3UGX | pdb_00003ugx

Crystal Structure of Visual Arrestin

PDB DOI: https://doi.org/10.2210/pdb3UGX/pdb

Classification: SIGNALING PROTEIN
Organism(s): Bos taurus
Expression System: Saccharomyces cerevisiae
Mutation(s): No

Deposited: 2011-11-03 Released: 2012-02-08
Deposition Author(s): Batra-Safferling, R., Granzin, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free:
0.253 (Depositor), 0.252 (DCC)
R-Value Work:
0.209 (Depositor), 0.206 (DCC)
R-Value Observed:
0.211 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Crystal Structure of p44, a Constitutively Active Splice Variant of Visual Arrestin.

Granzin, J., Cousin, A., Weirauch, M., Schlesinger, R., Buldt, G., Batra-Safferling, R.

(2012) J Mol Biology 416: 611-618

PubMed: 22306737 Search on PubMed
DOI: https://doi.org/10.1016/j.jmb.2012.01.028
Primary Citation Related Structures:
3UGU, 3UGX

PubMed Abstract:
Visual arrestin specifically binds to photoactivated and phosphorylated rhodopsin and inactivates phototransduction. In contrast, the p44 splice variant can terminate phototransduction by binding to nonphosphorylated light-activated rhodopsin. Here we report the crystal structure of bovine p44 at a resolution of 1.85 Å. Compared to native arrestin, the p44 structure reveals significant differences in regions crucial for receptor binding, namely flexible loop V-VI and polar core regions. Additionally, electrostatic potential is remarkably positive on the N-domain and the C-domain. The p44 structure represents an active conformation that serves as a model to explain the 'constitutive activity' found in arrestin variants.

Organizational Affiliation

Institute of Complex Systems, ICS-6: Structural Biochemistry, Forschungszentrum Jülich, 52425 Jülich, Germany.

Macromolecule Content

Total Structure Weight: 188.27 kDa
Atom Count: 11,230
Modeled Residue Count: 1,427
Deposited Residue Count: 1,656
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
S-arrestin	A, B, C, D	414	Bos taurus	Mutation(s): 0 Gene Names: SAG
UniProt
Find proteins for P08168 (Bos taurus) Explore P08168 Go to UniProtKB: P08168
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P08168
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PTD Query on PTD Download:Ideal Coordinates CCD File SDF format, chain DA [auth D] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain R [auth B] SDF format, chain U [auth C] SDF format, chain V [auth C] SDF format, chain W [auth C] SDF format, chain Q [auth B] SDF format, chain L [auth A] SDF format, chain I [auth A] MOL2 format, chain DA [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain R [auth B] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C] MOL2 format, chain Q [auth B] MOL2 format, chain L [auth A] MOL2 format, chain I [auth A] mmCIF format, chain DA [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain R [auth B] mmCIF format, chain U [auth C] mmCIF format, chain V [auth C] mmCIF format, chain W [auth C] mmCIF format, chain Q [auth B] mmCIF format, chain L [auth A] mmCIF format, chain I [auth A]	DA [auth D] E [auth A] F [auth A] G [auth A] H [auth A] DA [auth D], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], Q [auth B], R [auth B], U [auth C], V [auth C], W [auth C]	PENTANEDIAL C₅ H₈ O₂ SXRSQZLOMIGNAQ-UHFFFAOYSA-N		Interactions Focus chain DA [auth D] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Interactions & Density Focus chain DA [auth D] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C]
IMD Query on IMD Download:Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain CA [auth D] SDF format, chain P [auth B] MOL2 format, chain BA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain P [auth B] mmCIF format, chain BA [auth D] mmCIF format, chain CA [auth D] mmCIF format, chain P [auth B]	BA [auth D], CA [auth D], P [auth B]	IMIDAZOLE C₃ H₅ N₂ RAXXELZNTBOGNW-UHFFFAOYSA-O		Interactions Focus chain BA [auth D] Focus chain CA [auth D] Focus chain P [auth B] Interactions & Density Focus chain BA [auth D] Focus chain CA [auth D] Focus chain P [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain O [auth A] SDF format, chain T [auth B] SDF format, chain Y [auth C] SDF format, chain Z [auth C] SDF format, chain N [auth A] SDF format, chain EA [auth D] MOL2 format, chain AA [auth C] MOL2 format, chain O [auth A] MOL2 format, chain T [auth B] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth C] MOL2 format, chain N [auth A] MOL2 format, chain EA [auth D] mmCIF format, chain AA [auth C] mmCIF format, chain O [auth A] mmCIF format, chain T [auth B] mmCIF format, chain Y [auth C] mmCIF format, chain Z [auth C] mmCIF format, chain N [auth A] mmCIF format, chain EA [auth D]	AA [auth C] EA [auth D] N [auth A] O [auth A] T [auth B] AA [auth C], EA [auth D], N [auth A], O [auth A], T [auth B], Y [auth C], Z [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain EA [auth D] Focus chain N [auth A] Focus chain O [auth A] Focus chain T [auth B] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain EA [auth D] Focus chain N [auth A] Focus chain O [auth A] Focus chain T [auth B] Focus chain Y [auth C] Focus chain Z [auth C]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain X [auth C] MOL2 format, chain X [auth C] mmCIF format, chain X [auth C]	X [auth C]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain X [auth C] Interactions & Density Focus chain X [auth C]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain S [auth B] MOL2 format, chain M [auth A] MOL2 format, chain S [auth B] mmCIF format, chain M [auth A] mmCIF format, chain S [auth B]	M [auth A], S [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Focus chain S [auth B] Interactions & Density Focus chain M [auth A] Focus chain S [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free: 0.253 (Depositor), 0.252 (DCC)
R-Value Work: 0.209 (Depositor), 0.206 (DCC)
R-Value Observed: 0.211 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 168.363	α = 90
b = 184.329	β = 90
c = 90.404	γ = 90

Software Package:

Software Name	Purpose
MAR345	data collection
MOLREP	phasing
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2012-02-08

Deposition Author(s):

Batra-Safferling, R.

Granzin, J.

Revision History (Full details and data files)

Version 1.0: 2012-02-08
Type: Initial release
Version 1.1: 2012-02-15
Changes: Structure summary
Version 1.2: 2012-03-21
Changes: Database references
Version 1.3: 2017-11-08
Changes: Refinement description
Version 1.4: 2024-02-28
Changes: Data collection, Database references, Derived calculations