[English] 日本語
Yorodumi
- PDB-2jop: Solution structure of the N-terminal extracellular domain of the ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2jop
TitleSolution structure of the N-terminal extracellular domain of the lymphocyte receptor CD5 (CD5 domain 1)
ComponentsT-cell surface glycoprotein CD5
KeywordsIMMUNE SYSTEM / CD5 / domain 1 / scavenger receptor cysteine rich / SRCR
Function / homology
Function and homology information


cell recognition / T cell costimulation / apoptotic signaling pathway / signaling receptor activity / external side of plasma membrane / plasma membrane
Similarity search - Function
T-cell surface glycoprotein CD5 / Mac-2 Binding Protein / SRCR-like domain / Scavenger receptor cysteine-rich domain / SRCR domain / SRCR domain profile. / SRCR-like domain / SRCR-like domain superfamily / Scavenger receptor Cys-rich / Roll / Alpha Beta
Similarity search - Domain/homology
T-cell surface glycoprotein CD5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
AuthorsGarza-Garcia, A. / Harris, R. / Esposito, D. / Driscoll, P.C.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Three-dimensional solution structure and conformational plasticity of the N-terminal scavenger receptor cysteine-rich domain of human CD5
Authors: Garza-Garcia, A. / Esposito, D. / Rieping, W. / Harris, R. / Briggs, C. / Brown, M.H. / Driscoll, P.C.
History
DepositionMar 19, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 5, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Dec 20, 2023Group: Data collection / Other
Category: chem_comp_atom / chem_comp_bond / pdbx_database_status
Item: _pdbx_database_status.deposit_site

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: T-cell surface glycoprotein CD5


Theoretical massNumber of molelcules
Total (without water)14,7891
Polymers14,7891
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)50 / 500structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein T-cell surface glycoprotein CD5 / Lymphocyte antigen T1/Leu- 1


Mass: 14788.589 Da / Num. of mol.: 1 / Fragment: residues 25-134 / Mutation: V88D, V97K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD5, LEU1 / Production host: Escherichia coli (E. coli) / References: UniProt: P06127

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D 1H-15N NOESY
1313D 1H-15N TOCSY
1422D 1H-15N HSQC
1523D HNCA
1623D HNCO
1723D HA(CACO)NH
1823D CBCA(CO)NH
1923D HN(CA)CB
11032D 1H-13C HSQC
11133D 1H-13C NOESY

-
Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-15N] CD5d1, 50 mM sodium phosphate, 200 mM sodium chloride, 1 mM EDTA, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-13C; U-15N] CD5d1, 1 mM EDTA, 50 mM sodium phosphate, 200 mM sodium chloride, 90% H2O/10% D2O90% H2O/10% D2O
31 mM [U-13C; U-15N] CD5d1, 1 mM EDTA, 50 mM sodium phosphate, 200 mM sodium chloride, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMCD5d1[U-15N]1
50 mMsodium phosphate1
200 mMsodium chloride1
1 mMEDTA1
1 mMCD5d1[U-13C; U-15N]2
1 mMEDTA2
50 mMsodium phosphate2
200 mMsodium chloride2
1 mMCD5d1[U-13C; U-15N]3
1 mMEDTA3
50 mMsodium phosphate3
200 mMsodium chloride3
Sample conditionsIonic strength: 0.2 / pH: 5.0 / Pressure: ambient / Temperature: 318 K

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian UnityPlusVarianUNITYPLUS5002
Varian INOVAVarianINOVA8003

-
Processing

NMR software
NameVersionDeveloperClassification
NMRPipe3.3Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
ANSIG3.3Kraulisdata analysis
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 1092 / NOE intraresidue total count: 390 / NOE long range total count: 318 / NOE medium range total count: 92 / NOE sequential total count: 292 / Disulfide bond constraints total count: 8 / Hydrogen bond constraints total count: 68
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 500 / Conformers submitted total number: 50

+
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