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- PDB-6p2f: Structure of a nested set of N-terminally extended MHC I-peptides... -

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Basic information

Entry
Database: PDB / ID: 6p2f
TitleStructure of a nested set of N-terminally extended MHC I-peptides provides novel insights into antigen processing and presentation
Components
  • Beta-2-microglobulinBeta-2 microglobulin
  • HLA class I histocompatibility antigen, B-8 alpha chain
  • MHC I-peptide
KeywordsIMMUNE SYSTEM / MHC I antigen processing / MHC I antigen presentation / MHC I structure / MHC I immunopeptide
Function / homology
Function and homology information


regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / TAP binding / 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 / secretory granule membrane ...regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / TAP binding / 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 / secretory granule membrane / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / early endosome lumen / positive regulation of receptor binding / 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 / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / defense response / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / response to molecule of bacterial origin / regulation of erythrocyte differentiation / 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 / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / recycling endosome membrane / phagocytic vesicle membrane / specific granule lumen / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / negative regulation of epithelial cell proliferation / Modulation by Mtb of host immune system / positive regulation of T cell activation / Interferon alpha/beta signaling / sensory perception of smell / negative regulation of neuron projection development / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / positive regulation of protein binding / ER-Phagosome pathway / iron ion transport / protein-folding chaperone binding / protein refolding / early endosome membrane / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / adaptive immune response / learning or memory / immune response / Amyloid fiber formation / lysosomal membrane / endoplasmic reticulum lumen / external side of plasma membrane / Golgi membrane / signaling receptor binding / focal adhesion / innate immune response / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / 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
HLA class I histocompatibility antigen, B alpha chain / HLA class I histocompatibility antigen, B alpha chain / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.482 Å
AuthorsLi, L. / Batliwala, M. / Bouvier, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)AI114467 United States
CitationJournal: J.Biol.Chem. / Year: 2019
Title: ERAP1 enzyme-mediated trimming and structural analyses of MHC I-bound precursor peptides yield novel insights into antigen processing and presentation.
Authors: Li, L. / Batliwala, M. / Bouvier, M.
History
DepositionMay 21, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Database references / Category: citation / pdbx_audit_support
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _pdbx_audit_support.funding_organization
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 class I histocompatibility antigen, B-8 alpha chain
B: Beta-2-microglobulin
C: MHC I-peptide


Theoretical massNumber of molelcules
Total (without water)45,3353
Polymers45,3353
Non-polymers00
Water4,936274
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4310 Å2
ΔGint-24 kcal/mol
Surface area18940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.845, 81.919, 111.060
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 class I histocompatibility antigen, B-8 alpha chain / MHC class I antigen B*8


Mass: 31902.004 Da / Num. of mol.: 1 / Fragment: UNP residues 25-300 / Mutation: E76C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B, HLAB / Plasmid: pLM1 / Details (production host): PLM1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P30460, UniProt: P01889*PLUS
#2: Protein Beta-2-microglobulin / Beta-2 microglobulin


Mass: 11879.356 Da / Num. of mol.: 1 / Fragment: UNP residues 21-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Plasmid: pHN1 / Production host: Escherichia coli (E. coli) / Strain (production host): XA90 / References: UniProt: P61769
#3: Protein/peptide MHC I-peptide


Mass: 1553.898 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 274 / Source method: isolated from a natural source / Formula: H2O

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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: 2.59 Å3/Da / Density % sol: 52.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.2 M ammonium sulfate, 18% PEG4000, 0.1 M sodium cacodylate, pH 5.7

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 4, 2018
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.48→19.215 Å / Num. obs: 76357 / % possible obs: 98.8 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 11.67
Reflection shellResolution: 1.48→1.53 Å / Rmerge(I) obs: 0.58 / Num. unique obs: 7231 / CC1/2: 0.795

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Processing

Software
NameVersionClassification
PHENIX1.8.1_1168refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1AGB

1agb


Resolution: 1.482→19.215 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.77
RfactorNum. reflection% reflection
Rfree0.2452 3815 5 %
Rwork0.2145 --
obs0.216 76357 98.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.482→19.215 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3142 0 0 274 3416
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113230
X-RAY DIFFRACTIONf_angle_d1.3534378
X-RAY DIFFRACTIONf_dihedral_angle_d14.1421196
X-RAY DIFFRACTIONf_chiral_restr0.093446
X-RAY DIFFRACTIONf_plane_restr0.007580
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4817-1.50040.36841200.36082269X-RAY DIFFRACTION84
1.5004-1.52010.30171410.28122681X-RAY DIFFRACTION100
1.5201-1.5410.29211420.25242697X-RAY DIFFRACTION100
1.541-1.5630.24371410.22942684X-RAY DIFFRACTION100
1.563-1.58630.25521450.22192756X-RAY DIFFRACTION100
1.5863-1.61110.291410.20832676X-RAY DIFFRACTION100
1.6111-1.63750.25621430.20382718X-RAY DIFFRACTION100
1.6375-1.66570.26261420.20192688X-RAY DIFFRACTION100
1.6657-1.69590.24051440.20532736X-RAY DIFFRACTION100
1.6959-1.72850.23121410.19792679X-RAY DIFFRACTION100
1.7285-1.76380.24631420.20592709X-RAY DIFFRACTION100
1.7638-1.80210.27111420.23182700X-RAY DIFFRACTION100
1.8021-1.8440.25971440.23532720X-RAY DIFFRACTION100
1.844-1.89010.3131430.25872735X-RAY DIFFRACTION100
1.8901-1.94110.4371130.40682196X-RAY DIFFRACTION81
1.9411-1.99820.27711410.25772684X-RAY DIFFRACTION98
1.9982-2.06260.25351430.22372712X-RAY DIFFRACTION100
2.0626-2.13630.22761430.21792732X-RAY DIFFRACTION100
2.1363-2.22170.26621450.23442739X-RAY DIFFRACTION100
2.2217-2.32260.39311380.35432632X-RAY DIFFRACTION97
2.3226-2.44490.25121430.222729X-RAY DIFFRACTION100
2.4449-2.59770.23381450.2092752X-RAY DIFFRACTION100
2.5977-2.79770.28161440.20682741X-RAY DIFFRACTION100
2.7977-3.07820.19441460.21092764X-RAY DIFFRACTION100
3.0782-3.52130.23871460.1842772X-RAY DIFFRACTION99
3.5213-4.42740.19491460.17272788X-RAY DIFFRACTION99
4.4274-19.21620.17981510.14872853X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: -12.258 Å / Origin y: -9.6338 Å / Origin z: 18.695 Å
111213212223313233
T0.1318 Å20.0051 Å20.0125 Å2-0.1062 Å2-0.005 Å2--0.1249 Å2
L1.0662 °20.1209 °20.4594 °2-0.4575 °20.0098 °2--0.7479 °2
S-0.0322 Å °-0.0161 Å °0.0908 Å °-0.0528 Å °-0.0092 Å °0.0282 Å °-0.032 Å °-0.0541 Å °0.0354 Å °
Refinement TLS groupSelection details: all

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