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- PDB-3mv9: Crystal Structure of the TK3-Gln55Ala TCR in complex with HLA-B*3... -

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Basic information

Entry
Database: PDB / ID: 3mv9
TitleCrystal Structure of the TK3-Gln55Ala TCR in complex with HLA-B*3501/HPVG
Components
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, B-35 alpha chain
  • HPVG peptide from Epstein-Barr nuclear antigen 1
  • alpha chain of the TK3 TCR
  • beta chain of the TK3 TCR
KeywordsIMMUNE SYSTEM / HLA B*3501 / EBV / TCR / TCRpMHC complex / HPVG / TCR polymorphism
Function / homology
Function and homology information


host cell PML body / viral latency / regulation of interleukin-12 production / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / regulation of dendritic cell differentiation / regulation of T cell anergy / enzyme-substrate adaptor activity / regulation of interleukin-6 production / symbiont-mediated disruption of host cell PML body / regulation of DNA replication ...host cell PML body / viral latency / regulation of interleukin-12 production / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / regulation of dendritic cell differentiation / regulation of T cell anergy / enzyme-substrate adaptor activity / regulation of interleukin-6 production / symbiont-mediated disruption of host cell PML body / regulation of DNA replication / TAP binding / protection from natural killer cell mediated cytotoxicity / detection of bacterium / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / secretory granule membrane / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / DAP12 interactions / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / lumenal side of endoplasmic reticulum membrane / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor 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 / defense response / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / multicellular organismal-level iron ion homeostasis / MHC class II protein complex / cellular response to nicotine / specific granule lumen / positive regulation of cellular senescence / positive regulation of T cell mediated cytotoxicity / recycling endosome membrane / phagocytic vesicle membrane / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of immune response / Interferon gamma signaling / Modulation by Mtb of host immune system / positive regulation of T cell activation / Interferon alpha/beta signaling / sensory perception of smell / negative regulation of neuron projection development / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / protein-folding chaperone binding / iron ion transport / ER-Phagosome pathway / T cell differentiation in thymus / symbiont-mediated suppression of host NF-kappaB cascade / early endosome membrane / protein refolding / endonuclease activity / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / adaptive immune response / learning or memory / immune response / DNA-binding transcription factor activity / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / Golgi membrane / external side of plasma membrane / innate immune response / signaling receptor binding / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / positive regulation of DNA-templated transcription / structural molecule activity / Golgi apparatus / cell surface / endoplasmic reticulum / protein homodimerization activity
Similarity search - Function
Epstein Barr virus nuclear antigen-1, DNA-binding / Epstein Barr virus nuclear antigen-1, DNA-binding domain / Epstein Barr virus nuclear antigen-1, DNA-binding domain superfamily / E2/EBNA1, C-terminal / 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 ...Epstein Barr virus nuclear antigen-1, DNA-binding / Epstein Barr virus nuclear antigen-1, DNA-binding domain / Epstein Barr virus nuclear antigen-1, DNA-binding domain superfamily / E2/EBNA1, C-terminal / 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 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / : / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
HLA class I histocompatibility antigen, B alpha chain / Epstein-Barr nuclear antigen 1 / HLA class I histocompatibility antigen, B alpha chain / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / 2fyy, 3ffc / molecular replacement / Resolution: 2.7 Å
AuthorsGras, S. / Chen, Z. / Miles, J.J. / Liu, Y.C. / Bell, M.J. / Sullivan, L.C. / Kjer-Nielsen, L. / Brennan, R.M. / Burrows, J.M. / Neller, M.A. ...Gras, S. / Chen, Z. / Miles, J.J. / Liu, Y.C. / Bell, M.J. / Sullivan, L.C. / Kjer-Nielsen, L. / Brennan, R.M. / Burrows, J.M. / Neller, M.A. / Khanna, R. / Purcell, A.W. / Brooks, A.G. / McCluskey, J. / Rossjohn, J. / Burrows, S.R.
CitationJournal: J.Exp.Med. / Year: 2010
Title: Allelic polymorphism in the T cell receptor and its impact on immune responses
Authors: Gras, S. / Chen, Z. / Miles, J.J. / Liu, Y.C. / Bell, M.J. / Sullivan, L.C. / Kjer-Nielsen, L. / Brennan, R.M. / Burrows, J.M. / Neller, M.A. / Khanna, R. / Purcell, A.W. / Brooks, A.G. / ...Authors: Gras, S. / Chen, Z. / Miles, J.J. / Liu, Y.C. / Bell, M.J. / Sullivan, L.C. / Kjer-Nielsen, L. / Brennan, R.M. / Burrows, J.M. / Neller, M.A. / Khanna, R. / Purcell, A.W. / Brooks, A.G. / McCluskey, J. / Rossjohn, J. / Burrows, S.R.
History
DepositionMay 3, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 20, 2011Group: Database references
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HLA class I histocompatibility antigen, B-35 alpha chain
B: Beta-2-microglobulin
C: HPVG peptide from Epstein-Barr nuclear antigen 1
D: alpha chain of the TK3 TCR
E: beta chain of the TK3 TCR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,5536
Polymers94,4575
Non-polymers961
Water1,11762
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.900, 62.570, 98.140
Angle α, β, γ (deg.)92.040, 102.290, 109.180
Int Tables number1
Space group name H-MP1

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Components

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Protein , 4 types, 4 molecules ABDE

#1: Protein HLA class I histocompatibility antigen, B-35 alpha chain / HLA B*3501 heavy chain / MHC class I antigen B*35


Mass: 31940.246 Da / Num. of mol.: 1 / Fragment: Extracellular domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B, HLAB / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P30685, UniProt: P01889*PLUS
#2: Protein Beta-2-microglobulin / Beta-2-microglobulin form pI 5.3


Mass: 11879.356 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P61769
#4: Protein alpha chain of the TK3 TCR


Mass: 22185.492 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#5: Protein beta chain of the TK3 TCR


Mass: 27124.039 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Q55A mutant / Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)

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Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide HPVG peptide from Epstein-Barr nuclear antigen 1


Mass: 1327.374 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic peptide / References: UniProt: P03211

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Non-polymers , 2 types, 63 molecules

#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsTHE SEQUENCE DATABASE REFERENCE FOR CHAIN D, E DO NOT CURRENTLY EXIST IN UNP DATABASE. CHAIN D: ...THE SEQUENCE DATABASE REFERENCE FOR CHAIN D, E DO NOT CURRENTLY EXIST IN UNP DATABASE. CHAIN D: TRAV20/TRAJ58 TCR ALPHA CHAIN CHAIN E : TRBV9 WITH THE MUTATION Q55A, TRBJ2-2 TCR BETA CHAIN THE ABOVE CODES ARE FROM IMGT DATABASES.

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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: 2.68 Å3/Da / Density % sol: 54.04 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 15%PEG 3350, 0.2M LiSO4, 0.1M Na-citrate, pH 5.6, vapor diffusion, hanging drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.979457 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Aug 5, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979457 Å / Relative weight: 1
ReflectionNumber: 93853 / Rmerge(I) obs: 0.086 / D res high: 2.7 Å / Num. obs: 25447 / % possible obs: 94.5
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)IDRmerge(I) obs
610189698.510.044
56174798.510.047
45393897.310.05
3.54326080.110.095
3.43.5103690.910.18
33.459249710.171
2.93206197.210.252
2.82.9232597.610.333
2.72.8274997.210.459
ReflectionResolution: 2.7→100 Å / Num. obs: 25447 / % possible obs: 94.5 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 47.526 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 12.04
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.7-2.80.4592.910111274997.2
2.8-2.90.3333.98775232597.6
2.9-30.25257811206197.2
3-3.40.1717.622576592497
3.4-3.50.188.73672103690.9
3.5-40.09513.110422326080.1
4-50.0520.914830393897.3
5-60.04721.96717174798.5
6-100.04424.37120189698.5
100.03631.2181951195

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
PHENIX1.4_4refinement
RefinementMethod to determine structure: 2fyy, 3ffc / Resolution: 2.7→39.248 Å / Occupancy max: 1 / Occupancy min: 0.42 / FOM work R set: 0.715 / SU ML: 0.48 / σ(F): 0.02 / Phase error: 34.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.331 1131 5.02 %
Rwork0.234 --
obs0.238 22529 83.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.72 Å2 / ksol: 0.284 e/Å3
Displacement parametersBiso max: 138.21 Å2 / Biso mean: 47.782 Å2 / Biso min: 12.26 Å2
Baniso -1Baniso -2Baniso -3
1-1.262 Å20.237 Å2-3.537 Å2
2---12.161 Å2-5.365 Å2
3---10.899 Å2
Refinement stepCycle: LAST / Resolution: 2.7→39.248 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6659 0 5 62 6726
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076864
X-RAY DIFFRACTIONf_angle_d1.1219316
X-RAY DIFFRACTIONf_chiral_restr0.075975
X-RAY DIFFRACTIONf_plane_restr0.0041235
X-RAY DIFFRACTIONf_dihedral_angle_d19.1612482
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7-2.8230.4451170.2812417253475
2.823-2.9710.3551360.2682579271581
2.971-3.1580.3891510.2562713286485
3.158-3.4010.3541260.2642625275182
3.401-3.7430.4461210.3182178229968
3.743-4.2840.3161480.2192669281784
4.284-5.3960.2431640.1573091325597
5.396-39.2520.2411680.1743126329498

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