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- PDB-1zt7: crystal structure of class I MHC H-2Kk in complex with a nonapeptide -

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Basic information

Entry
Database: PDB / ID: 1zt7
Titlecrystal structure of class I MHC H-2Kk in complex with a nonapeptide
Components
  • Beta-2-microglobulin
  • H-2 class I histocompatibility antigen, K-K alpha chain
  • SV40 epitope, SEFLLEKRI
KeywordsIMMUNE SYSTEM / peptide binding groove
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 / beta-2-microglobulin binding ...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 / beta-2-microglobulin binding / cellular defense response / Neutrophil degranulation / 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 / 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 / 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 / multicellular organismal-level iron ion homeostasis / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / phagocytic vesicle membrane / positive regulation of cellular senescence / peptide antigen binding / negative regulation of epithelial cell proliferation / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / sensory perception of smell / positive regulation of T cell activation / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / iron ion transport / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / defense response to bacterium / immune response / lysosomal membrane / external side of plasma membrane / signaling receptor binding / protein-containing complex binding / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / cytosol
Similarity search - Function
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 ...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 / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Beta-2-microglobulin / H-2 class I histocompatibility antigen, K-K alpha chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsKellenberger, C. / Roussel, A. / Malissen, B.
Citation
Journal: J Immunol. / Year: 2005
Title: The H-2Kk MHC peptide-binding groove anchors the backbone of an octameric antigenic peptide in an unprecedented mode.
Authors: Kellenberger, C. / Roussel, A. / Malissen, B.
#1: Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 2004
Title: Expression, refolding, crystallization and preliminary crystallographic study of MHC H-2Kk complexed with octapeptides and nonapeptides
Authors: Kellenberger, C. / Porciero, S. / Roussel, A.
History
DepositionMay 26, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 18, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 6, 2019Group: Data collection / Database references / Category: citation / 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_ref_seq_dif.details
Revision 1.4Apr 3, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: H-2 class I histocompatibility antigen, K-K alpha chain
B: Beta-2-microglobulin
C: H-2 class I histocompatibility antigen, K-K alpha chain
D: Beta-2-microglobulin
P: SV40 epitope, SEFLLEKRI
Q: SV40 epitope, SEFLLEKRI


Theoretical massNumber of molelcules
Total (without water)90,4006
Polymers90,4006
Non-polymers00
Water2,630146
1
A: H-2 class I histocompatibility antigen, K-K alpha chain
B: Beta-2-microglobulin
P: SV40 epitope, SEFLLEKRI


Theoretical massNumber of molelcules
Total (without water)45,2003
Polymers45,2003
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4320 Å2
ΔGint-18 kcal/mol
Surface area19920 Å2
MethodPISA
2
C: H-2 class I histocompatibility antigen, K-K alpha chain
D: Beta-2-microglobulin
Q: SV40 epitope, SEFLLEKRI


Theoretical massNumber of molelcules
Total (without water)45,2003
Polymers45,2003
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4320 Å2
ΔGint-19 kcal/mol
Surface area19980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.135, 72.628, 88.793
Angle α, β, γ (deg.)90.00, 111.24, 90.00
Int Tables number3
Space group name H-MP121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12A
22C
13B
23D
14P
24Q

NCS domain segments:

Component-ID: 1 / Refine code: 2

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYASNASNAA1 - 1762 - 177
21GLYGLYASNASNCC1 - 1762 - 177
12THRTHRGLUGLUAA182 - 275183 - 276
22THRTHRGLUGLUCC182 - 275183 - 276
13ILEILEMETMETBB1 - 992 - 100
23ILEILEMETMETDD1 - 992 - 100
14SERSERILEILEPE1 - 91 - 9
24SERSERILEILEQF1 - 91 - 9

NCS ensembles :
ID
1
2
3
4

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Components

#1: Protein H-2 class I histocompatibility antigen, K-K alpha chain / class I mouse MHC H-2Kk heavy chain / H- 2KK


Mass: 32228.023 Da / Num. of mol.: 2 / Fragment: residues 0-275
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET3a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P04223
#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) / Plasmid: pET3a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P01887
#3: Protein/peptide SV40 epitope, SEFLLEKRI


Mass: 1136.341 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: chemically synthesized. This sequence occurs naturally in simian virus
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / 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: 2.83 Å3/Da / Density % sol: 57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.6M ammonium sulfate, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 30, 2003
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 3→20 Å / Num. obs: 18302 / % possible obs: 90.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.5 % / Biso Wilson estimate: 54.3 Å2 / Rsym value: 0.158
Reflection shellResolution: 3→3.05 Å / Redundancy: 2.4 % / Num. unique all: 937 / Rsym value: 0.397 / % possible all: 90.4

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: the complex between H-2Kk and the octapeptide HA(259-266)

Resolution: 3→15 Å / Cor.coef. Fo:Fc: 0.873 / Cor.coef. Fo:Fc free: 0.776 / SU B: 24.345 / SU ML: 0.461 / Cross valid method: THROUGHOUT / ESU R Free: 0.601 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.31074 866 4.8 %RANDOM
Rwork0.23094 ---
all0.23474 ---
obs0.23474 17330 89.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 4.551 Å2
Baniso -1Baniso -2Baniso -3
1-2 Å20 Å20.68 Å2
2--1.28 Å20 Å2
3----2.79 Å2
Refinement stepCycle: LAST / Resolution: 3→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6334 0 0 146 6480
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0216524
X-RAY DIFFRACTIONr_bond_other_d0.0020.025642
X-RAY DIFFRACTIONr_angle_refined_deg1.211.9318860
X-RAY DIFFRACTIONr_angle_other_deg0.835313134
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0745760
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0730.2906
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.027264
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021416
X-RAY DIFFRACTIONr_nbd_refined0.1980.21405
X-RAY DIFFRACTIONr_nbd_other0.2070.26838
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0850.24007
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2020.2126
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.290.253
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2210.2141
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0920.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.1851.53832
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.35926202
X-RAY DIFFRACTIONr_scbond_it0.64632692
X-RAY DIFFRACTIONr_scangle_it1.0694.52658
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

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

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1035tight positional0.020.05
2A551tight positional0.020.05
3B582tight positional0.010.05
4P53tight positional0.020.05
1A1716medium positional0.230.5
2A901medium positional0.140.5
3B963medium positional0.190.5
4P107medium positional0.180.5
1A1035tight thermal0.030.5
2A551tight thermal0.030.5
3B582tight thermal0.020.5
4P53tight thermal0.030.5
1A1716medium thermal0.22
2A901medium thermal0.122
3B963medium thermal0.112
4P107medium thermal0.172
LS refinement shellResolution: 3→3.075 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.374 51
Rwork0.267 1131

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