[English] 日本語
Yorodumi
- PDB-4ww1: Crystal structure of human TCR Alpha Chain-TRAV21-TRAJ8 and Beta ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ww1
TitleCrystal structure of human TCR Alpha Chain-TRAV21-TRAJ8 and Beta Chain-TRBV7-8
Components
  • TCR Alpha Chain-TRAV21-TRAJ8
  • TCR Beta Chain-TRBV7-8
KeywordsIMMUNE SYSTEM / Immunity / NKT cells
Function / homology
Function and homology information


alpha-beta T cell receptor complex / T cell receptor complex / alpha-beta T cell activation / immunoglobulin complex, circulating / immunoglobulin receptor binding / complement activation, classical pathway / antigen binding / response to bacterium / peptide antigen binding / T cell receptor signaling pathway ...alpha-beta T cell receptor complex / T cell receptor complex / alpha-beta T cell activation / immunoglobulin complex, circulating / immunoglobulin receptor binding / complement activation, classical pathway / antigen binding / response to bacterium / peptide antigen binding / T cell receptor signaling pathway / antibacterial humoral response / adaptive immune response / blood microparticle / extracellular exosome / plasma membrane
Similarity search - Function
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 ...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 21 / T cell receptor beta constant 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.38 Å
AuthorsLe Nours, J. / Praveena, T. / Pellicci, D.G. / Lim, R.T. / Besra, G. / Howell, A.R. / Godfrey, D.I. / Rossjohn, J. / Uldrich, A.P.
CitationJournal: Nat Commun / Year: 2016
Title: Atypical natural killer T-cell receptor recognition of CD1d-lipid antigens.
Authors: Le Nours, J. / Praveena, T. / Pellicci, D.G. / Gherardin, N.A. / Ross, F.J. / Lim, R.T. / Besra, G.S. / Keshipeddy, S. / Richardson, S.K. / Howell, A.R. / Gras, S. / Godfrey, D.I. / Rossjohn, J. / Uldrich, A.P.
History
DepositionNov 10, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 4, 2018Group: Data collection / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / diffrn_source / pdbx_struct_oper_list
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 / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TCR Alpha Chain-TRAV21-TRAJ8
B: TCR Beta Chain-TRBV7-8


Theoretical massNumber of molelcules
Total (without water)49,9422
Polymers49,9422
Non-polymers00
Water8,305461
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4050 Å2
ΔGint-28 kcal/mol
Surface area21470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.110, 73.120, 65.600
Angle α, β, γ (deg.)90.00, 94.49, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein TCR Alpha Chain-TRAV21-TRAJ8


Mass: 22573.988 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0B4J279*PLUS
#2: Protein TCR Beta Chain-TRBV7-8


Mass: 27368.352 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A5B9*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 461 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.06 Å3/Da / Density % sol: 40.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 20% PEG 3000 0.2M Na Acetate 0.1M Tris-HCl 7.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 18, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.38→37.28 Å / Num. obs: 83037 / % possible obs: 99.7 % / Redundancy: 4.1 % / Biso Wilson estimate: 15.28 Å2 / Net I/σ(I): 9.8
Reflection shellResolution: 1.38→1.45 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 2.1 / % possible all: 98.8

-
Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2PO6

2po6


Resolution: 1.38→27.6 Å / Cor.coef. Fo:Fc: 0.9526 / Cor.coef. Fo:Fc free: 0.9419 / SU R Cruickshank DPI: 0.065 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.067 / SU Rfree Blow DPI: 0.066 / SU Rfree Cruickshank DPI: 0.064
RfactorNum. reflection% reflectionSelection details
Rfree0.2129 4150 5 %RANDOM
Rwork0.193 ---
obs0.194 83037 99.69 %-
Displacement parametersBiso mean: 20 Å2
Baniso -1Baniso -2Baniso -3
1--1.0554 Å20 Å20.6332 Å2
2--0.4237 Å20 Å2
3---0.6317 Å2
Refine analyzeLuzzati coordinate error obs: 0.169 Å
Refinement stepCycle: LAST / Resolution: 1.38→27.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3510 0 0 461 3971
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013631HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.095010HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1703SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes102HARMONIC2
X-RAY DIFFRACTIONt_gen_planes566HARMONIC5
X-RAY DIFFRACTIONt_it3631HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion4.51
X-RAY DIFFRACTIONt_other_torsion2.59
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion489SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4460SEMIHARMONIC4
LS refinement shellResolution: 1.38→1.42 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.22 295 4.96 %
Rwork0.2103 5656 -
all0.2108 5951 -
obs--99.69 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.7141-0.02830.43990.4466-0.18170.7452-0.02320.0218-0.02960.01320.08120.0778-0.0461-0.0867-0.058-0.00880.0120.0125-0.02220.0174-0.0368-0.7918-4.684295.7034
20.0907-0.0606-0.13260.26150.0010.4531-0.0111-0.0094-0.0228-0.0282-0.02470.0006-0.0085-0.03120.0358-0.0128-0.00040.0005-0.0490.0008-0.053414.9455-0.865584.4898
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

+
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