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- PDB-6z9w: Human Class I Major Histocompatibility Complex, A02 allele, prese... -

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Basic information

Entry
Database: PDB / ID: 6z9w
TitleHuman Class I Major Histocompatibility Complex, A02 allele, presenting LLGWVFAQV
Components
  • Beta-2-microglobulin
  • LEU-LEU-GLY-TRP-VAL-PHE-ALA-GLN-VAL
  • MHC class I antigen
KeywordsIMMUNE SYSTEM / MHC Class I / A02 allele
Function / homology
Function and homology information


antigen processing and presentation of peptide antigen via MHC class I / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / Endosomal/Vacuolar pathway / T cell mediated cytotoxicity / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / lumenal side of endoplasmic reticulum membrane / regulation of iron ion transport / cellular response to iron(III) ion ...antigen processing and presentation of peptide antigen via MHC class I / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / Endosomal/Vacuolar pathway / T cell mediated cytotoxicity / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / lumenal side of endoplasmic reticulum membrane / regulation of iron ion transport / cellular response to iron(III) ion / negative regulation of iron ion transport / 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 erythrocyte differentiation / response to molecule of bacterial origin / HFE-transferrin receptor complex / transferrin transport / MHC class I peptide loading complex / cellular response to iron ion / negative regulation of receptor-mediated endocytosis / 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 assembly with MHC class II protein complex / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / multicellular organismal-level iron ion homeostasis / positive regulation of T cell mediated cytotoxicity / specific granule lumen / positive regulation of immune response / antigen processing and presentation of exogenous peptide antigen via MHC class II / peptide antigen binding / phagocytic vesicle membrane / recycling endosome membrane / positive regulation of T cell activation / negative regulation of epithelial cell proliferation / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Modulation by Mtb of host immune system / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / T cell differentiation in thymus / late endosome membrane / negative regulation of neuron projection development / ER-Phagosome pathway / protein refolding / early endosome membrane / amyloid fibril formation / protein homotetramerization / intracellular iron ion homeostasis / learning or memory / endoplasmic reticulum lumen / Amyloid fiber formation / Golgi membrane / external side of plasma membrane / lysosomal 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 exosome / extracellular region / membrane / identical protein binding / 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
Beta-2-microglobulin / MHC class I antigen
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 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 22, 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 / struct_ncs_dom_lim
Item: _diffrn_source.pdbx_synchrotron_site / _struct_ncs_dom_lim.beg_auth_comp_id ..._diffrn_source.pdbx_synchrotron_site / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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: LEU-LEU-GLY-TRP-VAL-PHE-ALA-GLN-VAL
D: MHC class I antigen
E: Beta-2-microglobulin
F: LEU-LEU-GLY-TRP-VAL-PHE-ALA-GLN-VAL


Theoretical massNumber of molelcules
Total (without water)89,5326
Polymers89,5326
Non-polymers00
Water1,65792
1
A: MHC class I antigen
B: Beta-2-microglobulin
C: LEU-LEU-GLY-TRP-VAL-PHE-ALA-GLN-VAL


Theoretical massNumber of molelcules
Total (without water)44,7663
Polymers44,7663
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4400 Å2
ΔGint-22 kcal/mol
Surface area18680 Å2
MethodPISA
2
D: MHC class I antigen
E: Beta-2-microglobulin
F: LEU-LEU-GLY-TRP-VAL-PHE-ALA-GLN-VAL


Theoretical massNumber of molelcules
Total (without water)44,7663
Polymers44,7663
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4320 Å2
ΔGint-22 kcal/mol
Surface area18740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.725, 69.208, 88.617
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
12B
22E

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYGLUGLUAA1 - 2751 - 275
21GLYGLYGLUGLUDD1 - 2751 - 275
12METMETMETMETBB0 - 991 - 100
22METMETMETMETEE0 - 991 - 100

NCS ensembles :
ID
1
2

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Components

#1: Protein MHC class I antigen


Mass: 31854.203 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: U5YJM1
#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
#3: Protein/peptide LEU-LEU-GLY-TRP-VAL-PHE-ALA-GLN-VAL


Mass: 1032.234 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / Source method: isolated from a natural source / Formula: H2O
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: 2.05 Å3/Da / Density % sol: 39.87 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5
Details: PACT premier screen, condition D02: 0.1M MMT buffer, 25% PEG 1500

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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 PILATUS 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
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.649
11-h,-k,l20.351
ReflectionResolution: 2.7→29.94 Å / Num. obs: 19779 / % possible obs: 99.8 % / Redundancy: 6.9 % / CC1/2: 0.991 / Rmerge(I) obs: 0.212 / Rpim(I) all: 0.088 / Rrim(I) all: 0.23 / Net I/σ(I): 7.8
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
2.7-2.777.51.39257727680.6250.5431.4961.499.9
12.08-29.855.40.0637671420.9970.0280.06917.794.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4.67 Å29.86 Å
Translation4.67 Å29.86 Å

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.5.32data scaling
PHASER2.8.3phasing
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EUL

5eul


Resolution: 2.7→29.94 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.86 / SU B: 18.806 / SU ML: 0.213 / SU R Cruickshank DPI: 0.0736 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.096
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2806 971 4.9 %RANDOM
Rwork0.1997 ---
obs0.2036 18791 98.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 108.57 Å2 / Biso mean: 42.764 Å2 / Biso min: 16.35 Å2
Baniso -1Baniso -2Baniso -3
1-12.65 Å20 Å2-4.05 Å2
2---1.89 Å2-0 Å2
3----10.76 Å2
Refinement stepCycle: final / Resolution: 2.7→29.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6316 0 0 92 6408
Biso mean---30.24 -
Num. residues----768
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0136502
X-RAY DIFFRACTIONr_bond_other_d0.0040.0175664
X-RAY DIFFRACTIONr_angle_refined_deg1.5371.6548826
X-RAY DIFFRACTIONr_angle_other_deg1.1941.58113120
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.8965762
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.78921.33406
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.119151054
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.7321556
X-RAY DIFFRACTIONr_chiral_restr0.0640.2794
X-RAY DIFFRACTIONr_gen_planes_refined0.010.027394
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021534
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A84920.12
12D84920.12
21B29200.11
22E29200.11
LS refinement shellResolution: 2.7→2.77 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 69 -
Rwork0.223 1397 -
all-1466 -
obs--99.32 %
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)
12.5166-0.50210.03721.4709-0.4313.2034-0.0563-0.14810.0237-0.00520.04860.1560.2111-0.23770.00760.0298-0.0279-0.00360.04330.00420.0352-3.8633-39.295649.8426
22.12031.9921-0.66734.4543-0.53521.64760.02670.06640.33620.1108-0.0371-0.1382-0.3334-0.19010.01040.07820.0374-0.04170.1452-0.02710.158526.3605-22.865740.541
33.5256-0.38220.50062.0467-0.39282.3490.04190.1756-0.1979-0.148-0.0339-0.06520.18260.1743-0.0080.1142-0.0374-0.02960.05990.00230.03115.8154-40.117530.7044
42.2920.0839-0.61661.423-0.09433.6578-0.04460.05570.032-0.04410.00320.1449-0.2459-0.10330.04140.05180.0224-0.04370.0213-0.02050.0553-3.9739-9.7374-5.5456
52.6146-1.4059-1.08213.37430.82251.7707-0.1463-0.0338-0.5752-0.2581-0.1671-0.27610.3428-0.2250.31350.1282-0.0360.13910.1796-0.00660.282126.3109-26.1663.5574
64.0640.6035-0.63761.20550.20721.7414-0.005-0.10840.10080.1430.0079-0.0601-0.16940.1286-0.00280.10460.0369-0.02990.052-0.01120.018515.6788-8.963213.617
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 180
2X-RAY DIFFRACTION1C0 - 9
3X-RAY DIFFRACTION2A181 - 276
4X-RAY DIFFRACTION3B0 - 99
5X-RAY DIFFRACTION4D0 - 180
6X-RAY DIFFRACTION4F0 - 9
7X-RAY DIFFRACTION5D181 - 276
8X-RAY DIFFRACTION6E0 - 99

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