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- PDB-6g3j: MHC A02 Allele presenting MTSAIGILVP -

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Basic information

Entry
Database: PDB / ID: 6g3j
TitleMHC A02 Allele presenting MTSAIGILVP
Components
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, A-2 alpha chain
  • MET-THR-SER-ALA-ILE-GLY-ILE-LEU-PRO-VAL
KeywordsIMMUNE SYSTEM / MHCI
Function / homology
Function and homology information


positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / beta-2-microglobulin binding ...positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / beta-2-microglobulin binding / endoplasmic reticulum exit site / TAP binding / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / protection from natural killer cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / detection of bacterium / T cell receptor binding / 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 / lumenal side of endoplasmic reticulum membrane / 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 / 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 / positive regulation of type II interferon production / 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 / Interferon alpha/beta signaling / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / antibacterial humoral response / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / T cell receptor signaling pathway / E3 ubiquitin ligases ubiquitinate target proteins / 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 / defense response to Gram-positive bacterium / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / signaling receptor binding / Golgi membrane / lysosomal membrane / innate immune response / external side of plasma membrane / focal adhesion / Neutrophil degranulation / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / cell surface / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / RNA binding / extracellular exosome
Similarity search - Function
MHC class I, alpha chain, C-terminal / MHC_I C-terminus / 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 class I, alpha chain, C-terminal / MHC_I C-terminus / 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
HLA class I histocompatibility antigen, A alpha chain / HLA class I histocompatibility antigen, A alpha chain / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsRizkallah, P.J. / Sewell, A.K.
CitationJournal: Front Immunol / Year: 2019
Title: Peptide Super-Agonist Enhances T-Cell Responses to Melanoma.
Authors: Galloway, S.A.E. / Dolton, G. / Attaf, M. / Wall, A. / Fuller, A. / Rius, C. / Bianchi, V. / Theaker, S. / Lloyd, A. / Caillaud, M.E. / Svane, I.M. / Donia, M. / Cole, D.K. / Szomolay, B. / ...Authors: Galloway, S.A.E. / Dolton, G. / Attaf, M. / Wall, A. / Fuller, A. / Rius, C. / Bianchi, V. / Theaker, S. / Lloyd, A. / Caillaud, M.E. / Svane, I.M. / Donia, M. / Cole, D.K. / Szomolay, B. / Rizkallah, P. / Sewell, A.K.
History
DepositionMar 26, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 20, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 27, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / pdbx_contact_author / pdbx_database_proc
Item: _citation.title / _citation_author.identifier_ORCID ..._citation.title / _citation_author.identifier_ORCID / _citation_author.name / _pdbx_contact_author.email / _pdbx_contact_author.identifier_ORCID / _pdbx_contact_author.name_last
Revision 1.2Apr 10, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 1.4Nov 13, 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: HLA class I histocompatibility antigen, A-2 alpha chain
B: Beta-2-microglobulin
C: MET-THR-SER-ALA-ILE-GLY-ILE-LEU-PRO-VAL
D: HLA class I histocompatibility antigen, A-2 alpha chain
E: Beta-2-microglobulin
F: MET-THR-SER-ALA-ILE-GLY-ILE-LEU-PRO-VAL


Theoretical massNumber of molelcules
Total (without water)89,6646
Polymers89,6646
Non-polymers00
Water43224
1
A: HLA class I histocompatibility antigen, A-2 alpha chain
B: Beta-2-microglobulin
C: MET-THR-SER-ALA-ILE-GLY-ILE-LEU-PRO-VAL


Theoretical massNumber of molelcules
Total (without water)44,8323
Polymers44,8323
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4350 Å2
ΔGint-24 kcal/mol
Surface area19380 Å2
MethodPISA
2
D: HLA class I histocompatibility antigen, A-2 alpha chain
E: Beta-2-microglobulin
F: MET-THR-SER-ALA-ILE-GLY-ILE-LEU-PRO-VAL


Theoretical massNumber of molelcules
Total (without water)44,8323
Polymers44,8323
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4280 Å2
ΔGint-23 kcal/mol
Surface area19380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)202.940, 50.280, 119.070
Angle α, β, γ (deg.)90.00, 122.86, 90.00
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 HLA class I histocompatibility antigen, A-2 alpha chain / MHC class I antigen A*2


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, HLAA / Production host: Escherichia coli (E. coli) / References: UniProt: P01892, UniProt: P04439*PLUS
#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 MET-THR-SER-ALA-ILE-GLY-ILE-LEU-PRO-VAL


Mass: 1001.241 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.: 24 / 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: 2.85 Å3/Da / Density % sol: 56.77 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96859 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96859 Å / Relative weight: 1
ReflectionResolution: 2.45→41.05 Å / Num. obs: 37034 / % possible obs: 98.7 % / Redundancy: 3.5 % / Biso Wilson estimate: 61.8 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.104 / Rrim(I) all: 0.123 / Net I/σ(I): 9.1
Reflection shellResolution: 2.45→2.51 Å / Redundancy: 3.6 % / Rmerge(I) obs: 1.155 / Mean I/σ(I) obs: 1 / Num. unique obs: 2764 / CC1/2: 0.594 / Rrim(I) all: 1.354 / % possible all: 97.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
xia2data reduction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EU5

5eu5


Resolution: 2.45→41.05 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.931 / SU B: 36.283 / SU ML: 0.331 / Cross valid method: THROUGHOUT / ESU R: 0.451 / ESU R Free: 0.288 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27021 1818 4.9 %RANDOM
Rwork0.22328 ---
obs0.22569 35216 98.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 84.848 Å2
Baniso -1Baniso -2Baniso -3
1-2.26 Å2-0 Å22.04 Å2
2---1 Å2-0 Å2
3----2.12 Å2
Refinement stepCycle: 1 / Resolution: 2.45→41.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6320 0 0 24 6344
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0196516
X-RAY DIFFRACTIONr_bond_other_d0.0020.025690
X-RAY DIFFRACTIONr_angle_refined_deg1.91.9228844
X-RAY DIFFRACTIONr_angle_other_deg1.111313193
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6745768
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.28423.13345
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.454151059
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.4321556
X-RAY DIFFRACTIONr_chiral_restr0.1120.2903
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0217308
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021460
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.1335.3183087
X-RAY DIFFRACTIONr_mcbond_other3.1285.3173086
X-RAY DIFFRACTIONr_mcangle_it4.8267.9733850
X-RAY DIFFRACTIONr_mcangle_other4.8277.9743851
X-RAY DIFFRACTIONr_scbond_it3.5945.6853429
X-RAY DIFFRACTIONr_scbond_other3.5925.6853429
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.5448.3894994
X-RAY DIFFRACTIONr_long_range_B_refined7.72358.2376854
X-RAY DIFFRACTIONr_long_range_B_other7.72358.2446855
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A171840.06
12D171840.06
21B61220.04
22E61220.04
LS refinement shellResolution: 2.45→2.513 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.39 148 -
Rwork0.402 2612 -
obs--99.17 %
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)
16.1409-1.24081.2543.2663-1.28143.5376-0.0303-0.15550.26730.0506-0.14090.2258-0.3291-0.54830.17120.20710.04350.10570.1431-0.08210.1460.082356.137256.0297
22.56130.0018-0.71615.2852.68367.1163-0.0195-0.0225-0.592-0.3285-0.1540.23080.6207-0.46810.17360.2043-0.0533-0.00910.33650.01570.2869-3.720442.607322.8023
32.60770.43890.31763.4302-1.85186.87680.00190.21120.0998-0.3185-0.2017-0.1132-0.10.09040.19970.102-0.00660.08210.0857-0.04540.119611.426257.42831.2112
44.86041.69321.51473.59310.22375.39460.15490.6454-0.4165-0.2811-0.1110.00670.1576-0.1761-0.04390.17980.03910.13460.1605-0.09650.2412-15.870855.029180.8235
55.5021-1.5347-1.48865.64070.3164.0056-0.09540.45730.6789-0.015-0.0350.4794-0.9454-0.3120.13040.31620.0743-0.08880.45890.04520.4862-47.698168.610791.2007
66.47631.4692-2.04573.42-1.58244.08760.161-0.2929-0.26260.108-0.23870.255-0.0059-0.230.07770.0829-0.02390.09590.0718-0.02390.16-33.906253.7638101.396
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 180
2X-RAY DIFFRACTION1C1 - 10
3X-RAY DIFFRACTION2A181 - 276
4X-RAY DIFFRACTION3B0 - 99
5X-RAY DIFFRACTION4D1 - 180
6X-RAY DIFFRACTION4F1 - 10
7X-RAY DIFFRACTION5D181 - 276
8X-RAY DIFFRACTION6E0 - 99

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