[English] 日本語
Yorodumi
- PDB-4mnh: Structure of the DP10.7 TCR -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4mnh
TitleStructure of the DP10.7 TCR
Components
  • Human nkt tcr alpha chain
  • T-cell receptor gamma chain V region PT-gamma-1/2, Human nkt tcr beta chain
KeywordsIMMUNE SYSTEM / Immunoglobulin / Histocompatibility antigens / T cell receptor / Immunological / lymphocytes / T cell recognition / activation / gamma delta T cell / Human / intraepithelial lymphocytes / CD1d / glycolipids / non-classical MHC / Glycoproteins / Cell-surface receptors
Function / homology
Function and homology information


Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / 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
Human nkt tcr beta chain / TRA@ protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsLuoma, A.M. / Adams, E.J.
CitationJournal: Immunity / Year: 2013
Title: Crystal Structure of V delta 1 T Cell Receptor in Complex with CD1d-Sulfatide Shows MHC-like Recognition of a Self-Lipid by Human gamma delta T Cells.
Authors: Luoma, A.M. / Castro, C.D. / Mayassi, T. / Bembinster, L.A. / Bai, L. / Picard, D. / Anderson, B. / Scharf, L. / Kung, J.E. / Sibener, L.V. / Savage, P.B. / Jabri, B. / Bendelac, A. / Adams, E.J.
History
DepositionSep 10, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2014Group: Database references
Revision 1.2Jun 14, 2017Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_src_gen ...entity / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: T-cell receptor gamma chain V region PT-gamma-1/2, Human nkt tcr beta chain
B: Human nkt tcr alpha chain
C: T-cell receptor gamma chain V region PT-gamma-1/2, Human nkt tcr beta chain
D: Human nkt tcr alpha chain


Theoretical massNumber of molelcules
Total (without water)109,3744
Polymers109,3744
Non-polymers00
Water0
1
A: T-cell receptor gamma chain V region PT-gamma-1/2, Human nkt tcr beta chain
B: Human nkt tcr alpha chain


Theoretical massNumber of molelcules
Total (without water)54,6872
Polymers54,6872
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4380 Å2
ΔGint-28 kcal/mol
Surface area20530 Å2
MethodPISA
2
C: T-cell receptor gamma chain V region PT-gamma-1/2, Human nkt tcr beta chain
D: Human nkt tcr alpha chain


Theoretical massNumber of molelcules
Total (without water)54,6872
Polymers54,6872
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4460 Å2
ΔGint-31 kcal/mol
Surface area20820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.261, 60.835, 99.086
Angle α, β, γ (deg.)90.00, 113.33, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
/ NCS ensembles :
ID
1
2

-
Components

#1: Protein T-cell receptor gamma chain V region PT-gamma-1/2, Human nkt tcr beta chain


Mass: 29284.555 Da / Num. of mol.: 2
Fragment: DP10.7 TCR gamma variable domain fused with human TCR beta constant domain
Mutation: S173C, C191A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRGV3, TCRB, B2M, HDCMA22P, B2M, HDCMA22P / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: K7N5M4
#2: Protein Human nkt tcr alpha chain


Mass: 25402.463 Da / Num. of mol.: 2
Fragment: DP10.7 TCR delta variable domain fused with human TCR alpha constant domain
Mutation: T167C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRA@ / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q6PJ56

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 47.31 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris pH 8.5, 20% PEG 10k, VAPOR DIFFUSION, SITTING DROP, temperature 292K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.0781 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 31, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0781 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. all: 15411 / Num. obs: 15411 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.2 %
Reflection shellResolution: 3.3→3.36 Å / Mean I/σ(I) obs: 2.07 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.3→49.415 Å / SU ML: 0.48 / σ(F): 1.36 / Phase error: 32.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2853 758 4.95 %
Rwork0.231 --
obs0.2337 15321 98.99 %
all-15321 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.3→49.415 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6440 0 0 0 6440
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026607
X-RAY DIFFRACTIONf_angle_d0.6329005
X-RAY DIFFRACTIONf_dihedral_angle_d10.5432199
X-RAY DIFFRACTIONf_chiral_restr0.0251013
X-RAY DIFFRACTIONf_plane_restr0.0041152
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.55480.37891740.2922877X-RAY DIFFRACTION99
3.5548-3.91240.34441450.2482896X-RAY DIFFRACTION99
3.9124-4.47820.25511410.20462923X-RAY DIFFRACTION99
4.4782-5.64070.25811490.20752897X-RAY DIFFRACTION99
5.6407-49.420.26531490.2362970X-RAY DIFFRACTION98

+
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