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- PDB-6v2q: HLA-B*57:03 presenting the peptide LSSPVTKSF -

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Basic information

Entry
Database: PDB / ID: 6v2q
TitleHLA-B*57:03 presenting the peptide LSSPVTKSF
Components
  • Beta-2-microglobulinBeta-2 microglobulin
  • HLA-B alpha chain (B*5703GB)
  • Peptide LEU-SER-SER-PRO-VAL-THR-LYS-SER-PHE
KeywordsIMMUNE SYSTEM / Peptide Antigen / HLA / MHC / Immunity
Function / homology
Function and homology information


antigen processing and presentation of peptide antigen via MHC class I / 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 / DAP12 interactions / negative regulation of receptor binding / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway ...antigen processing and presentation of peptide antigen via MHC class I / 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 / DAP12 interactions / negative regulation of receptor binding / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / 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 / response to molecule of bacterial origin / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / recycling endosome membrane / specific granule lumen / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / Modulation by Mtb of host immune system / sensory perception of smell / positive regulation of T cell activation / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / ER-Phagosome pathway / iron ion transport / early endosome membrane / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / immune response / Amyloid fiber formation / lysosomal membrane / external side of plasma membrane / endoplasmic reticulum lumen / Golgi membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / cell surface / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / membrane / identical protein binding / plasma membrane / cytosol
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 classes I/II-like antigen recognition protein ...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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / HLA-B alpha chain (B*5703GB) / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HLA-B alpha chain (B*5703GB)
B: Beta-2-microglobulin
C: Peptide LEU-SER-SER-PRO-VAL-THR-LYS-SER-PHE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7164
Polymers44,6573
Non-polymers591
Water11,187621
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4610 Å2
ΔGint-24 kcal/mol
Surface area18770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.922, 82.158, 110.821
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 HLA-B alpha chain (B*5703GB) / MHC class I antigen / Human Leukocyte Antigen B*57:03


Mass: 31811.285 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: I3ZN84
#2: Protein Beta-2-microglobulin / 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 LEU-SER-SER-PRO-VAL-THR-LYS-SER-PHE


Mass: 966.109 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


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


Mass: 18.015 Da / Num. of mol.: 621 / 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: 2.6 Å3/Da / Density % sol: 52.61 %
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 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 1.6→46.27 Å / Num. obs: 62191 / % possible obs: 100 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.127 / Net I/σ(I): 11.5
Reflection shellResolution: 1.6→1.63 Å / Rmerge(I) obs: 1.04 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 3036 / % possible all: 100

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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: 1.6→41.079 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.22
RfactorNum. reflection% reflection
Rfree0.1943 3099 4.99 %
Rwork0.1588 --
obs0.1605 62108 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.6→41.079 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3147 0 4 621 3772
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093412
X-RAY DIFFRACTIONf_angle_d1.1024658
X-RAY DIFFRACTIONf_dihedral_angle_d8.7512788
X-RAY DIFFRACTIONf_chiral_restr0.059484
X-RAY DIFFRACTIONf_plane_restr0.007614
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.6250.25831420.2132638X-RAY DIFFRACTION100
1.625-1.65170.25571400.21412668X-RAY DIFFRACTION100
1.6517-1.68020.2611410.20672627X-RAY DIFFRACTION100
1.6802-1.71070.24141570.19912614X-RAY DIFFRACTION100
1.7107-1.74360.24271560.19032636X-RAY DIFFRACTION100
1.7436-1.77920.25221290.18892647X-RAY DIFFRACTION100
1.7792-1.81790.23961460.18982688X-RAY DIFFRACTION100
1.8179-1.86020.20271250.18862640X-RAY DIFFRACTION100
1.8602-1.90670.21071450.18392669X-RAY DIFFRACTION100
1.9067-1.95820.22611310.16752661X-RAY DIFFRACTION100
1.9582-2.01590.19671560.16182656X-RAY DIFFRACTION100
2.0159-2.08090.1781210.1582647X-RAY DIFFRACTION100
2.0809-2.15530.17771360.1592684X-RAY DIFFRACTION100
2.1553-2.24160.16011300.15352669X-RAY DIFFRACTION100
2.2416-2.34360.16991530.14732699X-RAY DIFFRACTION100
2.3436-2.46710.17131370.14972675X-RAY DIFFRACTION100
2.4671-2.62170.1951470.15272685X-RAY DIFFRACTION100
2.6217-2.82410.17521410.16042703X-RAY DIFFRACTION100
2.8241-3.10820.19121370.15352708X-RAY DIFFRACTION100
3.1082-3.55770.18471470.14682729X-RAY DIFFRACTION100
3.5577-4.48150.15961490.13022750X-RAY DIFFRACTION100
4.4815-41.0790.22951330.15552916X-RAY DIFFRACTION100

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