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- PDB-9wbd: Crystal structure of HLA-B*07:02 in complex with SPR epitope and ... -

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Basic information

Entry
Database: PDB / ID: 9wbd
TitleCrystal structure of HLA-B*07:02 in complex with SPR epitope and Q04 TCR
Components
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, B alpha chain
  • Nucleoprotein
  • T cell receptor alpha variable 25,T cell receptor alpha chain constant
  • TCR beta
KeywordsIMMUNE SYSTEM / pMHC-TCR complex
Function / homology
Function and homology information


: / response to host immune response / viral RNA genome packaging / regulation of interleukin-12 production / negative regulation of interferon-beta production / regulation of dendritic cell differentiation / alpha-beta T cell receptor complex / regulation of T cell anergy / regulation of interleukin-6 production / poly(U) RNA binding ...: / response to host immune response / viral RNA genome packaging / regulation of interleukin-12 production / negative regulation of interferon-beta production / regulation of dendritic cell differentiation / alpha-beta T cell receptor complex / regulation of T cell anergy / regulation of interleukin-6 production / poly(U) RNA binding / Maturation of nucleoprotein / intracellular membraneless organelle / T cell receptor complex / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / positive regulation of NLRP3 inflammasome complex assembly / MHC class I protein binding / TAP binding / alpha-beta T cell activation / protection from natural killer cell mediated cytotoxicity / Generation of second messenger molecules / Co-inhibition by PD-1 / 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 / CD28 dependent PI3K/Akt signaling / detection of bacterium / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / protein sequestering activity / secretory granule membrane / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / VEGFR2 mediated vascular permeability / cellular response to iron ion / Endosomal/Vacuolar pathway / lumenal side of endoplasmic reticulum membrane / response to bacterium / 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 / MHC class II protein complex / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / molecular condensate scaffold activity / ER to Golgi transport vesicle membrane / 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 / defense response / NOD1/2 Signaling Pathway / TAK1-dependent IKK and NF-kappa-B activation / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / DDX58/IFIH1-mediated induction of interferon-alpha/beta / antigen processing and presentation of endogenous peptide antigen via MHC class I / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / positive regulation of T cell activation / 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 / RNA stem-loop binding / specific granule lumen / Interleukin-1 signaling / phagocytic vesicle membrane / recycling endosome membrane / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / Interferon alpha/beta signaling / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / viral capsid / positive regulation of cellular senescence / tertiary granule lumen / Downstream TCR signaling / DAP12 signaling / T cell differentiation in thymus / PIP3 activates AKT signaling / T cell receptor signaling pathway / negative regulation of neuron projection development / protein-folding chaperone binding / ER-Phagosome pathway / protein refolding / viral nucleocapsid / Transcription of SARS-CoV-2 sgRNAs / host cell endoplasmic reticulum-Golgi intermediate compartment / early endosome membrane / protein homotetramerization
Similarity search - Function
: / Nucleocapsid protein, betacoronavirus / Nucleocapsid protein, coronavirus / Nucleocapsid protein, C-terminal / Nucleocapsid protein, N-terminal / Nucleocapsid (N) protein, C-terminal domain, coronavirus / Nucleocapsid (N) protein, N-terminal domain, coronavirus / Coronavirus nucleocapsid / Coronavirus nucleocapsid (CoV N) protein N-terminal (NTD) domain profile. / Coronavirus nucleocapsid (CoV N) protein C-terminal (CTD) domain profile. ...: / Nucleocapsid protein, betacoronavirus / Nucleocapsid protein, coronavirus / Nucleocapsid protein, C-terminal / Nucleocapsid protein, N-terminal / Nucleocapsid (N) protein, C-terminal domain, coronavirus / Nucleocapsid (N) protein, N-terminal domain, coronavirus / Coronavirus nucleocapsid / Coronavirus nucleocapsid (CoV N) protein N-terminal (NTD) domain profile. / Coronavirus nucleocapsid (CoV N) protein C-terminal (CTD) domain profile. / T-cell receptor alpha chain, constant domain / Domain of unknown function (DUF1968) / 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 / 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
DI(HYDROXYETHYL)ETHER / T cell receptor alpha variable 25 / T cell receptor alpha chain constant / HLA class I histocompatibility antigen, B alpha chain / Nucleoprotein / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsPing, Y. / Daichao, W.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: To Be Published
Title: Crystal structure of HLA-B*07:02 in complex with SPR epitope and Q04 TCR
Authors: Ping, Y. / Daichao, W.
History
DepositionAug 13, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 19, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: T cell receptor alpha variable 25,T cell receptor alpha chain constant
B: TCR beta
C: HLA class I histocompatibility antigen, B alpha chain
D: Beta-2-microglobulin
E: Nucleoprotein
F: T cell receptor alpha variable 25,T cell receptor alpha chain constant
G: TCR beta
H: HLA class I histocompatibility antigen, B alpha chain
I: Beta-2-microglobulin
J: Nucleoprotein
K: T cell receptor alpha variable 25,T cell receptor alpha chain constant
L: TCR beta
M: HLA class I histocompatibility antigen, B alpha chain
N: Beta-2-microglobulin
O: Nucleoprotein
P: T cell receptor alpha variable 25,T cell receptor alpha chain constant
Q: TCR beta
R: HLA class I histocompatibility antigen, B alpha chain
S: Beta-2-microglobulin
T: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)382,69824
Polymers382,31620
Non-polymers3824
Water25214
1
A: T cell receptor alpha variable 25,T cell receptor alpha chain constant
B: TCR beta
C: HLA class I histocompatibility antigen, B alpha chain
D: Beta-2-microglobulin
E: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,6716
Polymers95,5795
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
F: T cell receptor alpha variable 25,T cell receptor alpha chain constant
G: TCR beta
H: HLA class I histocompatibility antigen, B alpha chain
I: Beta-2-microglobulin
J: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,6856
Polymers95,5795
Non-polymers1061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
K: T cell receptor alpha variable 25,T cell receptor alpha chain constant
L: TCR beta
M: HLA class I histocompatibility antigen, B alpha chain
N: Beta-2-microglobulin
O: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,6716
Polymers95,5795
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
P: T cell receptor alpha variable 25,T cell receptor alpha chain constant
Q: TCR beta
R: HLA class I histocompatibility antigen, B alpha chain
S: Beta-2-microglobulin
T: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,6716
Polymers95,5795
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.786, 102.564, 120.701
Angle α, β, γ (deg.)84.14, 68.60, 81.10
Int Tables number1
Space group name H-MP1

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Components

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Protein , 4 types, 16 molecules AFKPBGLQCHMRDINS

#1: Protein
T cell receptor alpha variable 25,T cell receptor alpha chain constant


Mass: 23105.703 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRAV25, TRAC, TCRA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0B4J276, UniProt: P01848
#2: Protein
TCR beta


Mass: 27205.227 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria)
#3: Protein
HLA class I histocompatibility antigen, B alpha chain / Human leukocyte antigen B / HLA-B


Mass: 32093.211 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B, HLAB / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P01889
#4: Protein
Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P61769

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Protein/peptide , 1 types, 4 molecules EJOT

#5: Protein/peptide
Nucleoprotein / SER-PRO-ARG-TRP-TYR-PHE-TYR-TYR-LEU / N / Nucleocapsid protein / NC / Protein N


Mass: 1295.464 Da / Num. of mol.: 4 / Source method: obtained synthetically
Source: (synth.) Severe acute respiratory syndrome coronavirus 2
References: UniProt: P0DTC9

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Non-polymers , 3 types, 18 molecules

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


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 2.64 Å3/Da / Density % sol: 53.43 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: Tris-HCl, calcium chloride, PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 3, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.75→48.53 Å / Num. obs: 100846 / % possible obs: 98.9 % / Redundancy: 3.4 % / CC1/2: 0.901 / Rmerge(I) obs: 0.204 / Net I/σ(I): 5.9
Reflection shellResolution: 2.75→2.82 Å / Redundancy: 3.5 % / Rmerge(I) obs: 1.192 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 7426 / CC1/2: 0.407 / % possible all: 98.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
PDB_EXTRACTdata extraction
XDSdata reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.75→48.52 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.877 / SU B: 16.768 / SU ML: 0.326 / Cross valid method: THROUGHOUT / ESU R Free: 0.39 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27004 5025 5 %RANDOM
Rwork0.21789 ---
obs0.2205 95744 98.57 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.381 Å2
Baniso -1Baniso -2Baniso -3
1--0.4 Å2-1.76 Å21.09 Å2
2--4.57 Å20.65 Å2
3----3.15 Å2
Refinement stepCycle: 1 / Resolution: 2.75→48.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25326 0 25 14 25365
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01226058
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6441.81535519
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.77453201
X-RAY DIFFRACTIONr_dihedral_angle_2_deg12.2675164
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.449103806
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1160.23777
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0220833
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.8564.5112915
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it7.5188.08816079
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.5664.58513143
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined12.40253.55103515
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.75→2.816 Å
RfactorNum. reflection% reflection
Rfree0.393 345 -
Rwork0.334 6820 -
obs--94.48 %

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