neuroscience › Photoreceptor and optogenetics research
Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
Keywords: rhodopsin, G protein-coupled receptors, cone visual pigments, opsin, homology modeling, membrane orientation, color vision
MeSH terms: Amino Acid Sequence, Animals, Anura, Binding Sites, Crystallography, Cytoplasm, Humans, Membrane Proteins, Models, Molecular, Molecular Sequence Data, Protein Conformation, Receptors, Cell Surface, Retinal Pigments, Rhodopsin, Rod Opsins, Retinal Cone Photoreceptor Cells, Cryoelectron Microscopy

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

Crystal structure of rhodopsin: a template for cone visual pigments and other G protein-coupled receptors

Abstract

Integrity signals

Claims the paper makes

Claims other papers make about this one

Self-check

Cites

Cited by

Related

Record

About these checks