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- PDB-2zok: Crystal structure of H-2Db in complex with JHMV epitope S510 -

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Basic information

Entry
Database: PDB / ID: 2zok
TitleCrystal structure of H-2Db in complex with JHMV epitope S510
Components
  • 9-meric peptide from Spike glycoprotein
  • Beta-2-microglobulin
  • H-2 class I histocompatibility antigen, D-B alpha chain
KeywordsIMMUNE SYSTEM / Ig fold / Glycoprotein / Immune response / Membrane / MHC I / Transmembrane / Immunoglobulin domain / Secreted / Cleavage on pair of basic residues / Envelope protein / Fusion protein / Host-virus interaction / Virion / Virulence
Function / homology
Function and homology information


Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / cellular defense response / Neutrophil degranulation / lumenal side of endoplasmic reticulum membrane ...Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / cellular defense response / Neutrophil degranulation / lumenal side of endoplasmic reticulum membrane / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / iron ion transport / 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 / 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 / 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 / phagocytic vesicle membrane / negative regulation of epithelial cell proliferation / sensory perception of smell / positive regulation of cellular senescence / T cell differentiation in thymus / negative regulation of neuron projection development / protein refolding / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / learning or memory / receptor-mediated virion attachment to host cell / endocytosis involved in viral entry into host cell / fusion of virus membrane with host plasma membrane / external side of plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / host cell plasma membrane / virion membrane / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / membrane / plasma membrane / cytosol
Similarity search - Function
Spike (S) protein S1 subunit, N-terminal domain, murine hepatitis virus-like / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / 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 ...Spike (S) protein S1 subunit, N-terminal domain, murine hepatitis virus-like / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / 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 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Beta-2-microglobulin / H-2 class I histocompatibility antigen, D-B alpha chain / Spike glycoprotein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsTheodossis, A. / Dunstone, M.A. / Rossjohn, J.
CitationJournal: J Immunol. / Year: 2008
Title: Structural and biological basis of CTL escape in coronavirus-infected mice.
Authors: Butler, N.S. / Theodossis, A. / Webb, A.I. / Dunstone, M.A. / Nastovska, R. / Ramarathinam, S.H. / Rossjohn, J. / Purcell, A.W. / Perlman, S.
History
DepositionMay 22, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 10, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 6, 2019Group: Data collection / Database references / Derived calculations
Category: citation / struct_conn / struct_ref_seq_dif
Item: _citation.journal_abbrev / _citation.journal_id_ASTM ..._citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.pdbx_database_id_DOI / _citation.title / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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: H-2 class I histocompatibility antigen, D-B alpha chain
D: Beta-2-microglobulin
E: H-2 class I histocompatibility antigen, D-B alpha chain
F: Beta-2-microglobulin
G: H-2 class I histocompatibility antigen, D-B alpha chain
H: Beta-2-microglobulin
I: 9-meric peptide from Spike glycoprotein
L: 9-meric peptide from Spike glycoprotein
J: 9-meric peptide from Spike glycoprotein
K: 9-meric peptide from Spike glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,98420
Polymers181,23112
Non-polymers7538
Water17,457969
1
A: H-2 class I histocompatibility antigen, D-B alpha chain
B: Beta-2-microglobulin
I: 9-meric peptide from Spike glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5926
Polymers45,3083
Non-polymers2843
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4650 Å2
ΔGint-32 kcal/mol
Surface area18480 Å2
MethodPISA
2
C: H-2 class I histocompatibility antigen, D-B alpha chain
D: Beta-2-microglobulin
J: 9-meric peptide from Spike glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4004
Polymers45,3083
Non-polymers921
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4620 Å2
ΔGint-33 kcal/mol
Surface area18590 Å2
MethodPISA
3
E: H-2 class I histocompatibility antigen, D-B alpha chain
F: Beta-2-microglobulin
K: 9-meric peptide from Spike glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4965
Polymers45,3083
Non-polymers1882
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4740 Å2
ΔGint-32 kcal/mol
Surface area18680 Å2
MethodPISA
4
G: H-2 class I histocompatibility antigen, D-B alpha chain
H: Beta-2-microglobulin
L: 9-meric peptide from Spike glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4965
Polymers45,3083
Non-polymers1882
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4640 Å2
ΔGint-35 kcal/mol
Surface area18620 Å2
MethodPISA
5
A: H-2 class I histocompatibility antigen, D-B alpha chain
B: Beta-2-microglobulin
C: H-2 class I histocompatibility antigen, D-B alpha chain
D: Beta-2-microglobulin
I: 9-meric peptide from Spike glycoprotein
J: 9-meric peptide from Spike glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,99210
Polymers90,6166
Non-polymers3764
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11150 Å2
ΔGint-81 kcal/mol
Surface area35190 Å2
MethodPISA
6
E: H-2 class I histocompatibility antigen, D-B alpha chain
F: Beta-2-microglobulin
G: H-2 class I histocompatibility antigen, D-B alpha chain
H: Beta-2-microglobulin
L: 9-meric peptide from Spike glycoprotein
K: 9-meric peptide from Spike glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,99210
Polymers90,6166
Non-polymers3764
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11260 Å2
ΔGint-84 kcal/mol
Surface area35430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.538, 86.056, 152.072
Angle α, β, γ (deg.)90.00, 90.01, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 8 molecules ACEGBDFH

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


Mass: 32463.109 Da / Num. of mol.: 4 / Fragment: extracellular domain, UNP residues 25-299
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: P01899
#2: Protein
Beta-2-microglobulin


Mass: 11835.555 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: P01887

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Protein/peptide , 1 types, 4 molecules ILJK

#3: Protein/peptide
9-meric peptide from Spike glycoprotein / peptidic epitope S510


Mass: 1009.139 Da / Num. of mol.: 4 / Fragment: UNP residues 510-518 / Source method: obtained synthetically / Details: Synthetic peptide / References: UniProt: Q02385

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Non-polymers , 3 types, 977 molecules

#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 969 / Source method: isolated from a natural source / Formula: H2O

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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: 2.87 Å3/Da / Density % sol: 57.17 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M sodium citrate, 28% PEG 3350, 0.2M lithium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 2, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→58.4 Å / Num. all: 113937 / Num. obs: 113937 / % possible obs: 95.4 % / Redundancy: 2.8 % / Biso Wilson estimate: 30.4 Å2 / Rmerge(I) obs: 0.056 / Rsym value: 0.056 / Net I/σ(I): 8.2
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.185 / Mean I/σ(I) obs: 4.8 / Num. unique all: 16934 / Rsym value: 0.185 / % possible all: 97.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1BZ9

1bz9


Resolution: 2.1→56.98 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.901 / SU B: 4.501 / SU ML: 0.124 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.217 / ESU R Free: 0.201 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: number water and peptide chains for final H2Db model
RfactorNum. reflection% reflectionSelection details
Rfree0.26614 5737 5 %RANDOM
Rwork0.20635 ---
all0.20936 108198 --
obs0.20936 108198 95.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.903 Å2
Baniso -1Baniso -2Baniso -3
1-1.2 Å20 Å20.13 Å2
2---1.07 Å20 Å2
3----0.13 Å2
Refinement stepCycle: LAST / Resolution: 2.1→56.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12061 0 44 969 13074
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.02112479
X-RAY DIFFRACTIONr_angle_refined_deg1.7411.93516932
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.17551432
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.85723.344649
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.038152032
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5111596
X-RAY DIFFRACTIONr_chiral_restr0.1240.21693
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.029724
X-RAY DIFFRACTIONr_nbd_refined0.2060.25244
X-RAY DIFFRACTIONr_nbtor_refined0.3050.27984
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2949
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2360.290
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1580.231
X-RAY DIFFRACTIONr_mcbond_it1.79127599
X-RAY DIFFRACTIONr_mcangle_it2.66311736
X-RAY DIFFRACTIONr_scbond_it3.67245918
X-RAY DIFFRACTIONr_scangle_it5.2165196
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 431 -
Rwork0.232 8158 -
obs--97.13 %

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