[English] 日本語
Yorodumi
- PDB-6k3f: Crystal Structure of beta-Arrestin 2 in Complex with CXCR7 Phosph... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6k3f
TitleCrystal Structure of beta-Arrestin 2 in Complex with CXCR7 Phosphopeptide
Components
  • Beta-arrestin-2
  • Peptide from Atypical chemokine receptor 3
KeywordsSIGNALING PROTEIN / Complex
Function / homology
Function and homology information


type 2A serotonin receptor binding / platelet activating factor receptor binding / postsynaptic signal transduction / negative regulation of opioid receptor signaling pathway / positive regulation of opioid receptor signaling pathway / positive regulation of synaptic transmission, dopaminergic / oculomotor nerve development / alpha-1A adrenergic receptor binding / follicle-stimulating hormone receptor binding / TGFBR3 regulates TGF-beta signaling ...type 2A serotonin receptor binding / platelet activating factor receptor binding / postsynaptic signal transduction / negative regulation of opioid receptor signaling pathway / positive regulation of opioid receptor signaling pathway / positive regulation of synaptic transmission, dopaminergic / oculomotor nerve development / alpha-1A adrenergic receptor binding / follicle-stimulating hormone receptor binding / TGFBR3 regulates TGF-beta signaling / positive regulation of mesenchymal stem cell migration / G alpha (s) signalling events / alpha-1B adrenergic receptor binding / follicle-stimulating hormone signaling pathway / WNT5A-dependent internalization of FZD4 / positive regulation of cardiac muscle cell differentiation / C-X-C chemokine binding / angiotensin receptor binding / protein kinase B binding / Ub-specific processing proteases / MAP2K and MAPK activation / C-X-C chemokine receptor activity / negative regulation of toll-like receptor signaling pathway / desensitization of G protein-coupled receptor signaling pathway / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / negative regulation of interleukin-12 production / C-C chemokine receptor activity / type 1 angiotensin receptor binding / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / regulation of G protein-coupled receptor signaling pathway / chemokine-mediated signaling pathway / C-C chemokine binding / G protein-coupled receptor internalization / positive regulation of calcium ion transport / arrestin family protein binding / negative regulation of natural killer cell mediated cytotoxicity / positive regulation of epithelial cell apoptotic process / mitogen-activated protein kinase binding / Chemokine receptors bind chemokines / adult walking behavior / Thrombin signalling through proteinase activated receptors (PARs) / positive regulation of DNA biosynthetic process / scavenger receptor activity / response to morphine / negative regulation of interleukin-1 beta production / negative regulation of release of cytochrome c from mitochondria / detection of temperature stimulus involved in sensory perception of pain / negative regulation of smooth muscle cell apoptotic process / negative regulation of interleukin-6 production / positive regulation of receptor internalization / negative regulation of tumor necrosis factor production / positive regulation of collagen biosynthetic process / endocytic vesicle / D1 dopamine receptor binding / vasculogenesis / coreceptor activity / clathrin-coated pit / 14-3-3 protein binding / positive regulation of glial cell proliferation / negative regulation of canonical NF-kappaB signal transduction / negative regulation of protein ubiquitination / transforming growth factor beta receptor signaling pathway / cell chemotaxis / calcium-mediated signaling / G protein-coupled receptor binding / modulation of chemical synaptic transmission / recycling endosome / receptor internalization / circadian rhythm / endocytosis / protein transport / positive regulation of cytosolic calcium ion concentration / cytoplasmic vesicle / angiogenesis / G alpha (i) signalling events / basolateral plasma membrane / molecular adaptor activity / dendritic spine / proteasome-mediated ubiquitin-dependent protein catabolic process / negative regulation of neuron apoptotic process / postsynaptic membrane / transcription by RNA polymerase II / early endosome / positive regulation of ERK1 and ERK2 cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein ubiquitination / endosome / cell adhesion / postsynaptic density / immune response / G protein-coupled receptor signaling pathway / protein domain specific binding / signaling receptor binding / negative regulation of cell population proliferation / external side of plasma membrane / intracellular membrane-bounded organelle / ubiquitin protein ligase binding / positive regulation of gene expression / protein-containing complex binding
Similarity search - Function
Atypical chemokine receptor 3 / : / Arrestin, conserved site / Arrestins signature. / Arrestin / Arrestin, N-terminal / Arrestin-like, N-terminal / Arrestin C-terminal-like domain / Arrestin (or S-antigen), N-terminal domain / Arrestin (or S-antigen), C-terminal domain ...Atypical chemokine receptor 3 / : / Arrestin, conserved site / Arrestins signature. / Arrestin / Arrestin, N-terminal / Arrestin-like, N-terminal / Arrestin C-terminal-like domain / Arrestin (or S-antigen), N-terminal domain / Arrestin (or S-antigen), C-terminal domain / Arrestin (or S-antigen), C-terminal domain / Arrestin-like, C-terminal / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family) / Immunoglobulin E-set
Similarity search - Domain/homology
Atypical chemokine receptor 3 / Beta-arrestin-2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMin, K.J. / Yoon, H.J. / Lee, H.H.
Funding support Korea, Republic Of, 3items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2015R1A5A1008958 Korea, Republic Of
National Research Foundation (NRF, Korea)2018R1A2B2008142 Korea, Republic Of
Ministry of Science, ICT and Future Planning (MSIP)2014M1A8A1049296 Korea, Republic Of
CitationJournal: Structure / Year: 2020
Title: Crystal Structure of beta-Arrestin 2 in Complex with CXCR7 Phosphopeptide.
Authors: Min, K. / Yoon, H.J. / Park, J.Y. / Baidya, M. / Dwivedi-Agnihotri, H. / Maharana, J. / Chaturvedi, M. / Chung, K.Y. / Shukla, A.K. / Lee, H.H.
History
DepositionMay 18, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 10, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 23, 2021Group: Database references / Structure summary / Category: citation / citation_author / struct
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct.title
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Beta-arrestin-2
U: Peptide from Atypical chemokine receptor 3
B: Beta-arrestin-2
V: Peptide from Atypical chemokine receptor 3
C: Beta-arrestin-2
W: Peptide from Atypical chemokine receptor 3
D: Beta-arrestin-2
X: Peptide from Atypical chemokine receptor 3
E: Beta-arrestin-2
Y: Peptide from Atypical chemokine receptor 3
F: Beta-arrestin-2
Z: Peptide from Atypical chemokine receptor 3


Theoretical massNumber of molelcules
Total (without water)266,30212
Polymers266,30212
Non-polymers00
Water9,440524
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24640 Å2
ΔGint-127 kcal/mol
Surface area106150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.170, 127.910, 206.040
Angle α, β, γ (deg.)90.000, 90.040, 90.000
Int Tables number5
Space group name H-MC121

-
Components

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


Mass: 42442.750 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Arrb2 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P29067
#2: Protein/peptide
Peptide from Atypical chemokine receptor 3 / chemokine-related protein 1 / C-X-C chemokine receptor type 7 / CXCR-7 / Chemokine orphan receptor ...chemokine-related protein 1 / C-X-C chemokine receptor type 7 / CXCR-7 / Chemokine orphan receptor 1 / G-protein coupled receptor 159 / G-protein coupled receptor RDC1 homolog / RDC-1


Mass: 1940.975 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P25106
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 524 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.54 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.2M Ammonium acetate, 0.1M Bis-Tris pH5.5, 25% (w/v) PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Nov 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→46.804 Å / Num. obs: 162425 / % possible obs: 99.67 % / Redundancy: 1 % / CC1/2: 0.711 / Net I/σ(I): 1.31
Reflection shellResolution: 1.95→2.07 Å / Num. unique obs: 49820 / CC1/2: 0.261

-
Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5W0P

5w0p


Resolution: 2.3→46.804 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 25.3 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.2461 5310 5.07 %RANDOM
Rwork0.2332 99472 --
obs0.2358 104788 99.99 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 89.25 Å2 / Biso mean: 25.3474 Å2 / Biso min: 13.58 Å2
Refinement stepCycle: final / Resolution: 2.3→46.804 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16746 0 0 524 17270
Biso mean---19.75 -
Num. residues----2105
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3001-2.33970.36232420.33454941518395
2.3397-2.38230.3182800.33564972525295
2.3823-2.42810.33172410.34284958519995
2.4281-2.47760.33322750.32024944521995
2.4776-2.53150.292650.31235043530895
2.5315-2.59040.33222590.30734896515595
2.5904-2.65520.27862540.3044946520095
2.6552-2.72690.30592560.28684986524295
2.7269-2.80720.27272600.26314980524095
2.8072-2.89780.25952730.25914959523295
2.8978-3.00130.27262490.24614948519795
3.0013-3.12150.25562410.23635012525395
3.1215-3.26350.24522820.22754970525295
3.2635-3.43550.22692680.22064943521195
3.4355-3.65060.23442980.20764957525594
3.6506-3.93240.22482690.19984980524995
3.9324-4.32780.2142720.17994974524695
4.3278-4.95340.18242990.17364943524294
4.9534-6.23820.22512400.21015044528495
6.2382-45.59390.25612860.22265076536295
Refinement TLS params.Method: refined / Origin x: 50.6348 Å / Origin y: 63.5994 Å / Origin z: 51.391 Å
111213212223313233
T0.1738 Å20.0024 Å20.0046 Å2-0.1899 Å2-0.0074 Å2--0.2867 Å2
L-0.015 °20.003 °2-0.0034 °2--0.0165 °2-0.0054 °2---0.0064 °2
S-0.008 Å °0.0056 Å °0.0072 Å °-0.0034 Å °0.0021 Å °-0.0099 Å °-0.0022 Å °-0.0004 Å °0.0042 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA8 - 350
2X-RAY DIFFRACTION1allU333 - 345
3X-RAY DIFFRACTION1allB8 - 346
4X-RAY DIFFRACTION1allV333 - 344
5X-RAY DIFFRACTION1allC8 - 350
6X-RAY DIFFRACTION1allW336 - 344
7X-RAY DIFFRACTION1allD8 - 350
8X-RAY DIFFRACTION1allX333 - 344
9X-RAY DIFFRACTION1allE8 - 346
10X-RAY DIFFRACTION1allY333 - 344
11X-RAY DIFFRACTION1allF8 - 350
12X-RAY DIFFRACTION1allZ336 - 344
13X-RAY DIFFRACTION1allS2 - 743

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
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

-
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