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- PDB-7na5: Structure of the H2DB-TCR ternary complex with HSF2 melanoma neoa... -

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Basic information

Entry
Database: PDB / ID: 7na5
TitleStructure of the H2DB-TCR ternary complex with HSF2 melanoma neoantigen
Components
  • 47BE7 TCR alpha chain
  • 47BE7 TCR beta chain
  • Beta-2-microglobulin
  • H-2 class I histocompatibility antigen, D-B alpha chain
  • Heat shock factor protein 2
KeywordsIMMUNE SYSTEM / neoantigen / cancer / melanoma / B16 / mouse / H2DB / TCR / TCR-MHC complex / anchor residue mutation / HSF2
Function / homology
Function and homology information


RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / beta-2-microglobulin binding / 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 ...RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / beta-2-microglobulin binding / 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 / 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 / peptide binding / 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 / 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 / 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 / iron ion transport / ER-Phagosome pathway / T cell differentiation in thymus / early endosome membrane / protein refolding / spermatogenesis / DNA-binding transcription activator activity, RNA polymerase II-specific / protein homotetramerization / intracellular iron ion homeostasis / sequence-specific DNA binding / amyloid fibril formation / learning or memory / immune response / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / Golgi membrane / external side of plasma membrane / signaling receptor binding / focal adhesion / Neutrophil degranulation / protein-containing complex binding / regulation of transcription by RNA polymerase II / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / DNA binding / extracellular space / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / membrane / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Vertebrate heat shock transcription factor, C-terminal domain / Vertebrate heat shock transcription factor / Heat shock factor (HSF)-type, DNA-binding / Heat shock transcription factor family / HSF-type DNA-binding / HSF-type DNA-binding domain signature. / heat shock factor / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I alpha chain, alpha1 alpha2 domains ...Vertebrate heat shock transcription factor, C-terminal domain / Vertebrate heat shock transcription factor / Heat shock factor (HSF)-type, DNA-binding / Heat shock transcription factor family / HSF-type DNA-binding / HSF-type DNA-binding domain signature. / heat shock factor / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / 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 / Winged helix DNA-binding domain superfamily / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Winged helix-like DNA-binding domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
H-2 class I histocompatibility antigen, D-B alpha chain / Heat shock factor protein 2 / Beta-2-microglobulin
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsPatskovsky, Y. / Finnigan, J. / Patskovska, L. / Newman, J. / Bhardwaj, N. / Krogsgaard, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)CA243486 United States
CitationJournal: To be Published
Title: Structure of the TCR-H2DB ternary complex with melanoma HSF2 neoantigen YGFRNVVHI
Authors: Patskovsky, Y. / Finnigan, J. / Patskovska, L. / Newman, J. / Bhardwaj, N. / Krogsgaard, M.
History
DepositionJun 19, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 22, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: H-2 class I histocompatibility antigen, D-B alpha chain
B: Beta-2-microglobulin
C: Heat shock factor protein 2
D: 47BE7 TCR alpha chain
E: 47BE7 TCR beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,38422
Polymers96,8025
Non-polymers1,58117
Water3,747208
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14230 Å2
ΔGint-101 kcal/mol
Surface area36770 Å2
Unit cell
Length a, b, c (Å)155.439, 191.710, 67.811
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 4 types, 4 molecules ABDE

#1: Protein H-2 class I histocompatibility antigen, D-B alpha chain / H-2D(B)


Mass: 32601.303 Da / Num. of mol.: 1 / Fragment: UNP residues 25-304
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-D1 / Production host: Escherichia coli (E. coli) / References: UniProt: P01899
#2: Protein Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 1 / Fragment: UNP residues 21-119
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
#4: Protein 47BE7 TCR alpha chain


Mass: 21426.936 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET30 / Production host: Escherichia coli BL21(DE3) (bacteria)
#5: Protein 47BE7 TCR beta chain


Mass: 29788.338 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET30 / Production host: Escherichia coli BL21(DE3) (bacteria)

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Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide Heat shock factor protein 2 / HSF 2 / Heat shock transcription factor 2 / HSTF 2


Mass: 1106.277 Da / Num. of mol.: 1 / Fragment: UNP residues 68-76 / Mutation: K5N / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) / References: UniProt: P38533

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Non-polymers , 3 types, 225 molecules

#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / Source method: isolated from a natural source / Formula: H2O

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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: 2.61 Å3/Da / Density % sol: 52.98 % / Description: rods
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 25% PEG3350, 0.1 M Bis-Tris, pH 5.5, 0.2 M lithium sulfate, 15% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 9, 2020 / Details: SI 111 CRYSTAL
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.5→50.01 Å / Num. obs: 35345 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 5.9 % / CC1/2: 0.987 / Rmerge(I) obs: 0.161 / Net I/σ(I): 7.8
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 3783 / CC1/2: 0.45 / % possible all: 95.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 7N9J

7n9j


Resolution: 2.5→50.01 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.919 / SU B: 11.616 / SU ML: 0.242 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.441 / ESU R Free: 0.278 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2487 1073 3 %RANDOM
Rwork0.1838 ---
obs0.1858 34250 99.32 %-
Solvent computationIon probe radii: 0.5 Å / Shrinkage radii: 0.5 Å / VDW probe radii: 0.8 Å / Solvent model: MASK
Displacement parametersBiso max: 167.09 Å2 / Biso mean: 51.318 Å2 / Biso min: 24.06 Å2
Baniso -1Baniso -2Baniso -3
1-2.25 Å20 Å2-0 Å2
2---0.41 Å20 Å2
3----1.84 Å2
Refinement stepCycle: final / Resolution: 2.5→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6370 0 98 208 6676
Biso mean--77.45 45.59 -
Num. residues----804
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0136660
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175744
X-RAY DIFFRACTIONr_angle_refined_deg1.4321.6479044
X-RAY DIFFRACTIONr_angle_other_deg1.1971.57313358
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5735800
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.69722.59363
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.972151015
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8511537
X-RAY DIFFRACTIONr_chiral_restr0.0580.2824
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027467
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021448
LS refinement shellResolution: 2.5→2.565 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 65 -
Rwork0.321 2411 -
all-2476 -
obs--95.38 %

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