3C9L

Structure of ground-state bovine rhodospin in a hexagonal crystal form

PDB DOI: https://doi.org/10.2210/pdb3C9L/pdb

Classification: SIGNALING PROTEIN
Organism(s): Bos taurus
Mutation(s): No
Membrane Protein: Yes PDBTMMemProtMD

Deposited: 2008-02-16 Released: 2008-08-05
Deposition Author(s): Stenkamp, R.E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free: 0.216
R-Value Work: 0.188
R-Value Observed: 0.190

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 1GZM

Literature

Alternative models for two crystal structures of bovine rhodopsin.

Stenkamp, R.E.

(2008) Acta Crystallogr D Biol Crystallogr 64: 902-904

PubMed: 18645239 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1107/S0907444908017162
Primary Citation of Related Structures:
3C9L, 3C9M

PubMed Abstract:
The space-group symmetry of two crystal forms of rhodopsin (PDB codes 1gzm and 2j4y; space group P3(1)) can be re-interpreted as hexagonal (space group P6(4)). Two molecules of the G protein-coupled receptor are present in the asymmetric unit in the trigonal models. However, the noncrystallographic twofold axes parallel to the c axis can be treated as crystallographic symmetry operations in the hexagonal space group. This halves the asymmetric unit and makes all of the protein molecules equivalent in these structures. Corrections for merohedral twinning were also applied in the refinement in the higher symmetry space group for one of the structures (2j4y).

Organizational Affiliation

Departments of Biological Structure and Biochemistry, Biomolecular Structure Center, University of Washington, Seattle, WA 98195, USA. stenkamp@u.washington.edu

Macromolecule Content

Total Structure Weight: 43.87 kDa
Atom Count: 2,888
Modelled Residue Count: 329
Deposited Residue Count: 348
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Rhodopsin	A	348	Bos taurus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P02699 (Bos taurus) Explore P02699 Go to UniProtKB: P02699
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P02699
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain A
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B, C	3		N-Glycosylation	Interactions Focus chain B Focus chain C Interactions & Density Focus chain B Focus chain C
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEF Query on PEF Download Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE C₃₇ H₇₄ N O₈ P SLKDGVPOSSLUAI-PGUFJCEWSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
C8E Query on C8E Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A]	K [auth A] L [auth A] M [auth A] N [auth A] O [auth A] K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A]	(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE C₁₆ H₃₄ O₅ FEOZZFHAVXYAMB-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Interactions & Density Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A]
RET Query on RET Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	RETINAL C₂₀ H₂₈ O NCYCYZXNIZJOKI-OVSJKPMPSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
PLM Query on PLM Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A]	G [auth A], H [auth A]	PALMITIC ACID C₁₆ H₃₂ O₂ IPCSVZSSVZVIGE-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain G [auth A] Focus chain H [auth A]
LDA Query on LDA Download Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A] mmCIF format, chain J [auth A]	J [auth A]	LAURYL DIMETHYLAMINE-N-OXIDE C₁₄ H₃₁ N O SYELZBGXAIXKHU-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
ACE Query on ACE Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	ACETYL GROUP C₂ H₄ O IKHGUXGNUITLKF-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free: 0.216
R-Value Work: 0.188
R-Value Observed: 0.190
Space Group: P 6₄

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.82	α = 90
b = 103.82	β = 90
c = 76.59	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
REFMAC	refinement

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2008-08-05

Deposition Author(s):

Stenkamp, R.E.

Revision History (Full details and data files)

Version 1.0: 2008-08-05
Type: Initial release
Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.2: 2011-08-10
Changes: Other
Version 1.3: 2011-10-05
Changes: Other
Version 1.4: 2019-07-24
Changes: Data collection, Derived calculations, Refinement description
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2023-08-30
Changes: Data collection, Database references, Refinement description, Structure summary