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- PDB-5ymv: Crystal structure of 9-mer peptide from influenza virus in comple... -

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Basic information

Entry
Database: PDB / ID: 5ymv
TitleCrystal structure of 9-mer peptide from influenza virus in complex with BF2*1201
Components
  • ALA-VAL-LYS-GLY-VAL-GLY-THR-MET-VAL
  • Beta-2-microglobulinBeta-2 microglobulin
  • Class I histocompatibility antigen, F10 alpha chain
KeywordsIMMUNE SYSTEM / MHC / chicken / influenza virus
Function / homology
Function and homology information


ER-Phagosome pathway / Endosomal/Vacuolar pathway / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / DAP12 signaling / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / antigen processing and presentation of peptide antigen via MHC class I / Neutrophil degranulation / negative regulation of forebrain neuron differentiation / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport ...ER-Phagosome pathway / Endosomal/Vacuolar pathway / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / DAP12 signaling / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / antigen processing and presentation of peptide antigen via MHC class I / Neutrophil degranulation / negative regulation of forebrain neuron differentiation / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / 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 / 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 / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / negative regulation of epithelial cell proliferation / positive regulation of T cell activation / MHC class II protein complex binding / late endosome membrane / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / immune response / lysosomal membrane / external side of plasma membrane / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular region / 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 / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. ...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
Class I histocompatibility antigen, F10 alpha chain / Beta-2-microglobulin
Similarity search - Component
Biological speciesGallus gallus (chicken)
unidentified influenza virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.197 Å
AuthorsXiao, J. / Xiang, W. / Qi, J. / Chai, Y. / Liu, W.J. / Gao, G.F.
CitationJournal: J Immunol. / Year: 2018
Title: An Invariant Arginine in Common with MHC Class II Allows Extension at the C-Terminal End of Peptides Bound to Chicken MHC Class I.
Authors: Xiao, J. / Xiang, W. / Zhang, Y. / Peng, W. / Zhao, M. / Niu, L. / Chai, Y. / Qi, J. / Wang, F. / Qi, P. / Pan, C. / Han, L. / Wang, M. / Kaufman, J. / Gao, G.F. / Liu, W.J.
History
DepositionOct 22, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 24, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2019Group: Data collection / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Class I histocompatibility antigen, F10 alpha chain
B: Beta-2-microglobulin
C: ALA-VAL-LYS-GLY-VAL-GLY-THR-MET-VAL
D: Class I histocompatibility antigen, F10 alpha chain
E: Beta-2-microglobulin
F: ALA-VAL-LYS-GLY-VAL-GLY-THR-MET-VAL


Theoretical massNumber of molelcules
Total (without water)86,0846
Polymers86,0846
Non-polymers00
Water5,441302
1
A: Class I histocompatibility antigen, F10 alpha chain
B: Beta-2-microglobulin
C: ALA-VAL-LYS-GLY-VAL-GLY-THR-MET-VAL


Theoretical massNumber of molelcules
Total (without water)43,0423
Polymers43,0423
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4860 Å2
ΔGint-20 kcal/mol
Surface area17650 Å2
MethodPISA
2
D: Class I histocompatibility antigen, F10 alpha chain
E: Beta-2-microglobulin
F: ALA-VAL-LYS-GLY-VAL-GLY-THR-MET-VAL


Theoretical massNumber of molelcules
Total (without water)43,0423
Polymers43,0423
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4790 Å2
ΔGint-18 kcal/mol
Surface area17690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.270, 101.531, 74.205
Angle α, β, γ (deg.)90.00, 106.25, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Class I histocompatibility antigen, F10 alpha chain / B-F histocompatibility F10 antigen / B-F-beta-IV / B12


Mass: 31117.568 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Production host: Escherichia coli (E. coli) / References: UniProt: P15979
#2: Protein Beta-2-microglobulin / Beta-2 microglobulin


Mass: 11062.404 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: B2M / Production host: Escherichia coli (E. coli) / References: UniProt: P21611
#3: Protein/peptide ALA-VAL-LYS-GLY-VAL-GLY-THR-MET-VAL


Mass: 862.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) unidentified influenza virus
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 302 / 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: 2.74 Å3/Da / Density % sol: 55.14 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 10%v/v polyethylene glycol 200, 0.1M BIS-Tris propane pH 9.0, 18% w/V polyethylene glycol 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.975 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975 Å / Relative weight: 1
ReflectionResolution: 2.197→50 Å / Num. obs: 47077 / % possible obs: 99.4 % / Redundancy: 5.7 % / Net I/σ(I): 10.4

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
SCALEPACKdata scaling
SHELXDphasing
RefinementResolution: 2.197→41.626 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.23
RfactorNum. reflection% reflection
Rfree0.2241 2379 5.06 %
Rwork0.1907 --
obs0.1924 47052 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.197→41.626 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6064 0 0 302 6366
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046250
X-RAY DIFFRACTIONf_angle_d0.8388486
X-RAY DIFFRACTIONf_dihedral_angle_d15.2722264
X-RAY DIFFRACTIONf_chiral_restr0.033854
X-RAY DIFFRACTIONf_plane_restr0.0051114
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1974-2.24220.28251250.22812376X-RAY DIFFRACTION90
2.2422-2.2910.28911410.23292612X-RAY DIFFRACTION100
2.291-2.34430.27151520.23972610X-RAY DIFFRACTION100
2.3443-2.40290.2931140.2282686X-RAY DIFFRACTION100
2.4029-2.46790.261430.22452645X-RAY DIFFRACTION100
2.4679-2.54050.24691440.22292611X-RAY DIFFRACTION100
2.5405-2.62250.24211570.22522638X-RAY DIFFRACTION100
2.6225-2.71620.28211350.22762638X-RAY DIFFRACTION100
2.7162-2.82490.28431630.23042586X-RAY DIFFRACTION100
2.8249-2.95340.23771040.2242686X-RAY DIFFRACTION100
2.9534-3.10910.26161390.2152652X-RAY DIFFRACTION100
3.1091-3.30380.22621330.20192627X-RAY DIFFRACTION100
3.3038-3.55880.25821360.19812668X-RAY DIFFRACTION100
3.5588-3.91670.19451470.17592628X-RAY DIFFRACTION100
3.9167-4.48280.18741400.15782664X-RAY DIFFRACTION100
4.4828-5.64570.19221500.14812651X-RAY DIFFRACTION100
5.6457-41.63320.1771560.16372695X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 56.0043 Å / Origin y: -28.858 Å / Origin z: 89.7567 Å
111213212223313233
T0.2319 Å20.0089 Å20.0006 Å2-0.2374 Å2-0.0227 Å2--0.1996 Å2
L0.4296 °20.0553 °20.1086 °2-0.6877 °2-0.2841 °2--0.2577 °2
S0.05 Å °0.0144 Å °-0.0037 Å °-0.0725 Å °-0.0312 Å °0.0958 Å °0.0298 Å °-0.0156 Å °0 Å °
Refinement TLS groupSelection details: all

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