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- PDB-43rh: Crystal structure of TCR C3K in complex with H2-Q9/VP2.139 -

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Basic information

Entry
Database: PDB / ID: 43rh
TitleCrystal structure of TCR C3K in complex with H2-Q9/VP2.139
Components
  • (T cell receptor ...) x 2
  • Beta-2-microglobulin
  • Histocompatibility 2, Q region locus 7
  • Minor capsid protein VP2
KeywordsIMMUNE SYSTEM / Complex / TCR / MHC / Viral
Function / homology
Function and homology information


NK T cell differentiation / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / alpha-beta T cell receptor complex / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / T cell receptor complex / Translocation of ZAP-70 to Immunological synapse ...NK T cell differentiation / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / alpha-beta T cell receptor complex / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / T cell receptor complex / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / regulation of membrane depolarization / alpha-beta T cell activation / Generation of second messenger molecules / Co-inhibition by PD-1 / antigen processing and presentation of peptide antigen via MHC class I / cellular defense response / response to bacterium / Neutrophil degranulation / lumenal side of endoplasmic reticulum membrane / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / regulation of iron ion transport / cellular response to iron(III) ion / negative regulation of iron ion transport / negative regulation of forebrain neuron differentiation / response to molecule of bacterial origin / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / iron ion transport / HFE-transferrin receptor complex / MHC class I peptide loading complex / transferrin transport / negative regulation of receptor-mediated endocytosis / cellular response to iron ion / positive regulation of T cell cytokine production / multicellular organismal-level iron ion homeostasis / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / peptide antigen assembly with MHC class II protein complex / positive regulation of T cell mediated cytotoxicity / negative regulation of epithelial cell proliferation / cellular response to nicotine / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / viral penetration into host nucleus / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / peptide antigen binding / phagocytic vesicle membrane / positive regulation of T cell activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / T cell differentiation in thymus / viral capsid / sensory perception of smell / positive regulation of cellular senescence / MHC class II protein complex binding / T cell receptor signaling pathway / negative regulation of neuron projection development / Downstream TCR signaling / late endosome membrane / host cell / antimicrobial humoral immune response mediated by antimicrobial peptide / cellular response to lipopolysaccharide / protein refolding / antibacterial humoral response / amyloid fibril formation / defense response to Gram-negative bacterium / protein homotetramerization / adaptive immune response / intracellular iron ion homeostasis / learning or memory / cell surface receptor signaling pathway / defense response to Gram-positive bacterium / immune response / host cell endoplasmic reticulum membrane / external side of plasma membrane / innate immune response / lysosomal membrane / symbiont entry into host cell / host cell nucleus / Golgi apparatus / structural molecule activity / protein homodimerization activity / DNA binding / : / membrane / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Polyomavirus coat protein VP2 / Polyomavirus coat protein / : / : / T-cell receptor alpha chain, constant domain / Domain of unknown function (DUF1968) / : / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Immunoglobulin V-Type ...Polyomavirus coat protein VP2 / Polyomavirus coat protein / : / : / T-cell receptor alpha chain, constant domain / Domain of unknown function (DUF1968) / : / 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 C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
T cell receptor alpha variable 13D-1 / T cell receptor beta joining 1-1 / T cell receptor beta, variable 2 / T cell receptor alpha joining 18 / T cell receptor alpha chain constant / T cell receptor beta constant 1 / Beta-2-microglobulin / Minor capsid protein VP2 / Histocompatibility 2, Q region locus 7
Similarity search - Component
Biological speciesMus musculus (house mouse)
Alphapolyomavirus muris
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.33 Å
AuthorsTennant, L. / Jobichen, C. / Tran, M.T. / Littler, D.R. / Farenc, C. / Gras, S. / Lukacher, A.E. / Sullivan, L.C. / Brooks, A.G. / Rossjohn, J.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC) Australia
CitationJournal: To Be Published
Title: A murine MHC-Ib molecule, H2-Q9, drives peptide-centric T cell receptor recognition of a viral antigen
Authors: Tennant, L. / Jobichen, C. / Tran, M.T. / Littler, D.R. / Farenc, C. / Gras, S. / Lukacher, A.E. / Sullivan, L.C. / Brooks, A.G. / Rossjohn, J.
History
DepositionJul 14, 2026Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 29, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histocompatibility 2, Q region locus 7
B: Beta-2-microglobulin
C: T cell receptor alpha variable 13D-1,T cell receptor alpha joining 18,T cell receptor alpha chain constant
D: T cell receptor beta, variable 2,T cell receptor beta joining 1-1,T cell receptor beta constant 1
P: Minor capsid protein VP2
E: T cell receptor alpha variable 13D-1,T cell receptor alpha joining 18,T cell receptor alpha chain constant
F: T cell receptor beta, variable 2,T cell receptor beta joining 1-1,T cell receptor beta constant 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,54016
Polymers143,6837
Non-polymers8579
Water00
1
A: Histocompatibility 2, Q region locus 7
B: Beta-2-microglobulin
C: T cell receptor alpha variable 13D-1,T cell receptor alpha joining 18,T cell receptor alpha chain constant
D: T cell receptor beta, variable 2,T cell receptor beta joining 1-1,T cell receptor beta constant 1
P: Minor capsid protein VP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,88914
Polymers94,0325
Non-polymers8579
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: T cell receptor alpha variable 13D-1,T cell receptor alpha joining 18,T cell receptor alpha chain constant
F: T cell receptor beta, variable 2,T cell receptor beta joining 1-1,T cell receptor beta constant 1


Theoretical massNumber of molelcules
Total (without water)49,6512
Polymers49,6512
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)275.695, 66.810, 90.596
Angle α, β, γ (deg.)90.00, 98.84, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Histocompatibility 2, Q region locus 7 / MHC class Ib antigen


Mass: 31628.252 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-Q9, H2-Q7 / Plasmid: pET-30a(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q52PG7
#2: Protein Beta-2-microglobulin


Mass: 11660.350 Da / Num. of mol.: 1 / Fragment: UNP resides 21-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2m / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P01887

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T cell receptor ... , 2 types, 4 molecules CEDF

#3: Protein T cell receptor alpha variable 13D-1,T cell receptor alpha joining 18,T cell receptor alpha chain constant


Mass: 22043.268 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Trav13d-1, Traj18, TRAC, TCRA / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A075B606, UniProt: A0A0G2JG46, UniProt: P01848
#4: Protein T cell receptor beta, variable 2,T cell receptor beta joining 1-1,T cell receptor beta constant 1


Mass: 27608.014 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Trbv2, Trbj1-1, TRBC1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A0B4J1G8, UniProt: A0A0A6YVY0, UniProt: P01850

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Protein/peptide , 1 types, 1 molecules P

#5: Protein/peptide Minor capsid protein VP2 / Minor structural protein VP2


Mass: 1092.206 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Alphapolyomavirus muris / References: UniProt: P03097

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Non-polymers , 2 types, 9 molecules

#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.85 Å3/Da / Density % sol: 56.86 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.2 M ammonium sulfate, 0.1 M Na3 Cit pH 5.6, 16 % (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Crystal support: Cryo-loop / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX3 / Wavelength: 0.95373 Å
DetectorType: STFC Large Pixel Detector / Detector: PIXEL / Date: Mar 3, 2026
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 3.33→29.99 Å / Num. obs: 23857 / % possible obs: 98.9 % / Redundancy: 4.4 % / Biso Wilson estimate: 101.23 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.132 / Rpim(I) all: 0.082 / Rrim(I) all: 0.172 / Χ2: 1 / Net I/σ(I): 8
Reflection shellResolution: 3.33→3.6 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.584 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 4850 / CC1/2: 0.771 / Rpim(I) all: 0.484 / Rrim(I) all: 0.763 / Χ2: 1.05 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX(1.21.2_5419: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.33→29.84 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / Phase error: 27.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2668 2368 9.94 %
Rwork0.2179 --
obs0.2227 23821 98.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.33→29.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10116 0 35 12 10163
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00210418
X-RAY DIFFRACTIONf_angle_d0.55314144
X-RAY DIFFRACTIONf_dihedral_angle_d13.9233812
X-RAY DIFFRACTIONf_chiral_restr0.0421498
X-RAY DIFFRACTIONf_plane_restr0.0041844

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