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- PDB-6z9v: Human Class I Major Histocompatibility Complex, A02 allele, prese... -

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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


antigen processing and presentation of peptide antigen via MHC class I / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex ...antigen processing and presentation of peptide antigen via MHC class I / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / lumenal side of endoplasmic reticulum membrane / cellular response to iron(III) ion / MHC class II protein complex / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / ER to Golgi transport vesicle membrane / 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 / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / positive regulation of T cell activation / 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 / specific granule lumen / phagocytic vesicle membrane / recycling endosome membrane / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / negative regulation of neuron projection development / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / endoplasmic reticulum lumen / Amyloid fiber formation / Golgi membrane / lysosomal membrane / external side of plasma membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / endoplasmic reticulum / Golgi apparatus / 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
Revision 1.4Nov 13, 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: 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

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Components

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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

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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)

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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

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Details

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: 2.71 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

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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

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Phasing

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

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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

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