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- PDB-4zus: Crystal structure of Equine MHC I(Eqca-N*00602) in complexed with... -

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Basic information

Entry
Database: PDB / ID: 4zus
TitleCrystal structure of Equine MHC I(Eqca-N*00602) in complexed with equine infectious anaemia virus (EIAV) derived peptide REV-QW11
Components
  • Beta-2-microglobulinBeta-2 microglobulin
  • Classical MHC class I antigen
  • GLN-ALA-GLU-VAL-LEU-GLN-GLU-ARG-LEU-GLU-TRP
KeywordsIMMUNE SYSTEM / lentivirus vaccine
Function / homology
Function and homology information


host cell nucleolus / antigen processing and presentation of peptide antigen via MHC class I / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / regulation of membrane depolarization / mRNA transport ...host cell nucleolus / antigen processing and presentation of peptide antigen via MHC class I / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / regulation of membrane depolarization / mRNA transport / cellular defense response / Neutrophil degranulation / lumenal side of endoplasmic reticulum membrane / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / 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 / multicellular organismal-level iron ion homeostasis / positive regulation of T cell mediated cytotoxicity / 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 / phagocytic vesicle membrane / 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 / antimicrobial humoral immune response mediated by antimicrobial peptide / sensory perception of smell / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / antibacterial humoral response / iron ion transport / protein refolding / protein homotetramerization / cellular response to lipopolysaccharide / intracellular iron ion homeostasis / defense response to Gram-negative bacterium / host cell cytoplasm / amyloid fibril formation / learning or memory / defense response to Gram-positive bacterium / immune response / lysosomal membrane / external side of plasma membrane / innate immune response / viral envelope / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / RNA binding / extracellular region / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Rev protein of equine infectious anaemia virus / Rev protein of equine infectious anaemia virus / Gp90 envelope polyprotein of equine infectious anemia virus (EIAV) / EIAV coat protein, gp90 / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / 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 ...Rev protein of equine infectious anaemia virus / Rev protein of equine infectious anaemia virus / Gp90 envelope polyprotein of equine infectious anemia virus (EIAV) / EIAV coat protein, gp90 / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / 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
Beta-2-microglobulin / Protein Rev / Classical MHC class I antigen
Similarity search - Component
Biological speciesEquus caballus (horse)
Mus musculus (house mouse)
Equine infectious anemia virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsYao, S. / Liu, J. / Qi, J. / Chen, R. / Zhang, N. / Liu, Y. / Xia, C.
CitationJournal: J Immunol. / Year: 2016
Title: Structural Illumination of Equine MHC Class I Molecules Highlights Unconventional Epitope Presentation Manner That Is Evolved in Equine Leukocyte Antigen Alleles
Authors: Yao, S. / Liu, J. / Qi, J. / Chen, R. / Zhang, N. / Liu, Y. / Wang, J. / Wu, Y. / Gao, G.F. / Xia, C.
History
DepositionMay 17, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 6, 2016Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Classical MHC class I antigen
B: Beta-2-microglobulin
C: GLN-ALA-GLU-VAL-LEU-GLN-GLU-ARG-LEU-GLU-TRP


Theoretical massNumber of molelcules
Total (without water)44,7063
Polymers44,7063
Non-polymers00
Water52229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4400 Å2
ΔGint-11 kcal/mol
Surface area18750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.970, 68.970, 205.460
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-301-

HOH

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Components

#1: Protein Classical MHC class I antigen


Mass: 31599.658 Da / Num. of mol.: 1 / Fragment: UNP residues 22-295
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Equus caballus (horse) / Production host: Escherichia coli (E. coli) / References: UniProt: Q860N6
#2: Protein Beta-2-microglobulin / Beta-2 microglobulin


Mass: 11704.359 Da / Num. of mol.: 1 / Fragment: UNP residues 21-119 / Mutation: A85D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2m / Production host: Escherichia coli (E. coli) / References: UniProt: P01887
#3: Protein/peptide GLN-ALA-GLU-VAL-LEU-GLN-GLU-ARG-LEU-GLU-TRP


Mass: 1401.542 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Equine infectious anemia virus / References: UniProt: P11305*PLUS
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 29 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.73 Å3/Da / Density % sol: 54.99 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.02 M magnesium chloride hexahydrare, 0.1 M HEPES, 22% w/v polyacrylic acid sodium salt 5,100

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 21, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 15689 / % possible obs: 94.9 % / Redundancy: 5 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 34.186
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 5.104 / % possible all: 98.6

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Processing

Software
NameVersionClassification
PHENIX1.5_2refinement
HKL-2000data reduction
HKL-2000data scaling
HKL-2000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→35.301 Å / SU ML: 0.34 / Cross valid method: NONE / σ(F): 0.14 / Phase error: 26.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2679 695 4.94 %
Rwork0.2117 --
obs0.2143 14081 85.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.565 Å2 / ksol: 0.322 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-11.0807 Å20 Å2-0 Å2
2--11.0807 Å20 Å2
3----22.1615 Å2
Refinement stepCycle: LAST / Resolution: 2.6→35.301 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3145 0 0 29 3174
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043234
X-RAY DIFFRACTIONf_angle_d0.7364387
X-RAY DIFFRACTIONf_dihedral_angle_d18.0551181
X-RAY DIFFRACTIONf_chiral_restr0.052444
X-RAY DIFFRACTIONf_plane_restr0.003585
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5737-2.77240.32461300.27352271X-RAY DIFFRACTION75
2.7724-3.05120.36141360.26892539X-RAY DIFFRACTION83
3.0512-3.49240.29011540.24132741X-RAY DIFFRACTION89
3.4924-4.39870.2711480.19972833X-RAY DIFFRACTION90
4.3987-35.30470.20481270.17923002X-RAY DIFFRACTION89
Refinement TLS params.Method: refined / Origin x: -1.135 Å / Origin y: 6.3423 Å / Origin z: -29.5017 Å
111213212223313233
T0.2448 Å20.0299 Å20.0258 Å2-0.4138 Å20.0602 Å2--0.3453 Å2
L0.2417 °20.2967 °20.4043 °2-0.4312 °20.4419 °2--1.469 °2
S-0.076 Å °-0.101 Å °0.0406 Å °0.0892 Å °-0.0058 Å °0.1397 Å °0.2175 Å °0.0826 Å °0 Å °
Refinement TLS groupSelection details: all

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