[English] 日本語
Yorodumi
- PDB-1cd8: CRYSTAL STRUCTURE OF A SOLUBLE FORM OF THE HUMAN T CELL CO-RECEPT... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1cd8
TitleCRYSTAL STRUCTURE OF A SOLUBLE FORM OF THE HUMAN T CELL CO-RECEPTOR CD8 AT 2.6 ANGSTROMS RESOLUTION
ComponentsT CELL CORECEPTOR CD8
KeywordsSURFACE GLYCOPROTEIN
Function / homology
Function and homology information


cytotoxic T cell differentiation / MHC class I protein complex binding / T cell mediated immunity / T cell receptor complex / antigen processing and presentation / MHC class I protein binding / plasma membrane raft / coreceptor activity / cell surface receptor protein tyrosine kinase signaling pathway / T cell activation ...cytotoxic T cell differentiation / MHC class I protein complex binding / T cell mediated immunity / T cell receptor complex / antigen processing and presentation / MHC class I protein binding / plasma membrane raft / coreceptor activity / cell surface receptor protein tyrosine kinase signaling pathway / T cell activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / T cell receptor signaling pathway / adaptive immune response / cell surface receptor signaling pathway / receptor complex / immune response / external side of plasma membrane / extracellular region / plasma membrane
Similarity search - Function
CD8 alpha subunit / Immunoglobulin V-Type / 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 ...CD8 alpha subunit / Immunoglobulin V-Type / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
T-cell surface glycoprotein CD8 alpha chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.6 Å
AuthorsLeahy, D.J. / Axel, R. / Hendrickson, W.A.
CitationJournal: Cell(Cambridge,Mass.) / Year: 1992
Title: Crystal structure of a soluble form of the human T cell coreceptor CD8 at 2.6 A resolution.
Authors: Leahy, D.J. / Axel, R. / Hendrickson, W.A.
History
DepositionJan 16, 1992Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: T CELL CORECEPTOR CD8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9462
Polymers12,8501
Non-polymers961
Water41423
1
A: T CELL CORECEPTOR CD8
hetero molecules

A: T CELL CORECEPTOR CD8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8914
Polymers25,6992
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+2/31
Unit cell
Length a, b, c (Å)101.000, 101.000, 55.850
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
Atom site foot note1: RESIDUE PRO 7 IS A CIS PROLINE.

-
Components

#1: Protein T CELL CORECEPTOR CD8


Mass: 12849.552 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P01732
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.2 Å3/Da / Density % sol: 61.54 %
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
125-30 %(w/v)PEG33501reservoir
23.75 %satammonium sulphate1reservoir
310 mMsodium citrate1reservoir
55-10 mg/mldH2O1drop
610 mMsodium citrate1drop
4sCD81drop0.001ml

-
Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 30 Å / Num. obs: 4347 / Observed criterion σ(F): 2 / Num. measured all: 19913 / Rmerge(I) obs: 0.105
Reflection shell
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 2.69 Å / % possible obs: 44 % / Num. unique obs: 226 / Num. measured obs: 597 / Rmerge(I) obs: 0.323

-
Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.6→8 Å / σ(F): 0
Details: THREE SHORT LOOP REGIONS HAVE POOR ELECTRON DENSITY AND AVERAGE B-FACTORS ABOVE 50A**2: (I) SER 27-SER 31, (II) GLN 54-LYS 56, (III) ARG 40-ALA 43. IN THESE REGIONS SUFFICIENT MAIN-CHAIN ...Details: THREE SHORT LOOP REGIONS HAVE POOR ELECTRON DENSITY AND AVERAGE B-FACTORS ABOVE 50A**2: (I) SER 27-SER 31, (II) GLN 54-LYS 56, (III) ARG 40-ALA 43. IN THESE REGIONS SUFFICIENT MAIN-CHAIN DENSITY IS PRESENT TO PROVIDE CONFIDENCE THAT THE COURSE OF THE MAIN-CHAIN IS GENERALLY CORRECT, BUT THE EXACT MAIN-CHAIN TORSION ANGLES AND SIDE-CHAIN POSITIONS ARE NOT WELL DEFINED.
RfactorNum. reflection
Rwork0.192 -
obs0.192 18872
Refinement stepCycle: LAST / Resolution: 2.6→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1111 0 5 69 1185
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3.1
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 8 Å / Num. reflection all: 18872 / σ(F): 0 / Rfactor all: 0.192
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 3.1

+
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