[English] 日本語
Yorodumi
- PDB-1g6r: A FUNCTIONAL HOT SPOT FOR ANTIGEN RECOGNITION IN A SUPERAGONIST T... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1g6r
TitleA FUNCTIONAL HOT SPOT FOR ANTIGEN RECOGNITION IN A SUPERAGONIST TCR/MHC COMPLEX
Components
  • ALPHA T CELL RECEPTOR
  • BETA T CELL RECEPTOR
  • BETA-2 MICROGLOBULIN
  • MAJOR HISTOCOMPATIBILITY COMPLEX CLASS I MOLECULE
  • SIYR PEPTIDE
KeywordsIMMUNE SYSTEM / T CELL ANTIGEN RECEPTOR / MAJOR HISTOCOMPATIBILITY COMPLEX / SUPERAGONIST
Function / homology
Function and homology information


alpha-beta T cell receptor complex / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / T cell receptor complex / antigen processing and presentation of exogenous peptide antigen via MHC class I / inner ear development ...alpha-beta T cell receptor complex / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / T cell receptor complex / antigen processing and presentation of exogenous peptide antigen via MHC class I / inner ear development / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / cellular defense response / Neutrophil degranulation / lumenal side of endoplasmic reticulum membrane / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / iron ion transport / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / regulation of erythrocyte differentiation / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / peptide antigen binding / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / phagocytic vesicle membrane / negative regulation of epithelial cell proliferation / sensory perception of smell / positive regulation of cellular senescence / T cell differentiation in thymus / negative regulation of neuron projection development / protein refolding / protein homotetramerization / amyloid fibril formation / adaptive immune response / intracellular iron ion homeostasis / learning or memory / defense response to bacterium / external side of plasma membrane / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / cytosol
Similarity search - Function
: / : / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Immunoglobulin V-Type / Beta-2-Microglobulin ...: / : / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Immunoglobulin V-Type / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / Immunoglobulin V-set domain / MHC classes I/II-like antigen recognition protein / Immunoglobulin V-set domain / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
T-cell receptor alpha chain V region PHDS58 / T-cell receptor beta-1 chain C region / Beta-2-microglobulin / H-2 class I histocompatibility antigen, K-B alpha chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsDegano, M. / Garcia, K.C. / Apostolopoulos, V. / Rudolph, M.G. / Teyton, L. / Wilson, I.A.
Citation
Journal: Immunity / Year: 2000
Title: A functional hot spot for antigen recognition in a superagonist TCR/MHC complex.
Authors: Degano, M. / Garcia, K.C. / Apostolopoulos, V. / Rudolph, M.G. / Teyton, L. / Wilson, I.A.
#1: Journal: Science / Year: 1998
Title: Structural basis of plasticity in T cell receptor recognition of a self peptide-MHC antigen
Authors: Garcia, K.C. / Degano, M. / Pease, L.R. / Huang, M. / Peterson, P.A. / Teyton, L. / Wilson, I.A.
History
DepositionNov 7, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 15, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ALPHA T CELL RECEPTOR
B: BETA T CELL RECEPTOR
H: MAJOR HISTOCOMPATIBILITY COMPLEX CLASS I MOLECULE
L: BETA-2 MICROGLOBULIN
P: SIYR PEPTIDE
C: ALPHA T CELL RECEPTOR
D: BETA T CELL RECEPTOR
I: MAJOR HISTOCOMPATIBILITY COMPLEX CLASS I MOLECULE
M: BETA-2 MICROGLOBULIN
Q: SIYR PEPTIDE


Theoretical massNumber of molelcules
Total (without water)185,94210
Polymers185,94210
Non-polymers00
Water00
1
A: ALPHA T CELL RECEPTOR
B: BETA T CELL RECEPTOR
H: MAJOR HISTOCOMPATIBILITY COMPLEX CLASS I MOLECULE
L: BETA-2 MICROGLOBULIN
P: SIYR PEPTIDE


Theoretical massNumber of molelcules
Total (without water)92,9715
Polymers92,9715
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: ALPHA T CELL RECEPTOR
D: BETA T CELL RECEPTOR
I: MAJOR HISTOCOMPATIBILITY COMPLEX CLASS I MOLECULE
M: BETA-2 MICROGLOBULIN
Q: SIYR PEPTIDE


Theoretical massNumber of molelcules
Total (without water)92,9715
Polymers92,9715
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)297.710, 94.570, 84.890
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein ALPHA T CELL RECEPTOR


Mass: 22298.889 Da / Num. of mol.: 2 / Fragment: EXTRACELLULAR DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P01738
#2: Protein BETA T CELL RECEPTOR


Mass: 26284.180 Da / Num. of mol.: 2 / Fragment: EXTRACELLULAR DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P01852
#3: Protein MAJOR HISTOCOMPATIBILITY COMPLEX CLASS I MOLECULE


Mass: 31648.322 Da / Num. of mol.: 2 / Fragment: EXTRACELLULAR DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P01901
#4: Protein BETA-2 MICROGLOBULIN


Mass: 11704.359 Da / Num. of mol.: 2 / Fragment: NON-COVALENTLY ASSOCIATED WITH ENTITY 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P01887
#5: Protein/peptide SIYR PEPTIDE


Mass: 1035.176 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthetic peptide
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.21 Å3/Da / Density % sol: 61.7 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 7.2
Details: 0.2 M Tris/acetate, 10% PEG 6000, pH 7.2, VAPOR DIFFUSION, temperature 22K
Crystal grow
*PLUS
Method: unknown
Details: used macroseeding, Garcia, K.C., (1997) Proc.Natl.Acad.Sci.USA., 94, 13838.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
112 %PEG400011
20.2 MTris acetate11
30.1 M11NaCl

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 52209 / % possible obs: 83.9 % / Redundancy: 4.5 % / Biso Wilson estimate: 62.4 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 20.3
Reflection shellResolution: 2.7→2.8 Å / Rmerge(I) obs: 0.389 / Mean I/σ(I) obs: 2.9 / % possible all: 93
Reflection
*PLUS
Lowest resolution: 50 Å
Reflection shell
*PLUS
% possible obs: 93 %

-
Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.3267 1316 RANDOM
Rwork0.2976 --
all-52177 -
Refinement stepCycle: LAST / Resolution: 2.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13100 0 0 0 13100
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.64
X-RAY DIFFRACTIONc_improper_angle_d0.86
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 50 Å / σ(F): 0 / % reflection Rfree: 2 % / Rfactor obs: 0.29
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.86

+
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