[English] 日本語
Yorodumi
- PDB-6oil: Crystal structure of human VISTA extracellular domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6oil
TitleCrystal structure of human VISTA extracellular domain
ComponentsV-type immunoglobulin domain-containing suppressor of T-cell activation
KeywordsSIGNALING PROTEIN / T cell activation / transmembrane / suppressor
Function / homology
Function and homology information


positive regulation of collagen catabolic process / negative regulation of CD8-positive, alpha-beta T cell proliferation / positive regulation of endopeptidase activity / negative regulation of alpha-beta T cell activation / negative regulation of CD4-positive, alpha-beta T cell proliferation / positive regulation of regulatory T cell differentiation / negative regulation of interleukin-17 production / zymogen activation / negative regulation of interleukin-10 production / negative regulation of type II interferon production ...positive regulation of collagen catabolic process / negative regulation of CD8-positive, alpha-beta T cell proliferation / positive regulation of endopeptidase activity / negative regulation of alpha-beta T cell activation / negative regulation of CD4-positive, alpha-beta T cell proliferation / positive regulation of regulatory T cell differentiation / negative regulation of interleukin-17 production / zymogen activation / negative regulation of interleukin-10 production / negative regulation of type II interferon production / negative regulation of tumor necrosis factor production / endopeptidase activator activity / regulation of immune response / positive regulation of cell migration / positive regulation of gene expression / enzyme binding / identical protein binding / plasma membrane
Similarity search - Function
V-type immunoglobulin domain-containing suppressor of T-cell activation / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
V-type immunoglobulin domain-containing suppressor of T-cell activation
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsMehta, N. / Cochran, J.R. / Mathews, I.I.
Funding support United States, 2items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-AC02-76SF00515 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41GM103393 United States
CitationJournal: Cell Rep / Year: 2019
Title: Structure and Functional Binding Epitope of V-domain Ig Suppressor of T Cell Activation.
Authors: Mehta, N. / Maddineni, S. / Mathews, I.I. / Andres Parra Sperberg, R. / Huang, P.S. / Cochran, J.R.
History
DepositionApr 9, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2019Group: Data collection / Structure summary / Category: struct / Item: _struct.title
Revision 1.2Nov 13, 2019Group: Database references / Category: citation / citation_author
Item: _citation.page_last / _citation.pdbx_database_id_PubMed ..._citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: V-type immunoglobulin domain-containing suppressor of T-cell activation
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4903
Polymers19,0471
Non-polymers4422
Water73941
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)29.169, 64.089, 37.695
Angle α, β, γ (deg.)90.000, 91.730, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein V-type immunoglobulin domain-containing suppressor of T-cell activation / Platelet receptor Gi24 / Stress-induced secreted protein-1 / Sisp-1 / V-set domain-containing ...Platelet receptor Gi24 / Stress-induced secreted protein-1 / Sisp-1 / V-set domain-containing immunoregulatory receptor / V-set immunoregulatory receptor


Mass: 19047.223 Da / Num. of mol.: 1 / Mutation: N59Q, N76Q, D155E, N158Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VSIR / Production host: Homo sapiens (human) / Strain (production host): Expi293 System / References: UniProt: Q9H7M9
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 1.85 Å3/Da / Density % sol: 33.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 18% PEG3350, 0.075M NaBr, 0.05M HAT buffer(combination of HEPES (7.5), ADA (6.5), and TrisHCl (8.0))
PH range: 6.5-8.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 19, 2019 / Details: Si(111) monochromator
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.85→29.156 Å / Num. obs: 11704 / % possible obs: 98.4 % / Redundancy: 9.222 % / Biso Wilson estimate: 37.395 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.096 / Rrim(I) all: 0.101 / Χ2: 0.971 / Net I/σ(I): 13 / Num. measured all: 107740
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.85-1.98.4371.4671.468430.6091.56296.2
1.9-1.959.531.1372.048570.7951.20299.2
1.95-2.019.4550.8722.618110.8150.92298.8
2.01-2.079.4320.6393.627980.9040.67598.9
2.07-2.149.3560.5364.347590.9450.56798.3
2.14-2.219.4190.3975.77560.9590.4299.2
2.21-2.299.1070.3067.127030.9820.32498.7
2.29-2.398.4550.2837.426900.9790.30197.5
2.39-2.499.230.2518.686610.9860.26699
2.49-2.629.6740.19411.026500.9910.20599.4
2.62-2.769.5830.15813.466040.9940.16799
2.76-2.939.3550.11617.375890.9960.12398.8
2.93-3.139.4290.09621.965220.9950.10298.7
3.13-3.388.8060.07826.234900.9960.08396.6
3.38-3.78.8690.06229.694590.9980.06595.4
3.7-4.149.4680.05235.724270.9980.055100
4.14-4.789.460.04739.223670.9990.04999.2
4.78-5.859.1420.04539.333170.9990.04897.5
5.85-8.278.7840.04537.692360.9990.04897.5
8.27-29.1569.2150.03941.651440.9990.042100

-
Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.24data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Rosetta generated models

Resolution: 1.85→29.156 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.28
RfactorNum. reflection% reflection
Rfree0.2226 605 5.17 %
Rwork0.1799 --
obs0.1821 11694 98.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 132.5 Å2 / Biso mean: 41.2578 Å2 / Biso min: 13.58 Å2
Refinement stepCycle: final / Resolution: 1.85→29.156 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1174 0 28 41 1243
Biso mean--74.2 43.28 -
Num. residues----148
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.85-2.03620.26371460.22582744289098
2.0362-2.33070.25051490.18962767291699
2.3307-2.9360.23931720.20162778295099
2.936-29.15940.19981380.16132800293898
Refinement TLS params.Method: refined / Origin x: 16.8608 Å / Origin y: 33.6278 Å / Origin z: 30.9665 Å
111213212223313233
T0.1694 Å20.003 Å20.0082 Å2-0.1458 Å20.0018 Å2--0.1519 Å2
L1.6248 °20.2335 °20.4678 °2-0.8509 °2-0.3127 °2--1.4671 °2
S0.0095 Å °-0.0895 Å °-0.0509 Å °-0.0106 Å °0.0006 Å °-0.0878 Å °-0.2116 Å °-0.0507 Å °0.0002 Å °
Refinement TLS groupSelection details: (chain A and resseq 1:151)

+
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://pdbjlvh1.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