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- PDB-6k3f: Crystal Structure of beta-Arrestin 2 in Complex with CXCR7 Phosph... -

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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 / negative regulation of opioid receptor signaling pathway / positive regulation of opioid receptor signaling pathway / postsynaptic signal transduction / positive regulation of synaptic transmission, dopaminergic / oculomotor nerve development / alpha-1A adrenergic receptor binding / follicle-stimulating hormone receptor binding / positive regulation of mesenchymal stem cell migration ...type 2A serotonin receptor binding / platelet activating factor receptor binding / negative regulation of opioid receptor signaling pathway / positive regulation of opioid receptor signaling pathway / postsynaptic signal transduction / positive regulation of synaptic transmission, dopaminergic / oculomotor nerve development / alpha-1A adrenergic receptor binding / follicle-stimulating hormone receptor binding / positive regulation of mesenchymal stem cell migration / TGFBR3 regulates TGF-beta signaling / G alpha (s) signalling events / follicle-stimulating hormone signaling pathway / alpha-1B adrenergic receptor binding / WNT5A-dependent internalization of FZD4 / C-X-C chemokine binding / protein kinase B binding / Ub-specific processing proteases / angiotensin receptor binding / MAP2K and MAPK activation / C-X-C chemokine receptor activity / desensitization of G protein-coupled receptor signaling pathway / negative regulation of toll-like receptor signaling pathway / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / positive regulation of cardiac muscle cell differentiation / negative regulation of interleukin-12 production / type 1 angiotensin receptor binding / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / C-C chemokine receptor activity / C-C chemokine binding / regulation of G protein-coupled receptor signaling pathway / positive regulation of calcium ion transport / positive regulation of epithelial cell apoptotic process / arrestin family protein binding / negative regulation of natural killer cell mediated cytotoxicity / G protein-coupled receptor internalization / mitogen-activated protein kinase binding / Chemokine receptors bind chemokines / adult walking behavior / scavenger receptor activity / Thrombin signalling through proteinase activated receptors (PARs) / chemokine-mediated signaling pathway / positive regulation of DNA biosynthetic process / negative regulation of interleukin-1 beta production / response to morphine / 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 collagen biosynthetic process / positive regulation of receptor internalization / positive regulation of glial cell proliferation / negative regulation of tumor necrosis factor production / endocytic vesicle / canonical NF-kappaB signal transduction / D1 dopamine receptor binding / vasculogenesis / coreceptor activity / 14-3-3 protein binding / clathrin-coated pit / sensory perception of pain / negative regulation of protein ubiquitination / transforming growth factor beta receptor signaling pathway / negative regulation of canonical NF-kappaB signal transduction / cell chemotaxis / calcium-mediated signaling / circadian rhythm / recycling endosome / G protein-coupled receptor binding / receptor internalization / modulation of chemical synaptic transmission / endocytosis / protein transport / positive regulation of cytosolic calcium ion concentration / cytoplasmic vesicle / angiogenesis / G alpha (i) signalling events / basolateral plasma membrane / protein-macromolecule adaptor activity / dendritic spine / negative regulation of neuron apoptotic process / transcription by RNA polymerase II / molecular adaptor activity / proteasome-mediated ubiquitin-dependent protein catabolic process / early endosome / postsynaptic membrane / positive regulation of ERK1 and ERK2 cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell adhesion / endosome / postsynaptic density / immune response / protein ubiquitination / G protein-coupled receptor signaling pathway / intracellular membrane-bounded organelle / protein domain specific binding / signaling receptor binding / negative regulation of cell population proliferation / external side of plasma membrane
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. / 7 transmembrane receptor (rhodopsin family) / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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

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Experimental details

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Experiment

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

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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

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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

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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

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