[English] 日本語
Yorodumi
- PDB-2atp: Crystal structure of a CD8ab heterodimer -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2atp
TitleCrystal structure of a CD8ab heterodimer
Components
  • T-cell surface glycoprotein CD8 alpha chain
  • T-cell surface glycoprotein CD8 beta chain
  • artifact linker
KeywordsIMMUNE SYSTEM / CD8ab / CD8aa / MHC
Function / homology
Function and homology information


cytotoxic T cell differentiation / T cell mediated immunity / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / MHC class I protein binding / coreceptor activity / positive regulation of calcium-mediated signaling / T cell activation / calcium-mediated signaling / T cell receptor signaling pathway / defense response to virus ...cytotoxic T cell differentiation / T cell mediated immunity / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / MHC class I protein binding / coreceptor activity / positive regulation of calcium-mediated signaling / T cell activation / calcium-mediated signaling / T cell receptor signaling pathway / defense response to virus / adaptive immune response / receptor complex / cell surface receptor signaling pathway / external side of plasma membrane / cell surface / identical protein binding / plasma membrane
Similarity search - Function
T-cell surface glycoprotein CD8 beta chain / 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 ...T-cell surface glycoprotein CD8 beta chain / 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 / T-cell surface glycoprotein CD8 beta chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsChang, H.C. / Tan, K. / Ouyang, J. / Parisini, E. / Liu, J.H. / Le, Y. / Wang, X. / Reinherz, E.L. / Wang, J.H.
CitationJournal: Immunity / Year: 2005
Title: Structural and Mutational Analyses of a CD8alphabeta Heterodimer and Comparison with the CD8alphaalpha Homodimer.
Authors: Chang, H.C. / Tan, K. / Ouyang, J. / Parisini, E. / Liu, J.H. / Le, Y. / Wang, X. / Reinherz, E.L. / Wang, J.H.
History
DepositionAug 25, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 27, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jul 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_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Aug 23, 2023Group: 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
Revision 1.5Oct 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 surface glycoprotein CD8 alpha chain
E: artifact linker
B: T-cell surface glycoprotein CD8 beta chain
C: T-cell surface glycoprotein CD8 alpha chain
F: artifact linker
D: T-cell surface glycoprotein CD8 beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4849
Polymers59,8206
Non-polymers6643
Water79344
1
A: T-cell surface glycoprotein CD8 alpha chain
E: artifact linker
B: T-cell surface glycoprotein CD8 beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1314
Polymers29,9103
Non-polymers2211
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: T-cell surface glycoprotein CD8 alpha chain
F: artifact linker
D: T-cell surface glycoprotein CD8 beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3525
Polymers29,9103
Non-polymers4422
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.668, 92.655, 79.330
Angle α, β, γ (deg.)90.00, 95.67, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein T-cell surface glycoprotein CD8 alpha chain / T-cell surface glycoprotein Lyt-2


Mass: 13842.911 Da / Num. of mol.: 2 / Fragment: CD8a ectodomain fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cd8a, Lyt-2, Lyt2 / Plasmid: pEE14 / Production host: Cricetulus griseus (Chinese hamster) / Strain (production host): CHO-Lec 3.8.2.1 / References: UniProt: P01731
#2: Protein/peptide artifact linker


Mass: 3028.172 Da / Num. of mol.: 2
Fragment: a peptide used to connect CD8a C-terminal and CD8b N-terminal
Source method: obtained synthetically / Details: synthetic linker
#3: Protein T-cell surface glycoprotein CD8 beta chain / T-cell surface glycoprotein Lyt-3 / T-cell membrane glycoprotein Ly-3


Mass: 13038.967 Da / Num. of mol.: 2 / Fragment: CD8b ectodomain fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cd8b, Lyt-3, Lyt3 / Plasmid: pEE14 / Production host: Cricetulus griseus (Chinese hamster) / Strain (production host): CHO-Lec 3.8.2.1 / References: UniProt: P10300
#4: 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.: 3
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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 25% PEG4000, 0.2M (NH4)2SO4, 0.1 M Tris , pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 5, 2004
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 21001 / Num. obs: 21001 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 51.2 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 17.8
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.1 / Num. unique all: 2071 / % possible all: 96.8

-
Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
PHASESphasing
CNS1.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BQH

1bqh


Resolution: 2.4→25 Å / Isotropic thermal model: Isotropic / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.294 1497 -RANDOM
Rwork0.242 ---
obs0.246 19292 90.9 %-
all-20984 --
Displacement parametersBiso mean: 52.314 Å2
Refine analyzeLuzzati coordinate error obs: 0.38 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.6 Å
Refinement stepCycle: LAST / Resolution: 2.4→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3750 0 42 44 3836
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d0.0092
X-RAY DIFFRACTIONc_angle_deg1.913
X-RAY DIFFRACTIONc_dihedral_angle_d27.842
X-RAY DIFFRACTIONc_improper_angle_d1.649
LS refinement shellResolution: 2.4→2.49 Å
RfactorNum. reflection
Rfree0.457 121
Rwork0.406 -
obs-1550

+
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