2J4Y

Crystal structure of a rhodopsin stabilizing mutant expressed in mammalian cells

PDB DOI: https://doi.org/10.2210/pdb2J4Y/pdb

Classification: SIGNALING PROTEIN
Organism(s): Bos taurus
Expression System: Chlorocebus aethiops
Mutation(s): Yes
Membrane Protein: Yes PDBTM

Deposited: 2006-09-07 Released: 2007-09-25
Deposition Author(s): Standfuss, J., Xie, G., Edwards, P.C., Burghammer, M., Oprian, D.D., Schertler, G.F.X.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.40 Å
R-Value Free: 0.330
R-Value Work: 0.290
R-Value Observed: 0.290

wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 3C9M

Macromolecule Content

Total Structure Weight: 79.08 kDa
Atom Count: 5,252
Modelled Residue Count: 656
Deposited Residue Count: 698
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, B	349	Bos taurus	Mutation(s): 3 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
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
RET Query on RET Download Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain C [auth A] MOL2 format, chain E [auth B] MOL2 format, chain C [auth A]	C [auth A], E [auth B]	RETINAL C₂₀ H₂₈ O NCYCYZXNIZJOKI-OVSJKPMPSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth B] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B]	D [auth A], F [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.40 Å
R-Value Free: 0.330
R-Value Work: 0.290
R-Value Observed: 0.290
Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.3	α = 90
b = 109.3	β = 90
c = 77.7	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2007-09-25

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2007-09-25
Type: Initial release
Version 1.1: 2012-12-12
Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Other, Refinement description, Source and taxonomy, Structure summary, Version format compliance
Version 1.2: 2019-05-08
Changes: Data collection, Derived calculations, Experimental preparation, Other
Version 1.3: 2019-10-23
Changes: Data collection, Database references, Other
Version 1.4: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.5: 2023-12-13
Changes: Data collection, Database references, Refinement description, Structure summary

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2J4Y

Crystal structure of a rhodopsin stabilizing mutant expressed in mammalian cells

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)