[English] 日本語
Yorodumi
- PDB-8hxs: Small_spotted catshark CD8alpha -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8hxs
TitleSmall_spotted catshark CD8alpha
ComponentsT-cell surface glycoprotein CD8 alpha chain
KeywordsCYTOKINE / Cartilaginous fishes / CD8alpha
Function / homology
Function and homology information


CD8 alpha subunit / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain ...CD8 alpha subunit / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / 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
Similarity search - Domain/homology
T-cell surface glycoprotein CD8 alpha chain
Similarity search - Component
Biological speciesScyliorhinus canicula (smaller spotted catshark)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsWang, J. / Zou, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32030112 China
CitationJournal: Front Immunol / Year: 2023
Title: The first crystal structure of CD8 alpha alpha from a cartilaginous fish.
Authors: Jia, Z. / Feng, J. / Dooley, H. / Zou, J. / Wang, J.
History
DepositionJan 5, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 22, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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
Revision 1.2Apr 17, 2024Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details ..._pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: T-cell surface glycoprotein CD8 alpha chain


Theoretical massNumber of molelcules
Total (without water)11,3231
Polymers11,3231
Non-polymers00
Water2,252125
1
A: T-cell surface glycoprotein CD8 alpha chain

A: T-cell surface glycoprotein CD8 alpha chain


Theoretical massNumber of molelcules
Total (without water)22,6462
Polymers22,6462
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area1710 Å2
ΔGint-14 kcal/mol
Surface area10470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.384, 40.446, 32.828
Angle α, β, γ (deg.)90.000, 92.556, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-242-

HOH

21A-325-

HOH

-
Components

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


Mass: 11322.787 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Scyliorhinus canicula (smaller spotted catshark)
Production host: Escherichia coli (E. coli) / References: UniProt: A0A8A5LLJ8
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 2.12 Å3/Da / Density % sol: 41.98 %
Crystal growTemperature: 291.5 K / Method: vapor diffusion, sitting drop
Details: 30% (w/v) PEG3000 and 100mM CHES/Sodium hydroxide pH9.5

-
Data collection

DiffractionMean temperature: 291.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 19, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9979 Å / Relative weight: 1
ReflectionResolution: 1.35→50 Å / Num. obs: 20802 / % possible obs: 99.2 % / Redundancy: 12.4 % / CC1/2: 0.96 / Net I/σ(I): 2.19
Reflection shellResolution: 1.35→1.37 Å / CC1/2: 0.96

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.35→35.324 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.965 / SU B: 0.006 / SU ML: 0 / Cross valid method: THROUGHOUT / ESU R: 0.063 / ESU R Free: 0.064
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2161 1113 5.35 %
Rwork0.2124 19689 -
all0.213 --
obs-20802 99.218 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 21.784 Å2
Baniso -1Baniso -2Baniso -3
1--0.188 Å2-0 Å2-0.506 Å2
2---0.232 Å2-0 Å2
3---0.463 Å2
Refinement stepCycle: LAST / Resolution: 1.35→35.324 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms786 0 0 125 911
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.3850.4830.4331416X-RAY DIFFRACTION96.0282
1.385-1.4230.412930.3841389X-RAY DIFFRACTION99.5299
1.423-1.4640.38790.3321356X-RAY DIFFRACTION99.308
1.464-1.5090.284780.2681329X-RAY DIFFRACTION99.3644
1.509-1.5590.341650.2571302X-RAY DIFFRACTION99.7082
1.559-1.6130.257620.2371267X-RAY DIFFRACTION99.4016
1.613-1.6740.26840.2271214X-RAY DIFFRACTION99.6163
1.674-1.7420.25680.2221146X-RAY DIFFRACTION99.5082
1.742-1.8190.288460.2341131X-RAY DIFFRACTION99.4928
1.819-1.9080.237430.2191096X-RAY DIFFRACTION99.3025
1.908-2.0110.248500.2161027X-RAY DIFFRACTION99.5379
2.011-2.1320.253500.218952X-RAY DIFFRACTION99.3062
2.132-2.2790.217790.2885X-RAY DIFFRACTION99.6898
2.279-2.4610.222400.208860X-RAY DIFFRACTION99.5575
2.461-2.6940.241330.205791X-RAY DIFFRACTION99.6372
2.694-3.010.172360.195722X-RAY DIFFRACTION99.6058
3.01-3.4720.181430.172620X-RAY DIFFRACTION99.5496
3.472-4.2430.145460.153514X-RAY DIFFRACTION100
4.243-5.9590.157210.184435X-RAY DIFFRACTION99.7812
5.959-35.3240.241140.259237X-RAY DIFFRACTION96.5385

+
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