[English] 日本語
Yorodumi
- PDB-5tv1: active arrestin-3 with inositol hexakisphosphate -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5tv1
Titleactive arrestin-3 with inositol hexakisphosphate
ComponentsBeta-arrestin-2Arrestin beta 2
KeywordsSIGNALING PROTEIN
Function / homology
Function and homology information


angiotensin receptor binding / desensitization of G protein-coupled receptor signaling pathway / inositol hexakisphosphate binding / G protein-coupled receptor internalization / positive regulation of receptor internalization / phosphatidylinositol-3,4,5-trisphosphate binding / endocytic vesicle / clathrin-coated pit / phosphatidylinositol binding / G protein-coupled receptor binding ...angiotensin receptor binding / desensitization of G protein-coupled receptor signaling pathway / inositol hexakisphosphate binding / G protein-coupled receptor internalization / positive regulation of receptor internalization / phosphatidylinositol-3,4,5-trisphosphate binding / endocytic vesicle / clathrin-coated pit / phosphatidylinositol binding / G protein-coupled receptor binding / receptor internalization / protein transport / positive regulation of ERK1 and ERK2 cascade / signal transduction / nucleus / cytoplasm
Similarity search - Function
Immunoglobulin-like - #640 / Arrestins signature. / Arrestin, conserved site / Arrestin, N-terminal / Arrestin / Arrestin (or S-antigen), N-terminal domain / Arrestin (or S-antigen), C-terminal domain / Arrestin C-terminal-like domain / Arrestin-like, N-terminal / Arrestin (or S-antigen), C-terminal domain ...Immunoglobulin-like - #640 / Arrestins signature. / Arrestin, conserved site / Arrestin, N-terminal / Arrestin / Arrestin (or S-antigen), N-terminal domain / Arrestin (or S-antigen), C-terminal domain / Arrestin C-terminal-like domain / Arrestin-like, N-terminal / Arrestin (or S-antigen), C-terminal domain / Arrestin-like, C-terminal / Immunoglobulin E-set / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
INOSITOL HEXAKISPHOSPHATE / Beta-arrestin-2
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsChen, Q. / Gilbert, N.C. / Perry, N.A. / Vishniveteskiy, S. / Gurevich, V.V. / Iverson, T.M.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM095633 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM077561 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM109955 United States
National Institutes of Health/National Eye Institute (NIH/NEI)EY011500 United States
CitationJournal: Nat Commun / Year: 2017
Title: Structural basis of arrestin-3 activation and signaling.
Authors: Chen, Q. / Perry, N.A. / Vishnivetskiy, S.A. / Berndt, S. / Gilbert, N.C. / Zhuo, Y. / Singh, P.K. / Tholen, J. / Ohi, M.D. / Gurevich, E.V. / Brautigam, C.A. / Klug, C.S. / Gurevich, V.V. / Iverson, T.M.
History
DepositionNov 7, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 14, 2020Group: Structure summary / Category: chem_comp / Item: _chem_comp.pdbx_synonyms

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Beta-arrestin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8606
Polymers44,2641
Non-polymers1,5965
Water79344
1
A: Beta-arrestin-2
hetero molecules

A: Beta-arrestin-2
hetero molecules

A: Beta-arrestin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,58018
Polymers132,7913
Non-polymers4,78915
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area10820 Å2
ΔGint-83 kcal/mol
Surface area49020 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)97.575, 97.575, 76.938
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

-
Components

#1: Protein Beta-arrestin-2 / Arrestin beta 2 / Arrestin beta-2 / Arrestin-3


Mass: 44263.531 Da / Num. of mol.: 1 / Fragment: UNP residues 8-393
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: ARRB2 / Production host: Enterobacteria phage L1 (virus) / References: UniProt: P32120
#2: Chemical ChemComp-IHP / INOSITOL HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE / Phytic acid


Mass: 660.035 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H18O24P6
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.51 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 100 mM Succinate/Phosphate/Glycine pH 8.5 and 25% PEG 1500

-
Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.4→37.03 Å / Num. obs: 15997 / % possible obs: 97 % / Redundancy: 3.4 % / Net I/σ(I): 26.2

-
Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data scaling
HKL-2000data reduction
PDB_EXTRACT3.2data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1G4M
Resolution: 2.4→37.03 Å / SU ML: 0.35 / Cross valid method: NONE / σ(F): 1.36 / Phase error: 27.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.245 765 4.78 %
Rwork0.197 --
obs0.199 15997 97.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 65.18 Å2
Refinement stepCycle: LAST / Resolution: 2.4→37.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2673 0 90 44 2807
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092822
X-RAY DIFFRACTIONf_angle_d1.2853841
X-RAY DIFFRACTIONf_dihedral_angle_d12.9471731
X-RAY DIFFRACTIONf_chiral_restr0.061434
X-RAY DIFFRACTIONf_plane_restr0.007479
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4001-2.58530.34891440.29233079X-RAY DIFFRACTION99
2.5853-2.84540.3131840.26593037X-RAY DIFFRACTION99
2.8454-3.25690.26221420.21973052X-RAY DIFFRACTION97
3.2569-4.10260.22561630.19212946X-RAY DIFFRACTION95
4.1026-37.03870.21781320.16443118X-RAY DIFFRACTION97

+
About Yorodumi

-
News

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

-
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more