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- PDB-6irl: Crystal structure of 8-mer peptide from avian influenza H5N1 viru... -

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Basic information

Entry
Database: PDB / ID: 6irl
TitleCrystal structure of 8-mer peptide from avian influenza H5N1 virus in complex with BF2*1501
Components
  • ARG-ARG-GLU-VAL-HIS-THR-TYR-TYR
  • Beta-2-microglobulin
  • MHC class I molecule
KeywordsIMMUNE SYSTEM / MHC class I / Chicken / Avian influenza virus / H5N1 / epitope / 8-mer
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 / cap snatching / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / antigen processing and presentation of peptide antigen via MHC class I / Neutrophil degranulation / cellular response to iron ion ...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 / cap snatching / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / antigen processing and presentation of peptide antigen via MHC class I / Neutrophil degranulation / cellular response to iron ion / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / negative regulation of forebrain neuron differentiation / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / HFE-transferrin receptor complex / MHC class I peptide loading complex / 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 / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / late endosome membrane / positive regulation of cellular senescence / endonuclease activity / protein homotetramerization / amyloid fibril formation / Hydrolases; Acting on ester bonds / intracellular iron ion homeostasis / host cell cytoplasm / learning or memory / immune response / viral translational frameshifting / lysosomal membrane / viral RNA genome replication / DNA-templated transcription / host cell nucleus / structural molecule activity / Golgi apparatus / protein homodimerization activity / RNA binding / extracellular region / metal ion binding / cytosol
Similarity search - Function
Polymerase acidic protein / Influenza RNA-dependent RNA polymerase subunit PA / Influenza RNA-dependent RNA polymerase subunit PA, endonuclease domain / Influenza RNA-dependent RNA polymerase subunit PA / 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 / : ...Polymerase acidic protein / Influenza RNA-dependent RNA polymerase subunit PA / Influenza RNA-dependent RNA polymerase subunit PA, endonuclease domain / Influenza RNA-dependent RNA polymerase subunit PA / 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
Beta-2-microglobulin / Polymerase acidic protein / MHC class I
Similarity search - Component
Biological speciesGallus gallus (chicken)
Influenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsXiao, L. / Zhang, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31572493 China
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Structures of the MHC-I molecule BF2*1501 disclose the preferred presentation of an H5N1 virus-derived epitope.
Authors: Li, X. / Zhang, L. / Liu, Y. / Ma, L. / Zhang, N. / Xia, C.
History
DepositionNov 13, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 18, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 4, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 22, 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 1.3Oct 16, 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: MHC class I molecule
B: Beta-2-microglobulin
C: ARG-ARG-GLU-VAL-HIS-THR-TYR-TYR


Theoretical massNumber of molelcules
Total (without water)43,6613
Polymers43,6613
Non-polymers00
Water7,134396
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5070 Å2
ΔGint-17 kcal/mol
Surface area18370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.103, 75.009, 101.896
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 MHC class I molecule


Mass: 31065.135 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: BF2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9GIP6
#2: Protein Beta-2-microglobulin


Mass: 11469.888 Da / Num. of mol.: 1
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 ARG-ARG-GLU-VAL-HIS-THR-TYR-TYR / RNA-directed RNA polymerase subunit P2


Mass: 1126.245 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Influenza A virus / References: UniProt: Q809J3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 396 / 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: 2.06 Å3/Da / Density % sol: 40.33 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop
Details: 0.1M BIS-TRIS pH6.5, 0.2M Sodium chloride, 1.5M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1.54178 Å
DetectorType: Nonius Kappa CCD / Detector: CCD / Date: Jan 8, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.6 % / CC1/2: 1 / Rmerge(I) obs: 0.112 / Net I/σ(I): 20.072
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.343 / Mean I/σ(I) obs: 6.477 / Num. unique obs: 165438 / Rsym value: 0.343 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.5_2refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4E0R

4e0r


Resolution: 2.1→25.176 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 0.13 / Phase error: 18.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2171 1079 5.08 %random
Rwork0.1865 ---
obs0.188 21224 97.62 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.281 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.8532 Å2-0 Å2-0 Å2
2---1.9852 Å20 Å2
3----0.868 Å2
Refinement stepCycle: LAST / Resolution: 2.1→25.176 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3053 0 0 396 3449
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0143143
X-RAY DIFFRACTIONf_angle_d1.2344271
X-RAY DIFFRACTIONf_dihedral_angle_d18.291115
X-RAY DIFFRACTIONf_chiral_restr0.109434
X-RAY DIFFRACTIONf_plane_restr0.005565
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1002-2.19570.24051260.19612392X-RAY DIFFRACTION94
2.1957-2.31140.22811360.19882446X-RAY DIFFRACTION97
2.3114-2.45610.2561340.20122468X-RAY DIFFRACTION97
2.4561-2.64550.20071440.2052471X-RAY DIFFRACTION98
2.6455-2.91140.27211130.20622525X-RAY DIFFRACTION98
2.9114-3.33190.2071520.19012534X-RAY DIFFRACTION99
3.3319-4.19460.19021440.15292591X-RAY DIFFRACTION99
4.1946-25.17740.20691300.1822718X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -14.5976 Å / Origin y: 1.8761 Å / Origin z: -3.6307 Å
111213212223313233
T0.0097 Å20.001 Å20.0034 Å2-0.0025 Å20.0021 Å2--0.018 Å2
L0.2189 °2-0.0132 °20.1123 °2-0.1446 °2-0.0138 °2--0.3831 °2
S0.0005 Å °0.0038 Å °-0.0072 Å °0.0061 Å °-0.0141 Å °0.0083 Å °0.008 Å °-0.0075 Å °0.0116 Å °
Refinement TLS groupSelection details: all

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