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- PDB-7zuc: Human Major Histocompatibility Complex A2 allele presenting LLLGIGILV -

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Basic information

Entry
Database: PDB / ID: 7zuc
TitleHuman Major Histocompatibility Complex A2 allele presenting LLLGIGILV
Components
  • Beta-2-microglobulin
  • LEU-LEU-LEU-GLY-ILE-GLY-ILE-LEU-VAL
  • MHC class I antigen
KeywordsIMMUNE SYSTEM / HUMAN / MHC / Melanoma
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 / lumenal side of endoplasmic reticulum membrane / Antigen Presentation: Folding, assembly and peptide loading of class I MHC ...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 / lumenal side of endoplasmic reticulum membrane / 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 / 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-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / 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 / : ...MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
MHC class I antigen / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.89 Å
AuthorsRizkallah, P.J. / Wall, A. / Sewell, A.K. / Fuller, A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Cell / Year: 2023
Title: Targeting of multiple tumor-associated antigens by individual T cell receptors during successful cancer immunotherapy.
Authors: Dolton, G. / Rius, C. / Wall, A. / Szomolay, B. / Bianchi, V. / Galloway, S.A.E. / Hasan, M.S. / Morin, T. / Caillaud, M.E. / Thomas, H.L. / Theaker, S. / Tan, L.R. / Fuller, A. / Topley, K. ...Authors: Dolton, G. / Rius, C. / Wall, A. / Szomolay, B. / Bianchi, V. / Galloway, S.A.E. / Hasan, M.S. / Morin, T. / Caillaud, M.E. / Thomas, H.L. / Theaker, S. / Tan, L.R. / Fuller, A. / Topley, K. / Legut, M. / Attaf, M. / Hopkins, J.R. / Behiry, E. / Zabkiewicz, J. / Alvares, C. / Lloyd, A. / Rogers, A. / Henley, P. / Fegan, C. / Ottmann, O. / Man, S. / Crowther, M.D. / Donia, M. / Svane, I.M. / Cole, D.K. / Brown, P.E. / Rizkallah, P. / Sewell, A.K.
History
DepositionMay 12, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 24, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / struct_ncs_dom_lim
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _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 1.2Feb 7, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.3Nov 6, 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: LEU-LEU-LEU-GLY-ILE-GLY-ILE-LEU-VAL
D: MHC class I antigen
E: Beta-2-microglobulin
F: LEU-LEU-LEU-GLY-ILE-GLY-ILE-LEU-VAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,85412
Polymers89,4826
Non-polymers3726
Water5,062281
1
A: MHC class I antigen
B: Beta-2-microglobulin
C: LEU-LEU-LEU-GLY-ILE-GLY-ILE-LEU-VAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9276
Polymers44,7413
Non-polymers1863
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4680 Å2
ΔGint-17 kcal/mol
Surface area18930 Å2
MethodPISA
2
D: MHC class I antigen
E: Beta-2-microglobulin
F: LEU-LEU-LEU-GLY-ILE-GLY-ILE-LEU-VAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9276
Polymers44,7413
Non-polymers1863
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4860 Å2
ΔGint-17 kcal/mol
Surface area19090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.259, 85.259, 213.486
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number153
Space group name H-MP3212
Components on special symmetry positions
IDModelComponents
11D-467-

HOH

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-LEU-GLY-ILE-GLY-ILE-LEU-VAL


Mass: 910.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 281 / Source method: isolated from a natural source / Formula: H2O
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: 2.5 Å3/Da / Density % sol: 50.86 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 20% PEG 3,350, 0.2 M Potassium Thiocyanate, 0.1 M BIS-TRIS Propane pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Apr 28, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.89→71.18 Å / Num. obs: 71594 / % possible obs: 100 % / Redundancy: 20.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.252 / Net I/σ(I): 6.5
Reflection shellResolution: 1.89→1.92 Å / Rmerge(I) obs: 3.949 / Num. unique obs: 3540 / CC1/2: 0.329

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.84 Å71.16 Å
Translation3.84 Å71.16 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
PHASER2.8.3phasing
PDB_EXTRACT3.27data extraction
DIALSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BNR

2bnr


Resolution: 1.89→71.16 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.941 / WRfactor Rfree: 0.2088 / WRfactor Rwork: 0.1733 / FOM work R set: 0.6347 / SU B: 16.046 / SU ML: 0.204 / SU R Cruickshank DPI: 0.1621 / SU Rfree: 0.1482 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.162 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2474 3414 4.8 %RANDOM
Rwork0.2116 ---
obs0.2133 68059 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 107.03 Å2 / Biso mean: 39.039 Å2 / Biso min: 7.26 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å2-0.07 Å20 Å2
2---0.14 Å2-0 Å2
3---0.46 Å2
Refinement stepCycle: final / Resolution: 1.89→71.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6310 0 24 281 6615
Biso mean--42.72 37.78 -
Num. residues----770
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0136510
X-RAY DIFFRACTIONr_bond_other_d0.0010.0155832
X-RAY DIFFRACTIONr_angle_refined_deg1.4081.6568824
X-RAY DIFFRACTIONr_angle_other_deg1.2211.58413422
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9395764
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.79221.3400
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.568151060
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2591556
X-RAY DIFFRACTIONr_chiral_restr0.0660.2798
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.027420
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021620
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A85800.12
12D85800.12
21B30920.09
22E30920.09
LS refinement shellResolution: 1.89→1.939 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.401 264 -
Rwork0.4 4981 -
all-5245 -
obs--99.19 %
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)
11.85690.0916-0.19533.6133-0.14671.371-0.01990.2119-0.2071-0.1563-0.00830.0730.14570.04790.02820.02130.00850.0050.1126-0.03260.216910.892929.242216.2378
26.5183-2.13070.77522.256-0.0481.3202-0.001-0.1501-0.05320.02490.06940.0564-0.1114-0.3118-0.06840.1448-0.0088-0.02820.11480.01240.1266-23.00222.88423.709
32.81591.2816-1.382.9207-1.31344.77550.1518-0.1554-0.04620.2619-0.01270.1702-0.0409-0.1458-0.13910.0474-0.0261-0.02330.0574-0.01960.2446-6.299430.028737.0607
40.36930.4879-0.94745.9746-2.65262.8259-0.04270.0019-0.0078-0.388-0.0127-0.13150.18280.07520.05540.1251-0.0147-0.01030.2199-0.01920.210717.429130.09213.2162
52.05620.0712-0.37492.3295-0.93292.3604-0.0114-0.0608-0.0125-0.0163-0.038-0.0143-0.10230.00590.04950.05290.0199-0.01440.00980.00030.229323.001521.565560.0317
65.227-4.656-1.79526.84053.56632.8673-0.3576-0.1502-0.12260.66880.453-0.21510.51750.4768-0.09540.22690.0368-0.0170.190.0360.250832.014-12.354563.0052
72.87451.9883-0.2876.1145-0.07122.5191-0.05560.2763-0.3684-0.33980.00930.32010.3422-0.29340.04630.15440.0087-0.05790.1316-0.03880.320117.5891-2.258548.5563
82.84192.2507-4.99432.6566-3.96328.79060.112-0.11650.08960.11880.00460.0664-0.16750.2184-0.11660.19460.0165-0.00430.17740.02490.204322.41528.963160.67
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 180
2X-RAY DIFFRACTION2A181 - 276
3X-RAY DIFFRACTION3B0 - 99
4X-RAY DIFFRACTION4C1 - 9
5X-RAY DIFFRACTION5D1 - 180
6X-RAY DIFFRACTION6D181 - 276
7X-RAY DIFFRACTION7E0 - 99
8X-RAY DIFFRACTION8F1 - 9

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