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- PDB-6lf9: Crystal structure of pSLA-1*1301 complex with dodecapeptide RVEDV... -

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Basic information

Entry
Database: PDB / ID: 6lf9
TitleCrystal structure of pSLA-1*1301 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 / antigen processing and presentation / MHC class I 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 / antigen processing and presentation / MHC class I protein complex / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / positive regulation of T cell activation / MHC class II protein complex binding / late endosome membrane / membrane => GO:0016020 / immune response / lysosomal membrane / extracellular region
Similarity search - Function
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. ...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 / Beta-2-microglobulin
Similarity search - Component
Biological speciesSus scrofa (pig)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsWei, X.H. / Wang, S. / Zhang, N.Z. / Xia, C.
CitationJournal: Front Immunol / Year: 2022
Title: Peptidomes and Structures Illustrate How SLA-I Micropolymorphism Influences the Preference of Binding Peptide Length.
Authors: Wei, X.H. / Wang, S. / Zhang, N.Z. / Xia, C.
History
DepositionNov 30, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 17, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2022Group: Database references / Category: citation / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
D: MHC class I antigen
E: Beta-2-microglobulin
F: ARG-VAL-GLU-ASP-VAL-THR-ASN-THR-ALA-GLU-TYR-TRP
A: MHC class I antigen
B: Beta-2-microglobulin
C: ARG-VAL-GLU-ASP-VAL-THR-ASN-THR-ALA-GLU-TYR-TRP
G: MHC class I antigen
H: Beta-2-microglobulin
I: ARG-VAL-GLU-ASP-VAL-THR-ASN-THR-ALA-GLU-TYR-TRP
J: MHC class I antigen
K: Beta-2-microglobulin
L: ARG-VAL-GLU-ASP-VAL-THR-ASN-THR-ALA-GLU-TYR-TRP


Theoretical massNumber of molelcules
Total (without water)176,48812
Polymers176,48812
Non-polymers00
Water5,314295
1
D: MHC class I antigen
E: Beta-2-microglobulin
F: ARG-VAL-GLU-ASP-VAL-THR-ASN-THR-ALA-GLU-TYR-TRP


Theoretical massNumber of molelcules
Total (without water)44,1223
Polymers44,1223
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4690 Å2
ΔGint-16 kcal/mol
Surface area18970 Å2
MethodPISA
2
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)44,1223
Polymers44,1223
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4700 Å2
ΔGint-16 kcal/mol
Surface area19020 Å2
MethodPISA
3
G: MHC class I antigen
H: Beta-2-microglobulin
I: ARG-VAL-GLU-ASP-VAL-THR-ASN-THR-ALA-GLU-TYR-TRP


Theoretical massNumber of molelcules
Total (without water)44,1223
Polymers44,1223
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4540 Å2
ΔGint-17 kcal/mol
Surface area19460 Å2
MethodPISA
4
J: MHC class I antigen
K: Beta-2-microglobulin
L: ARG-VAL-GLU-ASP-VAL-THR-ASN-THR-ALA-GLU-TYR-TRP


Theoretical massNumber of molelcules
Total (without water)44,1223
Polymers44,1223
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4670 Å2
ΔGint-18 kcal/mol
Surface area19260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.169, 44.240, 199.631
Angle α, β, γ (deg.)90.00, 90.03, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
MHC class I antigen


Mass: 31305.666 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0F6N4T3
#2: Protein
Beta-2-microglobulin / Lactollin


Mass: 11332.788 Da / Num. of mol.: 4
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.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 295 / 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: 2.38 Å3/Da / Density % sol: 48.35 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.2 M Ammonium fluoride, 20% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.97931 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2.16→199.63 Å / Num. obs: 55584 / % possible obs: 97.1 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.176 / Rsym value: 0.176 / Net I/σ(I): 6
Reflection shellResolution: 2.16→2.28 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.426 / Num. unique obs: 43280 / Rsym value: 0.426 / % possible all: 97.1

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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→199.63 Å / Cor.coef. Fo:Fc: 0.895 / Cor.coef. Fo:Fc free: 0.86 / SU B: 0.003 / SU ML: 0 / Cross valid method: THROUGHOUT / ESU R: 0.306 / ESU R Free: 0.355 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29127 2920 5 %RANDOM
Rwork0.25088 ---
obs0.25291 55584 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.458 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0.05 Å2
2--0.01 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: 1 / Resolution: 2.5→199.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12423 0 0 295 12718
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 217 -
Rwork0.261 4047 -
obs--99.51 %

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