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

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Basic information

Entry
Database: PDB / ID: 4zuv
TitleCrystal structure of Equine MHC I(Eqca-N*00602) in complexed with equine infectious anaemia virus (EIAV) derived peptide Env-RW12
Components
  • ARG-VAL-GLU-ASP-VAL-THR-ASN-THR-ALA-GLU-TYR-TRP
  • Beta-2-microglobulinBeta-2 microglobulin
  • Classical MHC class I antigen
KeywordsIMMUNE SYSTEM / lentivirus vaccine
Function / homology
Function and homology information


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 / cellular defense response / Neutrophil degranulation ...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 / cellular defense response / Neutrophil degranulation / lumenal side of endoplasmic reticulum membrane / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / 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 / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / positive regulation of T cell mediated cytotoxicity / MHC class II protein complex / 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 / negative regulation of epithelial cell proliferation / positive regulation of immune response / antimicrobial humoral immune response mediated by antimicrobial peptide / sensory perception of smell / positive regulation of T cell activation / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / iron ion transport / protein refolding / antibacterial humoral response / protein homotetramerization / intracellular iron ion homeostasis / cellular response to lipopolysaccharide / defense response to Gram-negative bacterium / amyloid fibril formation / learning or memory / defense response to Gram-positive bacterium / symbiont entry into host cell / immune response / lysosomal membrane / external side of plasma membrane / innate immune response / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular region / membrane / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Gp90 envelope polyprotein of equine infectious anemia virus (EIAV) / EIAV coat protein, gp90 / Retroviral envelope protein / Retroviral envelope protein GP41-like / 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 ...Gp90 envelope polyprotein of equine infectious anemia virus (EIAV) / EIAV coat protein, gp90 / Retroviral envelope protein / Retroviral envelope protein GP41-like / 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 / Envelope glycoprotein / Classical MHC class I antigen
Similarity search - Component
Biological speciesEquus caballus (horse)
Mus musculus (house mouse)
Equine infectious anemia virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.3 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
Revision 1.1Feb 19, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Classical MHC class I antigen
B: Beta-2-microglobulin
C: ARG-VAL-GLU-ASP-VAL-THR-ASN-THR-ALA-GLU-TYR-TRP
D: Classical MHC class I antigen
E: Beta-2-microglobulin
F: ARG-VAL-GLU-ASP-VAL-THR-ASN-THR-ALA-GLU-TYR-TRP


Theoretical massNumber of molelcules
Total (without water)89,5756
Polymers89,5756
Non-polymers00
Water6,269348
1
A: Classical MHC class I antigen
B: Beta-2-microglobulin
C: ARG-VAL-GLU-ASP-VAL-THR-ASN-THR-ALA-GLU-TYR-TRP


Theoretical massNumber of molelcules
Total (without water)44,7883
Polymers44,7883
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4280 Å2
ΔGint-15 kcal/mol
Surface area18940 Å2
MethodPISA
2
D: Classical MHC class I antigen
E: Beta-2-microglobulin
F: ARG-VAL-GLU-ASP-VAL-THR-ASN-THR-ALA-GLU-TYR-TRP


Theoretical massNumber of molelcules
Total (without water)44,7883
Polymers44,7883
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4290 Å2
ΔGint-14 kcal/mol
Surface area18940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.518, 71.441, 99.874
Angle α, β, γ (deg.)90.00, 102.94, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Classical MHC class I antigen


Mass: 31599.658 Da / Num. of mol.: 2 / 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.: 2 / 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 ARG-VAL-GLU-ASP-VAL-THR-ASN-THR-ALA-GLU-TYR-TRP


Mass: 1483.558 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Equine infectious anemia virus / References: UniProt: P16082*PLUS
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 348 / 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: 3.2 Å3/Da / Density % sol: 61.6 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.02 M magnesium chloride hexahydrare, 0.1 M HEPES, 22% w/v polyacrylic acid sodium salt 5,100
PH range: 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 0.97908 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 5, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97908 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 50912 / % possible obs: 99.5 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 12.988
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.464 / Mean I/σ(I) obs: 3.876 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.5_2refinement
HKL-2000data reduction
HKL-2000data scaling
HKL-2000phasing
RefinementMethod to determine structure: MIR
Starting model: 1Q94

1q94


Resolution: 2.3→31.836 Å / SU ML: 0.3 / Cross valid method: NONE / σ(F): 0.06 / Phase error: 25.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2335 2487 5.1 %
Rwork0.1996 --
obs0.2013 48752 91.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.816 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.1127 Å2-0 Å20.8928 Å2
2--0.5636 Å2-0 Å2
3---0.5491 Å2
Refinement stepCycle: LAST / Resolution: 2.3→31.836 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6302 0 0 348 6650
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066482
X-RAY DIFFRACTIONf_angle_d0.878798
X-RAY DIFFRACTIONf_dihedral_angle_d19.7572356
X-RAY DIFFRACTIONf_chiral_restr0.063892
X-RAY DIFFRACTIONf_plane_restr0.0031172
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2632-2.30680.2831460.2642843X-RAY DIFFRACTION30
2.3068-2.35380.27461250.25882420X-RAY DIFFRACTION87
2.3538-2.4050.29811270.25622441X-RAY DIFFRACTION88
2.405-2.46090.3091520.24092469X-RAY DIFFRACTION89
2.4609-2.52240.25861380.24342545X-RAY DIFFRACTION92
2.5224-2.59060.30261440.24052551X-RAY DIFFRACTION92
2.5906-2.66680.2921330.24142661X-RAY DIFFRACTION94
2.6668-2.75280.29051450.23792672X-RAY DIFFRACTION96
2.7528-2.85120.27051410.24772709X-RAY DIFFRACTION97
2.8512-2.96520.29231530.24472702X-RAY DIFFRACTION98
2.9652-3.10010.29651530.23932775X-RAY DIFFRACTION99
3.1001-3.26340.28821250.21942780X-RAY DIFFRACTION99
3.2634-3.46760.21651630.20572757X-RAY DIFFRACTION99
3.4676-3.7350.21391560.1852793X-RAY DIFFRACTION100
3.735-4.11010.18961510.16722778X-RAY DIFFRACTION99
4.1101-4.70320.1731450.15222793X-RAY DIFFRACTION99
4.7032-5.91940.20051480.15642834X-RAY DIFFRACTION100
5.9194-31.83880.20931420.19362742X-RAY DIFFRACTION95
Refinement TLS params.Method: refined / Origin x: 17.0423 Å / Origin y: 5.7926 Å / Origin z: -18.0377 Å
111213212223313233
T0.1794 Å20.0053 Å20.027 Å2-0.1862 Å20.0088 Å2--0.2052 Å2
L0.2502 °2-0.0111 °20.4044 °2-0.2664 °2-0.03 °2--0.6511 °2
S-0.0078 Å °-0.0261 Å °0.0597 Å °-0.0257 Å °-0.0403 Å °-0.0217 Å °0.0397 Å °-0.0505 Å °0.043 Å °
Refinement TLS groupSelection details: all

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