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- PDB-7cir: Peptide phosphorylation modification of MHC class I molecules -

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Basic information

Entry
Database: PDB / ID: 7cir
TitlePeptide phosphorylation modification of MHC class I molecules
Components
  • ARG-ARG-PHE-SEP-ARG-SER-PRO-ILE-ARG-ARG
  • Beta-2-microglobulin
  • MHC class I antigen
KeywordsIMMUNE SYSTEM / MHC I complex / P4-Son3
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 / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex ...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 / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / lumenal side of endoplasmic reticulum membrane / 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 / Resolution: 1.81 Å
AuthorsSun, M.W. / Feng, L. / Qi, J.X. / Liu, W.J. / Gao, G.F.
CitationJournal: Iscience / Year: 2022
Title: Phosphosite-dependent presentation of dual phosphorylated peptides by MHC class I molecules.
Authors: Zhao, Y. / Sun, M. / Zhang, N. / Liu, X. / Yue, C. / Feng, L. / Ji, S. / Liu, X. / Qi, J. / Wong, C.C.L. / Gao, G.F. / Liu, W.J.
History
DepositionJul 8, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 9, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _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
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 23, 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: ARG-ARG-PHE-SEP-ARG-SER-PRO-ILE-ARG-ARG


Theoretical massNumber of molelcules
Total (without water)45,2233
Polymers45,2233
Non-polymers00
Water6,882382
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4790 Å2
ΔGint-12 kcal/mol
Surface area18940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.725, 82.238, 108.441
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein MHC class I antigen


Mass: 31928.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B / Production host: Escherichia coli (E. coli) / References: UniProt: A3F718
#2: Protein Beta-2-microglobulin / Beta2m


Mass: 11879.356 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M / Production host: Escherichia coli (E. coli) / References: UniProt: P61769
#3: Protein/peptide ARG-ARG-PHE-SEP-ARG-SER-PRO-ILE-ARG-ARG


Mass: 1415.565 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 382 / 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: 50.81 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: 0.1M TRIS-HCl (PH7.9) 17.5%(w/v)PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 18, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 303959 / % possible obs: 98.5 % / Redundancy: 7.3 % / Biso Wilson estimate: 19.69 Å2 / Rmerge(I) obs: 0.111 / Net I/σ(I): 3.8
Reflection shellResolution: 1.8→1.86 Å / Rmerge(I) obs: 0.517 / Num. unique obs: 303959

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Processing

Software
NameVersionClassification
REFMAC1.13_2998refinement
Cootmodel building
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BST

2bst


Resolution: 1.81→31.94 Å / SU ML: 0.1844 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.7593 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2077 2098 5.05 %
Rwork0.1765 39462 -
obs0.1781 41560 97.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.75 Å2
Refinement stepCycle: LAST / Resolution: 1.81→31.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3187 0 0 382 3569
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00633276
X-RAY DIFFRACTIONf_angle_d0.84394450
X-RAY DIFFRACTIONf_chiral_restr0.0536453
X-RAY DIFFRACTIONf_plane_restr0.0052588
X-RAY DIFFRACTIONf_dihedral_angle_d8.6541956
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.81-1.850.2931130.22732316X-RAY DIFFRACTION87.91
1.85-1.890.23661300.2082622X-RAY DIFFRACTION97.76
1.89-1.940.2411410.1872566X-RAY DIFFRACTION97.03
1.94-20.21411450.19412555X-RAY DIFFRACTION97.19
2-2.070.26731340.19022589X-RAY DIFFRACTION98.06
2.07-2.140.22291320.18922623X-RAY DIFFRACTION97.76
2.14-2.230.24371280.17812603X-RAY DIFFRACTION97.89
2.23-2.330.23061490.18472628X-RAY DIFFRACTION98.76
2.33-2.450.20281680.18872603X-RAY DIFFRACTION98.61
2.45-2.60.23191330.19552675X-RAY DIFFRACTION98.91
2.6-2.80.25161580.18732642X-RAY DIFFRACTION99.4
2.8-3.090.20491360.19082707X-RAY DIFFRACTION99.75
3.09-3.530.18611500.1682700X-RAY DIFFRACTION99.75
3.53-4.450.17141470.14992733X-RAY DIFFRACTION99.83
4.45-31.940.17261340.15922900X-RAY DIFFRACTION99.8

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