[English] 日本語
Yorodumi
- PDB-3qjf: Crystal structure of the 2B4 TCR -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3qjf
TitleCrystal structure of the 2B4 TCR
Components
  • 2B4 alpha chain
  • 2B4 beta chain
KeywordsIMMUNE SYSTEM / immunoglobulin domain / T cell receptor
Function / homology
Function and homology information


alpha-beta 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 ...alpha-beta 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-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
T cell receptor alpha chain constant
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsEly, L.K. / Newell, E.W. / Davis, M.M. / Garcia, K.C.
CitationJournal: J.Immunol. / Year: 2011
Title: Structural basis of specificity and cross-reactivity in T cell receptors specific for cytochrome c-I-E(k).
Authors: Newell, E.W. / Ely, L.K. / Kruse, A.C. / Reay, P.A. / Rodriguez, S.N. / Lin, A.E. / Kuhns, M.S. / Garcia, K.C. / Davis, M.M.
History
DepositionJan 28, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 27, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 10, 2011Group: Database references

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 2B4 alpha chain
B: 2B4 beta chain
C: 2B4 alpha chain
D: 2B4 beta chain


Theoretical massNumber of molelcules
Total (without water)101,3234
Polymers101,3234
Non-polymers00
Water4,035224
1
A: 2B4 alpha chain
B: 2B4 beta chain


Theoretical massNumber of molelcules
Total (without water)50,6612
Polymers50,6612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4250 Å2
ΔGint-21 kcal/mol
Surface area20730 Å2
MethodPISA
2
C: 2B4 alpha chain
D: 2B4 beta chain


Theoretical massNumber of molelcules
Total (without water)50,6612
Polymers50,6612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4310 Å2
ΔGint-21 kcal/mol
Surface area20300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.850, 93.850, 388.751
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

-
Components

#1: Protein 2B4 alpha chain


Mass: 22807.115 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: P01848*PLUS
#2: Protein 2B4 beta chain


Mass: 27854.223 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / 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: 2.44 Å3/Da / Density % sol: 49.57 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 7.7
Details: 20 % PEG3350, 0.1 M calcium chloride and Tris, pH 7.7, VAPOR DIFFUSION, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 1, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→46.587 Å / Num. all: 40602 / Num. obs: 40602 / % possible obs: 99.5 % / Redundancy: 14.2 % / Rsym value: 0.132 / Net I/σ(I): 14.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.4-2.5314.50.73518367157540.73599.2
2.53-2.6814.50.5331.47970154820.53399.3
2.68-2.8714.50.3612.17455651400.36199.4
2.87-3.114.40.23536993448460.23599.5
3.1-3.3914.30.1574.46438644910.15799.6
3.39-3.7914.30.115.85834740770.1199.6
3.79-4.3814.10.0846.95154336500.08499.7
4.38-5.3713.90.0727.94371531410.07299.7
5.37-7.5913.50.0827.13377025080.08299.9
7.59-46.58712.20.0619.31846815130.06199.3

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
SCALA3.3.15data scaling
PHASERphasing
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→46.587 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8156 / SU ML: 0.36 / σ(F): 1.35 / Phase error: 24.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2587 2034 5.01 %
Rwork0.2096 --
obs0.212 40595 99.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.942 Å2 / ksol: 0.386 e/Å3
Displacement parametersBiso max: 96.07 Å2 / Biso mean: 39.1734 Å2 / Biso min: 15.5 Å2
Baniso -1Baniso -2Baniso -3
1-3.8279 Å20 Å2-0 Å2
2--3.8279 Å20 Å2
3----7.6558 Å2
Refinement stepCycle: LAST / Resolution: 2.4→46.587 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6817 0 0 224 7041
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016983
X-RAY DIFFRACTIONf_angle_d1.1689455
X-RAY DIFFRACTIONf_chiral_restr0.0771033
X-RAY DIFFRACTIONf_plane_restr0.0051243
X-RAY DIFFRACTIONf_dihedral_angle_d15.2022529
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4-2.48580.32521980.26063736393499
2.4858-2.58530.33982010.26453741394299
2.5853-2.7030.32811970.2633755395299
2.703-2.84540.33281930.23913803399699
2.8454-3.02370.29982070.22253780398799
3.0237-3.25710.24182300.20653792402299
3.2571-3.58480.26111980.20833833403199
3.5848-4.10320.22851950.19373905410099
4.1032-5.16850.19491910.16193980417199
5.1685-46.59560.27082240.225842364460100

+
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