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- PDB-7ji2: Crystal Structure of H2-Kb in complex with a OVA mutant peptide -

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Basic information

Entry
Database: PDB / ID: 7ji2
TitleCrystal Structure of H2-Kb in complex with a OVA mutant peptide
Components
  • Beta-2-microglobulin
  • H-2 class I histocompatibility antigen, K-B alpha chain
  • OVA mutant peptide
KeywordsIMMUNE SYSTEM / H2-Kb
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 / 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 / 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 / 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 / defense response to bacterium / external side of plasma membrane / 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 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 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 / Immunoglobulin-like fold
Similarity search - Domain/homology
Beta-2-microglobulin / H-2 class I histocompatibility antigen, K-B alpha chain
Similarity search - Component
Biological speciesMus musculus bactrianus (southwestern Asian house mouse)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsLi, X. / Mallis, R.J. / Mizsei, R. / Tan, K. / Reinherz, E.L. / Wang, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)R01AI136301 United States
CitationJournal: Science / Year: 2021
Title: Pre-T cell receptors topologically sample self-ligands during thymocyte beta-selection.
Authors: Li, X. / Mizsei, R. / Tan, K. / Mallis, R.J. / Duke-Cohan, J.S. / Akitsu, A. / Tetteh, P.W. / Dubey, A. / Hwang, W. / Wagner, G. / Lang, M.J. / Arthanari, H. / Wang, J.H. / Reinherz, E.L.
History
DepositionJul 22, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 20, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.3Oct 18, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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
D: H-2 class I histocompatibility antigen, K-B alpha chain
E: Beta-2-microglobulin
C: OVA mutant peptide
F: OVA mutant peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,15814
Polymers90,4226
Non-polymers7378
Water9,206511
1
A: H-2 class I histocompatibility antigen, K-B alpha chain
B: Beta-2-microglobulin
C: OVA mutant peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6718
Polymers45,2113
Non-polymers4605
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5270 Å2
ΔGint-17 kcal/mol
Surface area19190 Å2
MethodPISA
2
D: H-2 class I histocompatibility antigen, K-B alpha chain
E: Beta-2-microglobulin
F: OVA mutant peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4876
Polymers45,2113
Non-polymers2763
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4470 Å2
ΔGint-16 kcal/mol
Surface area19970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.427, 90.011, 89.674
Angle α, β, γ (deg.)90.000, 111.700, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 32388.150 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus bactrianus (southwestern Asian house mouse)
Gene: H2-K1, H2-K / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P01901
#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 bactrianus (southwestern Asian house mouse)
Gene: B2m / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P01887
#3: Protein/peptide OVA mutant peptide


Mass: 987.130 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 511 / Source method: isolated from a natural source / Formula: H2O
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: 2.78 Å3/Da / Density % sol: 55.82 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop
Details: 0.200 M Potassium Sodium Tartrate 20.000% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
Reflection twinOperator: h,-k,-h-l / Fraction: 0.33
ReflectionResolution: 1.95→50 Å / Num. obs: 70409 / % possible obs: 98.1 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.04 / Rrim(I) all: 0.105 / Χ2: 0.89 / Net I/σ(I): 4.8 / Num. measured all: 488045
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.95-1.9870.64234790.8830.2570.6920.4798.4
1.98-2.0270.58335250.880.2340.6290.46798.6
2.02-2.0670.47735220.9150.1920.5150.47698.5
2.06-2.170.44835180.9220.1810.4830.5498.6
2.1-2.1570.35535450.9420.1440.3840.50198.5
2.15-2.270.31235310.9560.1260.3370.51498.6
2.2-2.256.90.27535110.9580.1110.2970.56198.5
2.25-2.316.80.24935330.970.1020.2690.59298.2
2.31-2.386.40.20333300.9740.0860.2210.59993.5
2.38-2.466.80.18334390.980.0750.1980.63496.4
2.46-2.547.30.1735610.9820.0680.1830.67599.1
2.54-2.657.20.14535630.9850.0580.1570.73199.1
2.65-2.777.20.13235500.990.0530.1420.81999.2
2.77-2.917.10.11635440.9890.0470.1260.94999.1
2.91-3.170.10136040.9910.0410.1091.16899.2
3.1-3.336.60.09135340.990.0380.0991.37798.6
3.33-3.676.60.07933620.9930.0330.0861.68394.2
3.67-4.27.10.07136030.9940.0290.0771.75299.7
4.2-5.296.90.06736200.9950.0280.0721.77899.4
5.29-506.80.06235350.9960.0260.0671.55696.2

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1kpu

1kpu


Resolution: 1.95→45.01 Å / Cross valid method: THROUGHOUT / σ(F): 78.53 / Phase error: 31.52 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.1846 3628 5.15 %
Rwork0.1696 66824 -
obs0.1913 70388 97.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 92.31 Å2 / Biso mean: 33.4932 Å2 / Biso min: 14.22 Å2
Refinement stepCycle: final / Resolution: 1.95→45.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6235 0 48 512 6795
Biso mean--40.16 36.8 -
Num. residues----768
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.95-1.980.30981620.28883257341992
1.98-2.020.31891840.2843356354093
2.02-2.060.28131580.2773368352694
2.06-2.10.28131860.27923318350493
2.1-2.140.24971840.27663366355093
2.14-2.190.27182040.26023347355193
2.19-2.250.28792070.2543292349993
2.25-2.310.25951640.26243378354294
2.31-2.380.28661420.25943191333389
2.38-2.450.29541780.2493259343791
2.45-2.540.23821610.24083416357795
2.54-2.640.21321930.23053365355894
2.64-2.760.22942100.21993330354093
2.76-2.910.20641850.20493369355494
2.91-3.090.22391960.18823409360594
3.09-3.330.20271590.16693374353394
3.33-3.660.18371470.15453211335890
3.66-4.190.1491620.13333448361095
4.19-5.280.1241760.12493448362495
5.28-45.010.18882060.17653322352891

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