[English] 日本語
Yorodumi
- PDB-6z9v: Human Class I Major Histocompatibility Complex, A02 allele, prese... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6z9v
TitleHuman Class I Major Histocompatibility Complex, A02 allele, presenting IIGWMWIPV
Components
  • Beta-2-microglobulin
  • ILE-ILE-GLY-TRP-MET-TRP-ILE-PRO-VAL
  • MHC class I antigen
KeywordsIMMUNE SYSTEM / MHC I
Function / homology
Function and homology information


positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / DAP12 interactions / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / cellular response to iron ion ...positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / DAP12 interactions / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / 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 / ER to Golgi transport vesicle membrane / 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 / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / multicellular organismal-level iron ion homeostasis / MHC class II protein complex / cellular response to nicotine / specific granule lumen / positive regulation of cellular senescence / positive regulation of T cell mediated cytotoxicity / recycling endosome membrane / phagocytic vesicle membrane / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of immune response / Interferon gamma signaling / Modulation by Mtb of host immune system / positive regulation of T cell activation / sensory perception of smell / negative regulation of neuron projection development / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / iron ion transport / ER-Phagosome pathway / T cell differentiation in thymus / early endosome membrane / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / Golgi membrane / external side of plasma membrane / signaling receptor binding / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
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, 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
1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE / 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL / MHC class I antigen / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.01 Å
AuthorsRizkallah, P.J. / Man, S. / Redman, J.E.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust509517 United Kingdom
CitationJournal: J Immunol. / Year: 2021
Title: Synthetic Peptides with Inadvertent Chemical Modifications Can Activate Potentially Autoreactive T Cells.
Authors: Man, S. / Redman, J.E. / Cross, D.L. / Cole, D.K. / Can, I. / Davies, B. / Hashimdeen, S.S. / Reid, R. / Llewellyn-Lacey, S. / Miners, K.L. / Ladell, K. / Lissina, A. / Brown, P.E. / ...Authors: Man, S. / Redman, J.E. / Cross, D.L. / Cole, D.K. / Can, I. / Davies, B. / Hashimdeen, S.S. / Reid, R. / Llewellyn-Lacey, S. / Miners, K.L. / Ladell, K. / Lissina, A. / Brown, P.E. / Wooldridge, L. / Price, D.A. / Rizkallah, P.J.
History
DepositionJun 4, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 30, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 11, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Sep 29, 2021Group: Data collection / Database references / Category: citation / diffrn_source / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _diffrn_source.pdbx_synchrotron_site
Revision 1.3Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model
Item: _diffrn_source.pdbx_synchrotron_site

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: MHC class I antigen
B: Beta-2-microglobulin
C: ILE-ILE-GLY-TRP-MET-TRP-ILE-PRO-VAL
D: MHC class I antigen
E: Beta-2-microglobulin
F: ILE-ILE-GLY-TRP-MET-TRP-ILE-PRO-VAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,20631
Polymers89,8906
Non-polymers2,31525
Water8,845491
1
A: MHC class I antigen
B: Beta-2-microglobulin
C: ILE-ILE-GLY-TRP-MET-TRP-ILE-PRO-VAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,82114
Polymers44,9453
Non-polymers87611
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6310 Å2
ΔGint-59 kcal/mol
Surface area18900 Å2
MethodPISA
2
D: MHC class I antigen
E: Beta-2-microglobulin
F: ILE-ILE-GLY-TRP-MET-TRP-ILE-PRO-VAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,38517
Polymers44,9453
Non-polymers1,44014
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8170 Å2
ΔGint-30 kcal/mol
Surface area19110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.190, 85.190, 232.550
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number153
Space group name H-MP3212

-
Components

-
Protein , 2 types, 4 molecules ADBE

#1: Protein MHC class I antigen


Mass: 31951.316 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A / Production host: Escherichia coli (E. coli) / References: UniProt: A0A5B8RNS7
#2: Protein Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Escherichia coli (E. coli) / References: UniProt: P61769

-
Protein/peptide , 1 types, 2 molecules CF

#3: Protein/peptide ILE-ILE-GLY-TRP-MET-TRP-ILE-PRO-VAL


Mass: 1114.401 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

-
Non-polymers , 8 types, 516 molecules

#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Chemical ChemComp-P4G / 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE


Mass: 162.227 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O3
#9: Chemical ChemComp-PE8 / 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL


Mass: 370.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O9
#10: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 491 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.71 Å3/Da / Density % sol: 54.61 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PACT premier screen, condition G06: 0.2M Na Formate, 0.1M Bis-Tris Propane, 20% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97622 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97622 Å / Relative weight: 1
ReflectionResolution: 2.01→73.78 Å / Num. obs: 64808 / % possible obs: 100 % / Redundancy: 11.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.142 / Rpim(I) all: 0.044 / Rrim(I) all: 0.149 / Net I/σ(I): 13.4 / Num. measured all: 723829
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.01-2.0611.51.7555438847460.6050.5411.8381.5100
8.99-73.789.90.032798180710.010.03351.799.8

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4.85 Å73.78 Å
Translation4.85 Å73.78 Å

-
Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.5.32data scaling
PHASER2.8.2phasing
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EUL

5eul


Resolution: 2.01→73.78 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.953 / SU B: 9.634 / SU ML: 0.129 / SU R Cruickshank DPI: 0.1659 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.166 / ESU R Free: 0.15
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2164 3287 5.1 %RANDOM
Rwork0.1758 ---
obs0.1778 61437 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 130.12 Å2 / Biso mean: 35.743 Å2 / Biso min: 17.53 Å2
Baniso -1Baniso -2Baniso -3
1--0.84 Å2-0.42 Å20 Å2
2---0.84 Å2-0 Å2
3---2.72 Å2
Refinement stepCycle: final / Resolution: 2.01→73.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6340 0 145 491 6976
Biso mean--68.18 43.25 -
Num. residues----770
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0136752
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175933
X-RAY DIFFRACTIONr_angle_refined_deg1.7941.6599140
X-RAY DIFFRACTIONr_angle_other_deg1.391.58813757
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1675786
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.08421.214412
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.943151074
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9041558
X-RAY DIFFRACTIONr_chiral_restr0.0840.2813
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.027583
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021571
LS refinement shellResolution: 2.01→2.062 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 245 -
Rwork0.284 4489 -
all-4734 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.9057-0.49060.00134.15240.42750.8907-0.0484-0.1857-0.07520.26180.0241-0.00910.0759-0.06570.02430.0278-0.03080.00060.1370.00980.0042-13.180730.199820.0534
26.05292.1136-0.06462.3818-0.55791.63750.0198-0.0174-0.14150.0308-0.0223-0.1663-0.10030.27550.00250.0584-0.0015-0.00670.1101-0.01380.014221.719322.556315.0901
33.0125-1.4542-1.06473.29731.25563.84890.12760.30590.0734-0.3626-0.0576-0.13080.0320.1326-0.07010.0689-0.014-0.00520.14430.03150.02255.954329.68140.3323
40.9932-0.6579-0.49021.7871.41872.5073-0.0836-0.081-0.010.1450.0664-0.05390.06560.20930.01720.0389-0.0446-0.00180.1375-0.00150.006248.624443.842628.0346
57.2011.13222.20721.22240.27842.02710.1235-0.5742-0.08620.04030.03520.22560.0424-0.5514-0.15870.1071-0.0398-0.00440.23380.03140.114114.042553.439428.7362
62.3779-2.02540.35694.8005-0.40161.87920.05120.22810.2162-0.2693-0.10410.128-0.29950.02140.05290.1065-0.0533-0.01060.12930.01030.056730.703559.355514.333
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 180
2X-RAY DIFFRACTION1C1 - 9
3X-RAY DIFFRACTION2A181 - 276
4X-RAY DIFFRACTION3B0 - 99
5X-RAY DIFFRACTION4D1 - 180
6X-RAY DIFFRACTION4F1 - 9
7X-RAY DIFFRACTION5D181 - 276
8X-RAY DIFFRACTION6E0 - 99

+
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