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- PDB-2zol: Crystal structure of H-2Db in complex with the W513S variant of J... -

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Basic information

Entry
Database: PDB / ID: 2zol
TitleCrystal structure of H-2Db in complex with the W513S variant of 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 / Polymorphism / Secreted / Cleavage on pair of basic residues / Coiled coil / 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 / 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 / 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 / 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 / positive regulation of cellular senescence / negative regulation of epithelial cell proliferation / sensory perception of smell / T cell differentiation in thymus / negative regulation of neuron projection development / iron ion transport / 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 / endocytosis involved in viral entry into host cell / external side of plasma membrane / fusion of virus membrane with host 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, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / 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 / Spike S1 subunit, receptor binding domain superfamily, 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, 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 superfamily, coronavirus / 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: 2.7 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: Version format compliance
Revision 1.2Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 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 1.4Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id
Revision 1.6Nov 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, D-B alpha chain
C: H-2 class I histocompatibility antigen, D-B alpha chain
D: Beta-2-microglobulin
B: Beta-2-microglobulin
F: 9-meric peptide from Spike glycoprotein
E: 9-meric peptide from Spike glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,5137
Polymers90,4176
Non-polymers961
Water2,090116
1
A: H-2 class I histocompatibility antigen, D-B alpha chain
B: Beta-2-microglobulin
E: 9-meric peptide from Spike glycoprotein


Theoretical massNumber of molelcules
Total (without water)45,2093
Polymers45,2093
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4190 Å2
ΔGint-28 kcal/mol
Surface area18830 Å2
MethodPISA
2
C: H-2 class I histocompatibility antigen, D-B alpha chain
D: Beta-2-microglobulin
F: 9-meric peptide from Spike glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3054
Polymers45,2093
Non-polymers961
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3960 Å2
ΔGint-17 kcal/mol
Surface area18540 Å2
MethodPISA
3
C: H-2 class I histocompatibility antigen, D-B alpha chain
D: Beta-2-microglobulin
F: 9-meric peptide from Spike glycoprotein
hetero molecules

A: H-2 class I histocompatibility antigen, D-B alpha chain
B: Beta-2-microglobulin
E: 9-meric peptide from Spike glycoprotein


Theoretical massNumber of molelcules
Total (without water)90,5137
Polymers90,4176
Non-polymers961
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
Buried area9900 Å2
ΔGint-60 kcal/mol
Surface area35630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.561, 71.033, 86.999
Angle α, β, γ (deg.)90.00, 103.45, 90.00
Int Tables number3
Space group name H-MP121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12A
22C
13B
23D
14E
24F

NCS domain segments:

Component-ID: 1 / Refine code: 3

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROLEULEUAA2 - 1802 - 180
21PROPROLEULEUCB2 - 1802 - 180
12ARGARGTRPTRPAA181 - 274181 - 274
22ARGARGTRPTRPCB181 - 274181 - 274
13GLNGLNMETMETBD2 - 993 - 100
23GLNGLNMETMETDC2 - 993 - 100
14ABAABALEULEUEF1 - 91 - 9
24ABAABALEULEUFE1 - 91 - 9

NCS ensembles :
ID
1
2
3
4

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Components

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


Mass: 32463.109 Da / Num. of mol.: 2 / 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.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: P01887
#3: Protein/peptide 9-meric peptide from Spike glycoprotein / peptidic epitope S510


Mass: 910.007 Da / Num. of mol.: 2 / Fragment: UNP residues 510-518 / Mutation: W4S / Source method: obtained synthetically / Details: synthetic peptide / References: UniProt: Q02385
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 55.71 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 0.1M sodium citrate, 28% PEG 3350, 0.15M lithium sulfate, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.999 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 20, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
ReflectionResolution: 2.7→54.39 Å / Num. all: 27219 / Num. obs: 27219 / % possible obs: 99.3 % / Redundancy: 3 % / Biso Wilson estimate: 51.6 Å2 / Rmerge(I) obs: 0.083 / Rsym value: 0.083 / Net I/σ(I): 8.2
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 3 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 3.2 / Num. unique all: 3940 / Rsym value: 0.33 / % possible all: 99.1

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Processing

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

1bz9


Resolution: 2.7→33.7 Å / Cor.coef. Fo:Fc: 0.87 / Cor.coef. Fo:Fc free: 0.795 / SU B: 15.253 / SU ML: 0.321 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 1.46 / ESU R Free: 0.412 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: number water chains for final H2DbW4S model
RfactorNum. reflection% reflectionSelection details
Rfree0.30726 1368 5 %RANDOM
Rwork0.2537 ---
all0.2564 25849 --
obs0.2564 25849 99.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.996 Å2
Baniso -1Baniso -2Baniso -3
1-1 Å20 Å20.21 Å2
2--0.04 Å20 Å2
3----0.95 Å2
Refinement stepCycle: LAST / Resolution: 2.7→33.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5991 0 5 116 6112
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0216180
X-RAY DIFFRACTIONr_angle_refined_deg0.961.9338387
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1145716
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.54623.27318
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.33151008
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4721548
X-RAY DIFFRACTIONr_chiral_restr0.0660.2843
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.024826
X-RAY DIFFRACTIONr_nbd_refined0.1740.22461
X-RAY DIFFRACTIONr_nbtor_refined0.2960.24001
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1280.2200
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.190.262
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1340.28
X-RAY DIFFRACTIONr_mcbond_it0.52923758
X-RAY DIFFRACTIONr_mcangle_it0.95435861
X-RAY DIFFRACTIONr_scbond_it0.66342888
X-RAY DIFFRACTIONr_scangle_it1.06152526
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A708tight positional0.030.05
2A316tight positional0.020.05
3B392tight positional0.020.05
4E36tight positional0.020.05
1A760loose positional0.425
2A327loose positional0.615
3B421loose positional0.455
4E28loose positional0.045
1A708tight thermal0.020.5
2A316tight thermal0.020.5
3B392tight thermal0.030.5
4E36tight thermal0.020.5
1A760loose thermal0.5410
2A327loose thermal0.410
3B421loose thermal0.6510
4E28loose thermal0.4110
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 108 -
Rwork0.307 1861 -
obs--98.7 %

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