[English] 日本語
Yorodumi
- PDB-4udt: T cell receptor (TRAV22,TRBV7-9) structure -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4udt
TitleT cell receptor (TRAV22,TRBV7-9) structure
Components
  • PROTEIN TRBV7-9, T-CELL RECEPTOR BETA-2 CHAIN C REGION
  • T CELL RECEPTOR ALPHA CHAIN, T-CELL RECEPTOR ALPHA CHAIN C REGION
KeywordsIMMUNE SYSTEM / SUPERANTIGEN / STAPHYLCOCOCCAL ENTEROTOXIN / T CELL RECEPTOR / MAJOR HISTOCOMPATIBILITY COMPLEX
Function / homology
Function and homology information


alpha-beta T cell receptor complex / T cell receptor complex / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / alpha-beta T cell activation / Generation of second messenger molecules / PD-1 signaling / response to bacterium / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Downstream TCR signaling ...alpha-beta T cell receptor complex / T cell receptor complex / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / alpha-beta T cell activation / Generation of second messenger molecules / PD-1 signaling / response to bacterium / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Downstream TCR signaling / T cell receptor signaling pathway / adaptive immune response / plasma membrane
Similarity search - Function
T-cell receptor alpha chain, constant domain / Domain of unknown function (DUF1968) / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain ...T-cell receptor alpha chain, constant domain / Domain of unknown function (DUF1968) / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / 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 cell receptor alpha variable 22 / V_segment translation product / T cell receptor beta constant 2 / T cell receptor alpha chain constant
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsRodstrom, K.E.J. / Regenthal, P. / Lindkvist-Petersson, K.
CitationJournal: Plos One / Year: 2015
Title: Structure of Staphylococcal Enterotoxin E in Complex with Tcr Defines the Role of Tcr Loop Positioning in Superantigen Recognition.
Authors: Rodstrom, K.E.J. / Regenthal, P. / Lindkvist-Petersson, K.
History
DepositionDec 11, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 24, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2015Group: Database references
Revision 1.2Mar 15, 2017Group: Source and taxonomy
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: T CELL RECEPTOR ALPHA CHAIN, T-CELL RECEPTOR ALPHA CHAIN C REGION
B: PROTEIN TRBV7-9, T-CELL RECEPTOR BETA-2 CHAIN C REGION
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6703
Polymers50,5782
Non-polymers921
Water5,567309
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4530 Å2
ΔGint-28 kcal/mol
Surface area20640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.071, 79.747, 69.035
Angle α, β, γ (deg.)90.00, 105.86, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein T CELL RECEPTOR ALPHA CHAIN, T-CELL RECEPTOR ALPHA CHAIN C REGION


Mass: 22812.125 Da / Num. of mol.: 1
Fragment: VARIABLE DOMAIN TRAV22, RESIDUES 1-112, CONSTANT DOMAIN TRAC1, RESIDUES 2-95
Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell: T-LYMPHOCYTE / Gene: TRAC, TCRA / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): STAR / References: UniProt: P01848, UniProt: A0A0B4J277*PLUS
#2: Protein PROTEIN TRBV7-9, T-CELL RECEPTOR BETA-2 CHAIN C REGION


Mass: 27765.832 Da / Num. of mol.: 1
Fragment: VARIABLE DOMAIN TRBV7-9, RESIDUES 20-115, CONSTANT DOMAIN TRBC2, RESIDUES 1-129
Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell: T-LYMPHOCYTE / Gene: TCRBV6S4A1, TRBV7-9, TRBC2, TCRBC2 / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): STAR / References: UniProt: A0A5A3, UniProt: A0A5B9
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 309 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE STRUCTURE CONTAINS EXTRACELLULAR TCR ALPHA VARIABLE AND CONSTANT DOMAINS. DATABASE REFERENCE IS ...THE STRUCTURE CONTAINS EXTRACELLULAR TCR ALPHA VARIABLE AND CONSTANT DOMAINS. DATABASE REFERENCE IS ONLY AVAILABLE FOR THE CONSTANT DOMAIN. ENGINEERED DISULPHIDE BOND BETWEEN THE TRAC AND TRBC DOMAINS. THE STRUCTURE CONTAINS EXTRACELLULAR TCR BETA VARIABLE AND CONSTANT DOMAINS. DATABASE REFERENCE IS ONLY AVAILABLE FOR THE CONSTANT DOMAIN. ENGINEERED DISULPHIDE BOND BETWEEN THE TRAC AND TRBC DOMAINS.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.05 Å3/Da / Density % sol: 40 %
Description: TRAV, TRAC, TRBC DOMAINS FROM 2IAL. TRBV DOMAIN FROM 2DX9.
Crystal growpH: 8.5
Details: 22% W/V PEG 2000 MME, 0.1 M NH4CL PH 8.5, 0.1 M NACL

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 23, 2013 / Details: TOROIDAL MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.34→39.9 Å / Num. obs: 87661 / % possible obs: 97.1 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Biso Wilson estimate: 25.46 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 20.2
Reflection shellResolution: 1.34→1.43 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 3.5 / % possible all: 89.5

-
Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
Aimlessdata scaling
PHASER2.5.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2IAL, 2DX9

2ial

2dx9


Resolution: 1.35→39.91 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.966 / SU B: 2.249 / SU ML: 0.043 / Cross valid method: THROUGHOUT / ESU R: 0.063 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. INITIAL REFINEMENT IN BUSTER 2.10.0 AND CNS 1.3
RfactorNum. reflection% reflectionSelection details
Rfree0.19291 4341 5 %RANDOM
Rwork0.15569 ---
obs0.15752 82162 96.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.77 Å2
Baniso -1Baniso -2Baniso -3
1--0.94 Å20 Å2-0.42 Å2
2--0.4 Å2-0 Å2
3---0.57 Å2
Refinement stepCycle: LAST / Resolution: 1.35→39.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3472 0 6 309 3787
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0193819
X-RAY DIFFRACTIONr_bond_other_d0.0010.023425
X-RAY DIFFRACTIONr_angle_refined_deg1.1471.9295234
X-RAY DIFFRACTIONr_angle_other_deg0.6913.0037874
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3385491
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.32723.989188
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.6715598
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7281527
X-RAY DIFFRACTIONr_chiral_restr0.0730.2557
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214568
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02967
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.2862.2141898
X-RAY DIFFRACTIONr_mcbond_other2.26924.1621897
X-RAY DIFFRACTIONr_mcangle_it2.9873.3332411
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.8292.5391921
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.5833.6872824
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr1.5533814
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded17.47653695
LS refinement shellResolution: 1.346→1.38 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.443 261 -
Rwork0.374 4800 -
obs--76.51 %

+
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