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Basic information

Entry
Database: PDB / ID: 7wbg
TitleBF2*1901/RY8
Components
  • ARG-ARG-ARG-GLU-GLN-THR-ASP-TYR
  • Beta-2-microglobulinBeta-2 microglobulin
  • 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 / 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 ...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 / 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 / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / positive regulation of immune response / 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 / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular region / membrane / cytosol
Similarity search - Function
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 ...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 alpha chain 2 / Beta-2-microglobulin
Similarity search - Component
Biological speciesGallus gallus (chicken)
uncultured virus (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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

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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: ARG-ARG-ARG-GLU-GLN-THR-ASP-TYR
D: MHC class I alpha chain 2
E: Beta-2-microglobulin
F: ARG-ARG-ARG-GLU-GLN-THR-ASP-TYR


Theoretical massNumber of molelcules
Total (without water)85,9816
Polymers85,9816
Non-polymers00
Water10,611589
1
A: MHC class I alpha chain 2
B: Beta-2-microglobulin
C: ARG-ARG-ARG-GLU-GLN-THR-ASP-TYR


Theoretical massNumber of molelcules
Total (without water)42,9913
Polymers42,9913
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4950 Å2
ΔGint-13 kcal/mol
Surface area17620 Å2
MethodPISA
2
D: MHC class I alpha chain 2
E: Beta-2-microglobulin
F: ARG-ARG-ARG-GLU-GLN-THR-ASP-TYR


Theoretical massNumber of molelcules
Total (without water)42,9913
Polymers42,9913
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5060 Å2
ΔGint-9 kcal/mol
Surface area17550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.127, 85.025, 110.838
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.: 2
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 / 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 ARG-ARG-ARG-GLU-GLN-THR-ASP-TYR


Mass: 1126.205 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) uncultured virus (environmental samples)
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 589 / 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: 2.14 Å3/Da / Density % sol: 42.54 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 0.15 M Potassium bromide and 30% 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: SSRF / Beamline: BL17U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 49775 / % possible obs: 98.2 % / Redundancy: 6.3 % / Biso Wilson estimate: 23.42 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 13.1
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.142 / Num. unique obs: 4913

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PHASER1.13_2998phasing
Cootmodel building
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YEZ

2yez


Resolution: 2→33.4 Å / SU ML: 0.202 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 21.7077 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2358 2508 5.04 %
Rwork0.183 47267 -
obs0.1856 49775 98.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.36 Å2
Refinement stepCycle: LAST / Resolution: 2→33.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5994 0 0 589 6583
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00756170
X-RAY DIFFRACTIONf_angle_d0.90658388
X-RAY DIFFRACTIONf_chiral_restr0.0548844
X-RAY DIFFRACTIONf_plane_restr0.00571106
X-RAY DIFFRACTIONf_dihedral_angle_d6.88373596
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.040.26631350.192551X-RAY DIFFRACTION97.57
2.04-2.080.22061500.1822638X-RAY DIFFRACTION100
2.08-2.120.28481600.18282620X-RAY DIFFRACTION100
2.12-2.170.2451350.182660X-RAY DIFFRACTION100
2.17-2.230.26391280.17692653X-RAY DIFFRACTION100
2.23-2.290.26151490.17632641X-RAY DIFFRACTION100
2.29-2.350.24021350.18742656X-RAY DIFFRACTION99.96
2.35-2.430.24461300.19092651X-RAY DIFFRACTION100
2.43-2.520.21241540.18142648X-RAY DIFFRACTION100
2.52-2.620.26271310.18942662X-RAY DIFFRACTION100
2.62-2.740.251440.19642665X-RAY DIFFRACTION99.93
2.74-2.880.25931280.20152678X-RAY DIFFRACTION99.96
2.88-3.060.26151330.19892681X-RAY DIFFRACTION99.79
3.06-3.30.22961420.18782655X-RAY DIFFRACTION98.76
3.3-3.630.23421680.18562560X-RAY DIFFRACTION96.19
3.63-4.150.21611210.1682574X-RAY DIFFRACTION94.2
4.15-5.230.20541320.16312394X-RAY DIFFRACTION87.16
5.23-33.40.21531330.18112680X-RAY DIFFRACTION93.27

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