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- PDB-6avf: Crystal structure of the KFJ5 TCR-NY-ESO-1-HLA-B*07:02 complex -

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Basic information

Entry
Database: PDB / ID: 6avf
TitleCrystal structure of the KFJ5 TCR-NY-ESO-1-HLA-B*07:02 complex
Components
  • (T-cell receptor ...) x 2
  • ALA-PRO-ARG-GLY-PRO-HIS-GLY-GLY-ALA-ALA-SER-GLY-LEU
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, B-7 alpha chain
KeywordsIMMUNE SYSTEM / Human Leukocyte Antigen / Major histocompatibility complex / Immunoglobulin / T cell receptor
Function / homology
Function and homology information


tRNA threonylcarbamoyladenosine metabolic process / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / T cell receptor complex / TAP binding / protection from natural killer cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib ...tRNA threonylcarbamoyladenosine metabolic process / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / T cell receptor complex / TAP binding / protection from natural killer cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / detection of bacterium / secretory granule membrane / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / 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 / cellular response to iron ion / Endosomal/Vacuolar pathway / response to bacterium / lumenal side of endoplasmic reticulum membrane / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / 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 / MHC class II protein complex / 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 / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / antigen processing and presentation of exogenous peptide antigen via MHC class II / defense response / MHC class I protein complex / positive regulation of immune response / peptide antigen binding / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / positive regulation of T cell activation / multicellular organismal-level iron ion homeostasis / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / negative regulation of epithelial cell proliferation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / MHC class II protein complex binding / Modulation by Mtb of host immune system / Interferon alpha/beta signaling / late endosome membrane / sensory perception of smell / tertiary granule lumen / DAP12 signaling / positive regulation of protein binding / protein-folding chaperone binding / iron ion transport / negative regulation of neuron projection development / ER-Phagosome pathway / early endosome membrane / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response / amyloid fibril formation / learning or memory / cell surface receptor signaling pathway / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / Golgi membrane / external side of plasma membrane / signaling receptor binding / innate immune response / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / cell surface / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane
Similarity search - Function
CTAG/Pcc1 family / Transcription factor Pcc1 / : / : / 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 ...CTAG/Pcc1 family / Transcription factor Pcc1 / : / : / 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 / Immunoglobulin V-set domain / 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
T cell receptor alpha variable 4 / T cell receptor beta variable 28 / HLA class I histocompatibility antigen, B alpha chain / Beta-2-microglobulin / Cancer/testis antigen 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.028 Å
AuthorsGully, B.S. / Gras, S. / Rossjohn, J.
CitationJournal: Nat Commun / Year: 2018
Title: Divergent T-cell receptor recognition modes of a HLA-I restricted extended tumour-associated peptide.
Authors: Chan, K.F. / Gully, B.S. / Gras, S. / Beringer, D.X. / Kjer-Nielsen, L. / Cebon, J. / McCluskey, J. / Chen, W. / Rossjohn, J.
History
DepositionSep 2, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support
Revision 1.3Oct 9, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
M: Beta-2-microglobulin
A: T-cell receptor alpha variable 4,TCR alpha chain
B: T-cell receptor beta variable 28,TCR beta chain
P: ALA-PRO-ARG-GLY-PRO-HIS-GLY-GLY-ALA-ALA-SER-GLY-LEU
H: HLA class I histocompatibility antigen, B-7 alpha chain


Theoretical massNumber of molelcules
Total (without water)104,6865
Polymers104,6865
Non-polymers00
Water8,053447
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10310 Å2
ΔGint-39 kcal/mol
Surface area38010 Å2
Unit cell
Length a, b, c (Å)64.366, 67.679, 105.716
Angle α, β, γ (deg.)90.00, 102.93, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 2 molecules MH

#1: Protein Beta-2-microglobulin


Mass: 11748.160 Da / Num. of mol.: 1 / Fragment: UNP residues 13-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Escherichia coli (E. coli) / References: UniProt: P61769
#5: Protein HLA class I histocompatibility antigen, B-7 alpha chain / MHC class I antigen B*7


Mass: 40508.988 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B, HLAB / Production host: Escherichia coli (E. coli) / References: UniProt: P01889

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T-cell receptor ... , 2 types, 2 molecules AB

#2: Protein T-cell receptor alpha variable 4,TCR alpha chain


Mass: 23191.744 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRAV4 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0B4J268
#3: Protein T-cell receptor beta variable 28,TCR beta chain / V_segment translation product


Mass: 28087.447 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TCRBV3S1, TRBV28 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A5B6

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Protein/peptide / Non-polymers , 2 types, 448 molecules P

#4: Protein/peptide ALA-PRO-ARG-GLY-PRO-HIS-GLY-GLY-ALA-ALA-SER-GLY-LEU


Mass: 1149.262 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P78358*PLUS
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 447 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.1 Å3/Da / Density % sol: 41.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1 M MIB pH 7.0 and 25 % (w/v) PEG 1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.028→46.01 Å / Num. obs: 109701 / % possible obs: 99.1 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 9.3
Reflection shellResolution: 2.03→2.14 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 8094 / % possible all: 96.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.028→46.008 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2559 3854 3.51 %
Rwork0.2038 --
obs0.2056 109701 97.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.028→46.008 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6559 0 0 447 7006
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096761
X-RAY DIFFRACTIONf_angle_d1.1719176
X-RAY DIFFRACTIONf_dihedral_angle_d15.4082467
X-RAY DIFFRACTIONf_chiral_restr0.049967
X-RAY DIFFRACTIONf_plane_restr0.0061205
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0276-2.05240.34671340.33493312X-RAY DIFFRACTION85
2.0524-2.07830.34711060.31293753X-RAY DIFFRACTION96
2.0783-2.10570.31641520.3013840X-RAY DIFFRACTION99
2.1057-2.13450.30381470.27733814X-RAY DIFFRACTION99
2.1345-2.1650.31681480.27783868X-RAY DIFFRACTION99
2.165-2.19740.31281470.26723810X-RAY DIFFRACTION99
2.1974-2.23170.28511260.26783847X-RAY DIFFRACTION99
2.2317-2.26830.31131570.26743726X-RAY DIFFRACTION96
2.2683-2.30740.29921200.25763866X-RAY DIFFRACTION99
2.3074-2.34930.2991370.24683836X-RAY DIFFRACTION99
2.3493-2.39450.28511240.24233878X-RAY DIFFRACTION99
2.3945-2.44340.30661700.24573805X-RAY DIFFRACTION99
2.4434-2.49650.28291350.23173918X-RAY DIFFRACTION99
2.4965-2.55460.31551480.22983780X-RAY DIFFRACTION99
2.5546-2.61850.24641250.22313858X-RAY DIFFRACTION99
2.6185-2.68930.30721460.24163836X-RAY DIFFRACTION98
2.6893-2.76840.39311420.24983813X-RAY DIFFRACTION99
2.7684-2.85770.28511410.23613847X-RAY DIFFRACTION99
2.8577-2.95990.30311320.20733862X-RAY DIFFRACTION99
2.9599-3.07830.21731470.20923858X-RAY DIFFRACTION99
3.0783-3.21840.29041450.20913810X-RAY DIFFRACTION98
3.2184-3.3880.25161250.18613771X-RAY DIFFRACTION97
3.388-3.60020.26491410.17553707X-RAY DIFFRACTION96
3.6002-3.87810.17511340.16413719X-RAY DIFFRACTION96
3.8781-4.26810.21021360.15353758X-RAY DIFFRACTION96
4.2681-4.88510.17281370.13743644X-RAY DIFFRACTION94
4.8851-6.15240.23361310.15413675X-RAY DIFFRACTION95
6.1524-46.02020.20951210.16713636X-RAY DIFFRACTION93

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