[English] 日本語
Yorodumi
- PDB-7ji2: Crystal Structure of H2-Kb in complex with a OVA mutant peptide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ji2
TitleCrystal Structure of H2-Kb in complex with a OVA mutant peptide
Components
  • Beta-2-microglobulinBeta-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


TAP1 binding / TAP2 binding / positive regulation of antibody-dependent cellular cytotoxicity / regulation of natural killer cell mediated immunity / positive regulation of TRAIL production / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / MHC class Ib protein complex / positive regulation of natural killer cell mediated immunity / positive regulation of natural killer cell cytokine production / natural killer cell tolerance induction ...TAP1 binding / TAP2 binding / positive regulation of antibody-dependent cellular cytotoxicity / regulation of natural killer cell mediated immunity / positive regulation of TRAIL production / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / MHC class Ib protein complex / positive regulation of natural killer cell mediated immunity / positive regulation of natural killer cell cytokine production / natural killer cell tolerance induction / natural killer cell lectin-like receptor binding / negative regulation of natural killer cell activation / cis-Golgi network membrane / positive regulation of natural killer cell activation / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / negative regulation of natural killer cell mediated cytotoxicity / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of interleukin-13 production / positive regulation of natural killer cell mediated cytotoxicity / regulation of membrane depolarization / inner ear development / positive regulation of natural killer cell proliferation / T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / positive regulation of memory T cell activation / positive regulation of immunoglobulin production / TAP complex binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of interleukin-4 production / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / MHC class I protein binding / cellular defense response / endoplasmic reticulum exit site / beta-2-microglobulin binding / TAP binding / protection from natural killer cell mediated cytotoxicity / negative regulation of T cell proliferation / 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 / detection of bacterium / Neutrophil degranulation / T cell receptor binding / 14-3-3 protein binding / lumenal side of endoplasmic reticulum membrane / peptide binding / 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 / response to molecule of bacterial origin / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / 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 / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / negative regulation of epithelial cell proliferation / positive regulation of T cell activation / antimicrobial humoral immune response mediated by antimicrobial peptide / positive regulation of type II interferon production / sensory perception of smell / negative regulation of neuron projection development / positive regulation of tumor necrosis factor production / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / antibacterial humoral response / iron ion transport / T cell receptor signaling pathway / protein-folding chaperone binding / protein refolding / early endosome membrane / protein homotetramerization / cellular response to lipopolysaccharide / intracellular iron ion homeostasis / defense response to Gram-negative bacterium / amyloid fibril formation
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 / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. ...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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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 / 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 / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 511 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more