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- PDB-7wbi: BF2*1901-FLU -

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Basic information

Entry
Database: PDB / ID: 7wbi
TitleBF2*1901-FLU
Components
  • Beta-2-microglobulin
  • ILE-ARG-HIS-GLU-ASN-ARG-MET-VAL-LEU
  • MHC class I alpha chain 2
KeywordsIMMUNE SYSTEM / MHC I
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 / cellular response to iron ion / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex ...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 / 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 / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / immune response / lysosomal membrane / structural molecule activity / Golgi apparatus / protein homodimerization activity / 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 / : ...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
MHC class I alpha chain 2 / Beta-2-microglobulin
Similarity search - Component
Biological speciesGallus gallus (chicken)
uncultured virus (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLiu, W.J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: J Immunol. / Year: 2023
Title: A Wider and Deeper Peptide-Binding Groove for the Class I Molecules from B15 Compared with B19 Chickens Correlates with Relative Resistance to Marek's Disease.
Authors: Han, L. / Wu, S. / Zhang, T. / Peng, W. / Zhao, M. / Yue, C. / Wen, W. / Cai, W. / Li, M. / Wallny, H.J. / Avila, D.W. / Mwangi, W. / Nair, V. / Ternette, N. / Guo, Y. / Zhao, Y. / Chai, Y. ...Authors: Han, L. / Wu, S. / Zhang, T. / Peng, W. / Zhao, M. / Yue, C. / Wen, W. / Cai, W. / Li, M. / Wallny, H.J. / Avila, D.W. / Mwangi, W. / Nair, V. / Ternette, N. / Guo, Y. / Zhao, Y. / Chai, Y. / Qi, J. / Liang, H. / Gao, G.F. / Kaufman, J. / Liu, W.J.
History
DepositionDec 16, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 21, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 5, 2023Group: 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
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 13, 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 alpha chain 2
B: Beta-2-microglobulin
C: ILE-ARG-HIS-GLU-ASN-ARG-MET-VAL-LEU


Theoretical massNumber of molelcules
Total (without water)43,0353
Polymers43,0353
Non-polymers00
Water8,305461
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5050 Å2
ΔGint-17 kcal/mol
Surface area17930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.955, 76.148, 102.911
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein MHC class I alpha chain 2 / MHC class I molecule


Mass: 30801.967 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: A0ZXM5
#2: Protein Beta-2-microglobulin


Mass: 11062.404 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 ILE-ARG-HIS-GLU-ASN-ARG-MET-VAL-LEU


Mass: 1170.408 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) uncultured virus (environmental samples)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 461 / 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: 2.18 Å3/Da / Density % sol: 43.66 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M BIS-TRIS pH 6.5 and 28% w/v Polyethylene glycol monomethyl ether 2,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 1.54178 Å
DetectorType: RIGAKU / Detector: PIXEL / Date: Jun 14, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 35678 / % possible obs: 99.9 % / Redundancy: 10.7 % / Biso Wilson estimate: 16.36 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 11.7
Reflection shellResolution: 1.8→1.86 Å / Rmerge(I) obs: 0.207 / Num. unique obs: 35671

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PHASERphasing
HKL-2000data scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YEZ

2yez


Resolution: 1.8→35.71 Å / SU ML: 0.1604 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 18.7213 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.1997 1788 5.01 %
Rwork0.1666 33890 -
obs0.1683 35678 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.38 Å2
Refinement stepCycle: LAST / Resolution: 1.8→35.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3026 0 0 461 3487
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00643115
X-RAY DIFFRACTIONf_angle_d0.87834236
X-RAY DIFFRACTIONf_chiral_restr0.0586429
X-RAY DIFFRACTIONf_plane_restr0.0064558
X-RAY DIFFRACTIONf_dihedral_angle_d9.81361816
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.850.21631360.16872552X-RAY DIFFRACTION99.85
1.85-1.90.22371510.1722561X-RAY DIFFRACTION100
1.9-1.960.20491210.17122554X-RAY DIFFRACTION100
1.96-2.030.21971350.16512589X-RAY DIFFRACTION100
2.03-2.120.19491270.16932590X-RAY DIFFRACTION100
2.12-2.210.20871350.16782562X-RAY DIFFRACTION100
2.21-2.330.23011380.16192588X-RAY DIFFRACTION100
2.33-2.470.19621310.1712602X-RAY DIFFRACTION100
2.47-2.670.22221490.17882619X-RAY DIFFRACTION100
2.67-2.930.19561370.17752587X-RAY DIFFRACTION100
2.93-3.360.17931450.16842628X-RAY DIFFRACTION100
3.36-4.230.1791310.15062682X-RAY DIFFRACTION100
4.23-35.710.19691520.16582776X-RAY DIFFRACTION99.59

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