[English] 日本語
Yorodumi
- PDB-4rwh: Crystal structure of T cell costimulatory ligand B7-1 (CD80) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4rwh
TitleCrystal structure of T cell costimulatory ligand B7-1 (CD80)
ComponentsT-lymphocyte activation antigen CD80
KeywordsSIGNALING PROTEIN / Ig fold / T cell costimulatory ligand B7-1
Function / homology
Function and homology information


CD28 dependent PI3K/Akt signaling / CD28 dependent Vav1 pathway / CD28 co-stimulation / CTLA4 inhibitory signaling / protein complex involved in cell adhesion / PIP3 activates AKT signaling / positive regulation of alpha-beta T cell proliferation / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / coreceptor activity / positive regulation of T cell proliferation ...CD28 dependent PI3K/Akt signaling / CD28 dependent Vav1 pathway / CD28 co-stimulation / CTLA4 inhibitory signaling / protein complex involved in cell adhesion / PIP3 activates AKT signaling / positive regulation of alpha-beta T cell proliferation / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / coreceptor activity / positive regulation of T cell proliferation / negative regulation of T cell proliferation / T cell costimulation / positive regulation of peptidyl-tyrosine phosphorylation / cellular response to lipopolysaccharide / membrane => GO:0016020 / cell surface receptor signaling pathway / immune response / external side of plasma membrane / cell surface / signal transduction
Similarity search - Function
CD80, IgC-like domain / CD80, immunoglobulin variable domain / CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain ...CD80, IgC-like domain / CD80, immunoglobulin variable domain / CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
T-lymphocyte activation antigen CD80
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.802 Å
AuthorsFedorov, A.A. / Fedorov, E.V. / Samanta, D. / Hillerich, B. / Seidel, R.D. / Almo, S.C.
CitationJournal: To be Published
Title: Crystal structure of T cell costimulatory ligand B7-1 (CD80)
Authors: Fedorov, A.A. / Fedorov, E.V. / Samanta, D. / Hillerich, B. / Seidel, R.D. / Almo, S.C.
History
DepositionDec 4, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 17, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: T-lymphocyte activation antigen CD80


Theoretical massNumber of molelcules
Total (without water)12,3351
Polymers12,3351
Non-polymers00
Water77543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.001, 54.001, 85.879
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41
Components on special symmetry positions
IDModelComponents
11A-219-

HOH

21A-239-

HOH

-
Components

#1: Protein T-lymphocyte activation antigen CD80 / Activation B7-1 antigen / B7


Mass: 12335.271 Da / Num. of mol.: 1 / Fragment: UNP residues 44-144
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cd80, B7 / Production host: Escherichia coli (E. coli) / References: UniProt: Q00609
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 43 / 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: 1.81 Å3/Da / Density % sol: 31.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2.4M sodium malonate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 3, 2014
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.802→28.534 Å / Num. all: 11322 / Num. obs: 11322 / % possible obs: 99.46 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

-
Processing

Software
NameVersionClassification
CBASSdata collection
BALBESphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DR9

1dr9


Resolution: 1.802→28.534 Å / SU ML: 0.15 / σ(F): 0 / Phase error: 31.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2178 339 2.99 %RANDOM
Rwork0.1867 ---
all0.1877 11322 --
obs0.1877 11322 99.46 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.802→28.534 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms843 0 0 43 886
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006859
X-RAY DIFFRACTIONf_angle_d0.9671157
X-RAY DIFFRACTIONf_dihedral_angle_d11.339327
X-RAY DIFFRACTIONf_chiral_restr0.069134
X-RAY DIFFRACTIONf_plane_restr0.004139
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.802-2.26970.26951690.22845456X-RAY DIFFRACTION99
2.2697-28.53770.20721700.17825527X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 68.0483 Å / Origin y: 11.3089 Å / Origin z: 1.2083 Å
111213212223313233
T0.3161 Å20.0011 Å20.0056 Å2-0.4275 Å2-0.0033 Å2--0.1815 Å2
L5.4531 °2-1.3481 °2-1.7733 °2-5.9184 °2-0.5347 °2--4.9708 °2
S0.0138 Å °0.0592 Å °0.1196 Å °-0.0023 Å °0.0259 Å °0.1725 Å °-0.5014 Å °-0.6802 Å °-0.036 Å °
Refinement TLS groupSelection details: chain A

+
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