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- PDB-6p2c: Structure of a nested set of N-terminally extended MHC I-peptides... -

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Basic information

Entry
Database: PDB / ID: 6p2c
TitleStructure of a nested set of N-terminally extended MHC I-peptides provides novel insights into antigen processing and presentation
Components
  • Beta-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 / 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 / defense response / 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 / Interferon alpha/beta signaling / 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 / protein-folding chaperone binding / negative regulation of neuron projection development / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / adaptive immune response / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / Golgi membrane / signaling receptor binding / lysosomal membrane / innate immune response / external side of plasma membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / cell surface / 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, 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, 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: 1.396 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
Revision 1.4Oct 23, 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, B-8 alpha chain
B: Beta-2-microglobulin
C: MHC I-peptide


Theoretical massNumber of molelcules
Total (without water)45,9613
Polymers45,9613
Non-polymers00
Water5,603311
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4280 Å2
ΔGint-22 kcal/mol
Surface area18930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.790, 81.767, 111.871
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 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P30460, UniProt: P01889*PLUS
#2: Protein Beta-2-microglobulin


Mass: 11748.160 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 / Details (production host): PHN1 / Production host: Escherichia coli (E. coli) / Strain (production host): XA90 / References: UniProt: P61769
#3: Protein/peptide MHC I-peptide


Mass: 2310.841 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 311 / 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: 2.6 Å3/Da / Density % sol: 52.72 %
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-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 8, 2019
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.39→37.61 Å / Num. obs: 93207 / % possible obs: 99.9 % / Redundancy: 9.2 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 19.1
Reflection shellResolution: 1.4→1.45 Å / Rmerge(I) obs: 0.39 / Num. unique obs: 9169 / CC1/2: 0.965

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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: 1.396→37.602 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.71
RfactorNum. reflection% reflection
Rfree0.2098 9325 10 %
Rwork0.1961 --
obs0.1975 93207 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.396→37.602 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3139 0 0 311 3450
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053227
X-RAY DIFFRACTIONf_angle_d1.0214374
X-RAY DIFFRACTIONf_dihedral_angle_d14.3311196
X-RAY DIFFRACTIONf_chiral_restr0.083446
X-RAY DIFFRACTIONf_plane_restr0.004579
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3956-1.41150.2693090.24952775X-RAY DIFFRACTION99
1.4115-1.42810.25183010.23942694X-RAY DIFFRACTION100
1.4281-1.44550.25153090.22992780X-RAY DIFFRACTION100
1.4455-1.46380.23553090.21762781X-RAY DIFFRACTION100
1.4638-1.4830.23393080.22292766X-RAY DIFFRACTION100
1.483-1.50340.20963060.2012760X-RAY DIFFRACTION100
1.5034-1.52480.21793070.20072765X-RAY DIFFRACTION100
1.5248-1.54760.23273090.19552777X-RAY DIFFRACTION100
1.5476-1.57180.20733090.19372778X-RAY DIFFRACTION100
1.5718-1.59760.20443050.18582755X-RAY DIFFRACTION100
1.5976-1.62510.20233070.18342758X-RAY DIFFRACTION100
1.6251-1.65470.19433070.18382767X-RAY DIFFRACTION100
1.6547-1.68650.20363090.18372780X-RAY DIFFRACTION100
1.6865-1.72090.19493090.18632779X-RAY DIFFRACTION100
1.7209-1.75830.19043100.18432794X-RAY DIFFRACTION100
1.7583-1.79920.20993100.20032780X-RAY DIFFRACTION100
1.7992-1.84420.20753080.19942772X-RAY DIFFRACTION100
1.8442-1.89410.22223110.19782800X-RAY DIFFRACTION100
1.8941-1.94980.27513110.24482794X-RAY DIFFRACTION100
1.9498-2.01270.22533090.19252783X-RAY DIFFRACTION100
2.0127-2.08470.18143100.19072797X-RAY DIFFRACTION100
2.0847-2.16810.20253120.19332797X-RAY DIFFRACTION100
2.1681-2.26680.24423090.22772781X-RAY DIFFRACTION100
2.2668-2.38630.21533140.1922831X-RAY DIFFRACTION100
2.3863-2.53580.22473140.20622818X-RAY DIFFRACTION100
2.5358-2.73150.23533140.20452828X-RAY DIFFRACTION100
2.7315-3.00630.2123170.21182855X-RAY DIFFRACTION100
3.0063-3.4410.20633160.20372838X-RAY DIFFRACTION100
3.441-4.33430.1963210.17552893X-RAY DIFFRACTION100
4.3343-37.61540.17543350.16933006X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -12.2357 Å / Origin y: -9.5869 Å / Origin z: 18.8016 Å
111213212223313233
T0.0884 Å20.0012 Å20.0061 Å2-0.0744 Å2-0.0045 Å2--0.0797 Å2
L0.5721 °20.0464 °20.2837 °2-0.1629 °2-0.0201 °2--0.3239 °2
S-0.0179 Å °-0.029 Å °0.0498 Å °-0.03 Å °-0.0086 Å °-0.0067 Å °0.0017 Å °-0.0335 Å °-0.0014 Å °
Refinement TLS groupSelection details: all

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