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- PDB-6z9x: Human Class I Major Histocompatibility Complex, A02 allele, prese... -

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Basic information

Entry
Database: PDB / ID: 6z9x
TitleHuman Class I Major Histocompatibility Complex, A02 allele, presenting LLS (t-butyl)Y FGTPT
Components
  • Beta-2-microglobulin
  • LEU-LEU-SER-TUR-PHE-GLY-THR-PRO-THR
  • 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 / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC ...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 / 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 / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / MHC class II protein complex / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / MHC class I peptide loading complex / response to molecule of bacterial origin / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / antigen processing and presentation of exogenous peptide antigen via MHC class II / MHC class I protein complex / positive regulation of immune response / peptide antigen binding / negative regulation of neurogenesis / positive regulation of T cell activation / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / positive regulation of T cell mediated cytotoxicity / cellular response to nicotine / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / Interferon gamma signaling / MHC class II protein complex binding / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / tertiary granule lumen / DAP12 signaling / positive regulation of protein binding / iron ion transport / T cell differentiation in thymus / negative regulation of neuron projection development / ER-Phagosome pathway / early endosome membrane / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / Golgi membrane / external side of plasma membrane / 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
MHC class I antigen / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.68 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 / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim
Item: _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag ..._diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag / _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 2.0Jul 10, 2024Group: Data collection / Derived calculations ...Data collection / Derived calculations / Non-polymer description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / entity / struct_conn
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _entity.formula_weight / _struct_conn.pdbx_leaving_atom_flag

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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-SER-TUR-PHE-GLY-THR-PRO-THR
D: MHC class I antigen
E: Beta-2-microglobulin
F: LEU-LEU-SER-TUR-PHE-GLY-THR-PRO-THR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,15410
Polymers89,7706
Non-polymers3844
Water1,08160
1
A: MHC class I antigen
B: Beta-2-microglobulin
C: LEU-LEU-SER-TUR-PHE-GLY-THR-PRO-THR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0775
Polymers44,8853
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4780 Å2
ΔGint-49 kcal/mol
Surface area19160 Å2
MethodPISA
2
D: MHC class I antigen
E: Beta-2-microglobulin
F: LEU-LEU-SER-TUR-PHE-GLY-THR-PRO-THR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0775
Polymers44,8853
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4760 Å2
ΔGint-49 kcal/mol
Surface area19240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)206.240, 49.350, 115.900
Angle α, β, γ (deg.)90.000, 123.850, 90.000
Int Tables number5
Space group name H-MC121
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
11GLYGLYPROPROAA1 - 2761 - 276
21GLYGLYPROPRODD1 - 2761 - 276
12METMETMETMETBB0 - 991 - 100
22METMETMETMETEE0 - 991 - 100

NCS ensembles :
ID
1
2

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Components

#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
#3: Protein/peptide LEU-LEU-SER-TUR-PHE-GLY-THR-PRO-THR


Mass: 1054.236 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.73 Å3/Da / Density % sol: 54.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 25% PEG 4000, 0.1 M Cacodylate buffer, 5% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.6
11H+4/2L, -K, -L20.4
ReflectionResolution: 2.68→51.34 Å / Num. obs: 22144 / % possible obs: 81.9 % / Redundancy: 2.5 % / CC1/2: 0.916 / Rmerge(I) obs: 0.173 / Rpim(I) all: 0.127 / Rrim(I) all: 0.216 / Net I/σ(I): 6
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
2.7-2.832.30.76681529700.2070.580.9612.783.4
8.95-51.342.80.06417386160.9870.0430.0779.677.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.7 Å51.34 Å
Translation2.7 Å51.34 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
Aimless0.5.27data scaling
PHASER2.6.1phasing
REFMAC5.8.0257refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EUL

5eul


Resolution: 2.68→51.34 Å / Cor.coef. Fo:Fc: 0.891 / Cor.coef. Fo:Fc free: 0.828 / SU B: 20.185 / SU ML: 0.206 / SU R Cruickshank DPI: 0.0656 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.083
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2409 1034 4.7 %RANDOM
Rwork0.1861 ---
obs0.1886 21104 80.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 49.32 Å2 / Biso mean: 21.665 Å2 / Biso min: 3.81 Å2
Baniso -1Baniso -2Baniso -3
1-13.23 Å20 Å2-2.82 Å2
2---6.29 Å2-0 Å2
3----6.95 Å2
Refinement stepCycle: final / Resolution: 2.68→51.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6332 0 20 60 6412
Biso mean--32.27 16.63 -
Num. residues----770
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0136536
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175678
X-RAY DIFFRACTIONr_angle_refined_deg1.651.6638882
X-RAY DIFFRACTIONr_angle_other_deg1.2051.58713160
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.4575764
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.00121.294402
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.651151050
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4461556
X-RAY DIFFRACTIONr_chiral_restr0.0720.2800
X-RAY DIFFRACTIONr_gen_planes_refined0.010.027402
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021526
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A84680.12
12D84680.12
21B29310.13
22E29310.13
LS refinement shellResolution: 2.685→2.754 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 64 -
Rwork0.229 1215 -
all-1279 -
obs--62.57 %
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)
11.81880.46440.04281.0018-0.08041.5008-0.01220.19690.0885-0.1072-0.0324-0.0928-0.02850.21880.04450.0963-0.01140.14380.1124-0.00230.2291-33.5718.814-5.983
21.43070.4426-0.58824.1416-2.56693.79930.02680.0876-0.15830.1127-0.00290.00090.1970.0255-0.0240.06250.03680.04370.1444-0.02380.1885-29.81-5.43126.808
31.39490.09340.31.58241.65232.7902-0.02970.0370.07520.0285-0.00150.11340.0817-0.21410.03120.0501-0.00550.10210.05020.0370.2724-44.8329.07318.615
41.1340.32420.28731.59520.41422.26390.02280.2194-0.0641-0.15850.0080.01680.07160.0652-0.03080.10280.00010.14950.1842-0.02440.311415.44510.6927.731
52.0743-1.0824-1.27021.6911-0.12753.28050.24170.26480.1466-0.0797-0.1554-0.0865-0.4964-0.2137-0.08640.1009-0.00260.0730.2310.00340.2808-16.85120.97740.547
63.34660.3147-0.48350.6173-0.43551.84490.1132-0.2333-0.20780.0975-0.08560.04740.13840.0275-0.02750.0985-0.0040.10350.06280.02580.2372-1.5446.17848.636
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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