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- PDB-6lf8: Crystal structure of pSLA-1*0401 complex with dodecapeptide RVEDV... -

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Basic information

Entry
Database: PDB / ID: 6lf8
TitleCrystal structure of pSLA-1*0401 complex with dodecapeptide RVEDVTNTAEYW
Components
  • ARG-VAL-GLU-ASP-VAL-THR-ASN-THR-ALA-GLU-TYR-TRP
  • Beta-2-microglobulin
  • MHC class I antigen
KeywordsSTRUCTURAL PROTEIN / MHC class I structure / A single-amino acid mutation / Peptide motifs / Random peptide library
Function / homology
Function and homology information


ER-Phagosome pathway / Endosomal/Vacuolar pathway / DAP12 interactions / DAP12 signaling / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Neutrophil degranulation / antigen processing and presentation of peptide antigen via MHC class I / lumenal side of endoplasmic reticulum membrane / peptide antigen assembly with MHC class II protein complex ...ER-Phagosome pathway / Endosomal/Vacuolar pathway / DAP12 interactions / DAP12 signaling / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Neutrophil degranulation / antigen processing and presentation of peptide antigen via MHC class I / lumenal side of endoplasmic reticulum membrane / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / 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 / phagocytic vesicle membrane / MHC class II protein complex binding / late endosome membrane / immune response / lysosomal membrane / viral envelope / symbiont entry into host cell / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / extracellular region / membrane
Similarity search - Function
Gp90 envelope polyprotein of equine infectious anemia virus (EIAV) / EIAV coat protein, gp90 / Retroviral envelope protein / Retroviral envelope protein GP41-like / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : ...Gp90 envelope polyprotein of equine infectious anemia virus (EIAV) / EIAV coat protein, gp90 / Retroviral envelope protein / Retroviral envelope protein GP41-like / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / 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
Similarity search - Domain/homology
MHC class I antigen / MHC class I antigen / Envelope glycoprotein / Beta-2-microglobulin
Similarity search - Component
Biological speciesSus scrofa (pig)
unidentified influenza virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsWei, X.H. / Wang, S. / Zhang, N.Z. / Xia, C.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31201887 China
CitationJournal: J Immunol. / Year: 2022
Title: Structure and Peptidomes of Swine MHC Class I with Long Peptides Reveal the Cross-Species Characteristics of the Novel N-Terminal Extension Presentation Mode.
Authors: Wei, X. / Wang, S. / Wang, S. / Xie, X. / Zhang, N.
History
DepositionNov 30, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 3, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2022Group: Database references / Category: citation / citation_author / database_2
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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 22, 2023Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MHC class I antigen
B: Beta-2-microglobulin
C: ARG-VAL-GLU-ASP-VAL-THR-ASN-THR-ALA-GLU-TYR-TRP


Theoretical massNumber of molelcules
Total (without water)44,4983
Polymers44,4983
Non-polymers00
Water3,315184
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4800 Å2
ΔGint-17 kcal/mol
Surface area18850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)217.150, 45.280, 44.900
Angle α, β, γ (deg.)90.00, 90.45, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein MHC class I antigen


Mass: 31681.988 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0F6N4U7, UniProt: O19244*PLUS
#2: Protein Beta-2-microglobulin / Lactollin


Mass: 11332.788 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: B2M / Production host: Escherichia coli (E. coli) / References: UniProt: Q07717
#3: Protein/peptide ARG-VAL-GLU-ASP-VAL-THR-ASN-THR-ALA-GLU-TYR-TRP


Mass: 1483.558 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) unidentified influenza virus / References: UniProt: P16082*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / 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: 2.48 Å3/Da / Density % sol: 50.41 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M Bis-Tris pH 6.5, 25% w/v Polyethylene Glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97931 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2.3→108.57 Å / Num. obs: 19715 / % possible obs: 99.9 % / Redundancy: 7.4 % / Rpim(I) all: 0.0776 / Rsym value: 0.0776 / Net I/σ(I): 12.1
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.1405 / Mean I/σ(I) obs: 6.4 / Num. unique obs: 4296 / Rsym value: 0.1405 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0218refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QQ3

3qq3


Resolution: 2.5→108.57 Å / Cor.coef. Fo:Fc: 0.838 / Cor.coef. Fo:Fc free: 0.795 / SU B: 0.002 / SU ML: 0 / Cross valid method: THROUGHOUT / ESU R: 0.303 / ESU R Free: 0.346 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28513 759 4.9 %RANDOM
Rwork0.24991 ---
obs0.25175 14602 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.533 Å2
Baniso -1Baniso -2Baniso -3
1--0.66 Å2-0 Å2-0.13 Å2
2--0.34 Å2-0 Å2
3---0.32 Å2
Refinement stepCycle: 1 / Resolution: 2.5→108.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3136 0 0 184 3320
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 54 -
Rwork0.257 1040 -
obs--99.82 %

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