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- PDB-6v2o: HLA-B*57:01 presenting the peptide ASLNLPAVSW -

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Basic information

Entry
Database: PDB / ID: 6v2o
TitleHLA-B*57:01 presenting the peptide ASLNLPAVSW
Components
  • Beta-2-microglobulin
  • MHC class I antigen
  • Peptide ALA-SER-LEU-ASN-LEU-PRO-ALA-VAL-SER-TRP
KeywordsIMMUNE SYSTEM / Peptide Antigen / HLA / MHC / Immunity
Function / homology
Function and homology information


negative regulation of integrin-mediated signaling pathway / CDH11 homotypic and heterotypic interactions / Regulation of CDH19 Expression and Function / Regulation of CDH11 function / gamma-catenin binding / epithelial cell-cell adhesion / zonula adherens / gap junction assembly / cellular response to indole-3-methanol / flotillin complex ...negative regulation of integrin-mediated signaling pathway / CDH11 homotypic and heterotypic interactions / Regulation of CDH19 Expression and Function / Regulation of CDH11 function / gamma-catenin binding / epithelial cell-cell adhesion / zonula adherens / gap junction assembly / cellular response to indole-3-methanol / flotillin complex / vinculin binding / catenin complex / apical junction assembly / negative regulation of cell motility / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of smoothened signaling pathway / Adherens junctions interactions / negative regulation of protein localization to nucleus / axon regeneration / negative regulation of neuroblast proliferation / smoothened signaling pathway / Myogenesis / establishment or maintenance of cell polarity / odontogenesis of dentin-containing tooth / intercalated disc / neuroblast proliferation / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / RHO GTPases activate IQGAPs / ovarian follicle development / extrinsic apoptotic signaling pathway in absence of ligand / acrosomal vesicle / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / VEGFR2 mediated vascular permeability / cellular response to iron ion / integrin-mediated signaling pathway / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / adherens junction / 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 / cell-cell adhesion / 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 / beta-catenin binding / 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 / response to estrogen / specific granule lumen / male gonad development / 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 / actin filament binding / Modulation by Mtb of host immune system / cell-cell junction / late endosome membrane / cell junction / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / intracellular protein localization / DAP12 signaling / cell migration / T cell differentiation in thymus / lamellipodium / actin cytoskeleton / 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
Similarity search - Function
Alpha-catenin / Vinculin, conserved site / Vinculin family talin-binding region signature. / Vinculin/alpha-catenin / Vinculin family / Alpha-catenin/vinculin-like superfamily / 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 ...Alpha-catenin / Vinculin, conserved site / Vinculin family talin-binding region signature. / Vinculin/alpha-catenin / Vinculin family / Alpha-catenin/vinculin-like superfamily / 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
ACETATE ION / Catenin alpha-1 / Beta-2-microglobulin / MHC class I antigen
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.27 Å
AuthorsMaclachlan, B. / Rossjohn, J. / Vivian, J.P.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: The molecular basis of how buried human leukocyte antigen polymorphism modulates natural killer cell function.
Authors: Saunders, P.M. / MacLachlan, B.J. / Pymm, P. / Illing, P.T. / Deng, Y. / Wong, S.C. / Oates, C.V.L. / Purcell, A.W. / Rossjohn, J. / Vivian, J.P. / Brooks, A.G.
History
DepositionNov 25, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2020Provider: repository / Type: Initial release
Revision 1.1May 27, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jun 10, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Oct 11, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 30, 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: Peptide ALA-SER-LEU-ASN-LEU-PRO-ALA-VAL-SER-TRP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7324
Polymers44,6733
Non-polymers591
Water9,584532
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4440 Å2
ΔGint-21 kcal/mol
Surface area19170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.762, 81.950, 110.487
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein MHC class I antigen / Human Leukocyte Antigen B*57:01


Mass: 31736.172 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B / Plasmid: pET30 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: U6BR87
#2: Protein Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Plasmid: pET30 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P61769
#3: Protein/peptide Peptide ALA-SER-LEU-ASN-LEU-PRO-ALA-VAL-SER-TRP


Mass: 1057.200 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others) / References: UniProt: P35221*PLUS
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 532 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.57 Å3/Da / Density % sol: 52.18 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: 20 % PEG 4000, 0.2 M ammonium acetate, 0.1 M tri-sodium citrate pH 5.4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.954 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 1.268→46 Å / Num. obs: 121661 / % possible obs: 99.3 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 15.1
Reflection shellResolution: 1.27→1.29 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.69 / Num. unique obs: 5564 / % possible all: 93

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Processing

Software
NameVersionClassification
PHENIX(1.16_3549: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2RFX

2rfx


Resolution: 1.27→40.975 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 13.68
RfactorNum. reflection% reflection
Rfree0.1594 6130 5.04 %
Rwork0.1343 --
obs0.1356 121563 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.27→40.975 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3149 0 4 532 3685
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073324
X-RAY DIFFRACTIONf_angle_d0.9434537
X-RAY DIFFRACTIONf_dihedral_angle_d6.7252479
X-RAY DIFFRACTIONf_chiral_restr0.081467
X-RAY DIFFRACTIONf_plane_restr0.006602
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.27-1.28260.21211860.20563438X-RAY DIFFRACTION90
1.2826-1.29770.2112070.1723768X-RAY DIFFRACTION98
1.2977-1.31350.20871980.15793750X-RAY DIFFRACTION99
1.3135-1.33010.18981960.15533816X-RAY DIFFRACTION99
1.3301-1.34760.19831800.14733811X-RAY DIFFRACTION99
1.3476-1.36610.18571920.14123811X-RAY DIFFRACTION99
1.3661-1.38560.16152030.1363805X-RAY DIFFRACTION99
1.3856-1.40630.15742010.12923801X-RAY DIFFRACTION99
1.4063-1.42820.14971960.12523817X-RAY DIFFRACTION99
1.4282-1.45170.17061880.1263834X-RAY DIFFRACTION99
1.4517-1.47670.16581980.12183817X-RAY DIFFRACTION100
1.4767-1.50360.14571980.11943839X-RAY DIFFRACTION99
1.5036-1.53250.15582060.11343864X-RAY DIFFRACTION100
1.5325-1.56380.14342140.10783781X-RAY DIFFRACTION99
1.5638-1.59780.15271940.10663859X-RAY DIFFRACTION99
1.5978-1.63490.1442330.10973830X-RAY DIFFRACTION100
1.6349-1.67580.14121980.11063838X-RAY DIFFRACTION100
1.6758-1.72110.14431880.11753885X-RAY DIFFRACTION100
1.7211-1.77180.14772210.11983825X-RAY DIFFRACTION100
1.7718-1.8290.14592380.12553841X-RAY DIFFRACTION100
1.829-1.89430.1382190.13133849X-RAY DIFFRACTION100
1.8943-1.97020.14992110.12573891X-RAY DIFFRACTION100
1.9702-2.05980.15382140.1243886X-RAY DIFFRACTION100
2.0598-2.16840.15251850.12533905X-RAY DIFFRACTION100
2.1684-2.30430.13832210.12253907X-RAY DIFFRACTION100
2.3043-2.48220.13742060.12793906X-RAY DIFFRACTION100
2.4822-2.73190.15522200.14213906X-RAY DIFFRACTION100
2.7319-3.12710.19512020.1493983X-RAY DIFFRACTION100
3.1271-3.93930.17542030.14094007X-RAY DIFFRACTION100
3.9393-40.9750.16052140.14764163X-RAY DIFFRACTION100

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