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- PDB-2zsv: Crystal structure of H-2Kb in complex with JHMV epitope S598 -

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Basic information

Entry
Database: PDB / ID: 2zsv
TitleCrystal structure of H-2Kb in complex with JHMV epitope S598
Components
  • 8-mer peptide from spike glycoprotein
  • Beta-2-microglobulin
  • H-2 class I histocompatibility antigen, K-B alpha chain
KeywordsIMMUNE SYSTEM / Ig Fold / protein-protein interactions / subdominant epitope / Glycoprotein / Immune response / Membrane / MHC I / Transmembrane / Immunoglobulin domain / Secreted
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 exogenous peptide antigen via MHC class I / inner ear development / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / cellular defense response ...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 exogenous peptide antigen via MHC class I / inner ear development / 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 / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / iron ion transport / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / 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 / MHC class I protein complex / peptide antigen binding / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / positive regulation of T cell mediated cytotoxicity / cellular response to nicotine / 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 / learning or memory / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / defense response to bacterium / 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 / 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
CYSTEINE / Beta-2-microglobulin / H-2 class I histocompatibility antigen, K-B alpha chain / Spike glycoprotein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsTheodossis, A. / Dunstone, M.A. / Rossjohn, J.
CitationJournal: Plos Pathog. / Year: 2008
Title: Prevention of cytotoxic T cell escape using a heteroclitic subdominant viral T cell determinant.
Authors: Butler, N.S. / Theodossis, A. / Webb, A.I. / Nastovska, R. / Ramarathinam, S.H. / Dunstone, M.A. / Rossjohn, J. / Purcell, A.W. / Perlman, S.
History
DepositionSep 18, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 4, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 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_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 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

Downloads & links

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Assembly

Deposited unit
A: H-2 class I histocompatibility antigen, K-B alpha chain
B: Beta-2-microglobulin
C: H-2 class I histocompatibility antigen, K-B alpha chain
D: Beta-2-microglobulin
E: 8-mer peptide from spike glycoprotein
F: 8-mer peptide from spike glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,48317
Polymers89,4406
Non-polymers1,04211
Water11,097616
1
A: H-2 class I histocompatibility antigen, K-B alpha chain
B: Beta-2-microglobulin
E: 8-mer peptide from spike glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1187
Polymers44,7203
Non-polymers3974
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4670 Å2
ΔGint-15 kcal/mol
Surface area19380 Å2
MethodPISA
2
C: H-2 class I histocompatibility antigen, K-B alpha chain
D: Beta-2-microglobulin
F: 8-mer peptide from spike glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,36510
Polymers44,7203
Non-polymers6457
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5570 Å2
ΔGint-16 kcal/mol
Surface area19230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.487, 89.539, 89.932
Angle α, β, γ (deg.)90.00, 111.68, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D
13E
23F

NCS domain segments:

Component-ID: 1 / Refine code: 5

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYPROPROAA1 - 2781 - 278
21GLYGLYPROPROCC1 - 2781 - 278
12ILEILEMETMETBB1 - 991 - 99
22ILEILEMETMETDD1 - 991 - 99
13ARGARGILEILEEE1 - 81 - 8
23ARGARGILEILEFF1 - 81 - 8

NCS ensembles :
IDDetails
1A C
2B D
3E F

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Components

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Protein , 2 types, 4 molecules ACBD

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


Mass: 32068.777 Da / Num. of mol.: 2 / Fragment: extracellular domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-K1, H2-K / Production host: Escherichia coli (E. coli) / References: UniProt: P01901
#2: Protein Beta-2-microglobulin


Mass: 11704.359 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2m / Production host: Escherichia coli (E. coli) / References: UniProt: P01887

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Protein/peptide , 1 types, 2 molecules EF

#3: Protein/peptide 8-mer peptide from spike glycoprotein


Mass: 947.113 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The sequence of the peptide is naturally found in Mouse Hepatitis Virus JHM strain
References: UniProt: P11225*PLUS

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Non-polymers , 3 types, 627 molecules

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


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CYS / CYSTEINE


Type: L-peptide linking / Mass: 121.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2S
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 616 / 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: 2.78 Å3/Da / Density % sol: 55.77 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 0.1M cacodylate, 16% PEG 8K, 0.2M Ca(OAc)2, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 8, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.8→24.46 Å / Num. all: 90277 / Num. obs: 90277 / % possible obs: 99.6 % / Redundancy: 2.9 % / Biso Wilson estimate: 24.9 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 18
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.385 / Mean I/σ(I) obs: 2 / Num. unique all: 13114 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.4.0077refinement
CrystalCleardata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1G7Q

1g7q


Resolution: 1.8→24.4 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.935 / SU B: 2.785 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.133 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24975 4528 5 %RANDOM
Rwork0.21023 ---
obs0.21222 85747 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.616 Å2
Baniso -1Baniso -2Baniso -3
1--0.66 Å20 Å2-0.23 Å2
2--1.3 Å2-0 Å2
3----0.82 Å2
Refinement stepCycle: LAST / Resolution: 1.8→24.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6164 0 66 616 6846
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0216486
X-RAY DIFFRACTIONr_angle_refined_deg1.6181.9458823
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.395777
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.41323.639316
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.873151024
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9311543
X-RAY DIFFRACTIONr_chiral_restr0.1240.2911
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215055
X-RAY DIFFRACTIONr_mcbond_it1.35723881
X-RAY DIFFRACTIONr_mcangle_it2.34736284
X-RAY DIFFRACTIONr_scbond_it3.18142605
X-RAY DIFFRACTIONr_scangle_it4.67652537
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1094MEDIUM POSITIONAL0.120.5
12A1088LOOSE POSITIONAL0.275
11C1094MEDIUM THERMAL1.592
12C1088LOOSE THERMAL1.7210
21B392MEDIUM POSITIONAL0.040.5
22B402LOOSE POSITIONAL0.175
21D392MEDIUM THERMAL0.772
22D402LOOSE THERMAL1.110
31E32MEDIUM POSITIONAL0.040.5
32E32LOOSE POSITIONAL0.065
31F32MEDIUM THERMAL0.792
32F32LOOSE THERMAL1.2810
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.426 315 -
Rwork0.404 6245 -
obs--99 %

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