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

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Basic information

Entry
Database: PDB / ID: 4zut
TitleCrystal structure of Equine MHC I(Eqca-N*00602) in complexed with equine infectious anaemia virus (EIAV) derived peptide Gag-GW12
Components
  • Beta-2-microglobulin
  • Classical MHC class I antigen
  • GLY-SER-GLN-LYS-LEU-THR-THR-GLY-ASN-CYS-ASN-TRP
KeywordsIMMUNE SYSTEM / lentivirus vaccine
Function / homology
Function and homology information


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 / viral budding via host ESCRT complex / cellular defense response / Neutrophil degranulation / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent ...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 / viral budding via host ESCRT complex / cellular defense response / Neutrophil degranulation / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / 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 / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / 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 / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / negative regulation of epithelial cell proliferation / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / positive regulation of T cell activation / sensory perception of smell / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / iron ion transport / T cell differentiation in thymus / protein refolding / viral nucleocapsid / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / nucleic acid binding / structural constituent of virion / learning or memory / immune response / external side of plasma membrane / lysosomal membrane / signaling receptor binding / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / zinc ion binding / cytosol
Similarity search - Function
Gag protein p15 / Gag protein p15 / : / 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 / : ...Gag protein p15 / Gag protein p15 / : / 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 / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retrovirus capsid, C-terminal / Retroviral matrix protein / : / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / 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 / Gag polyprotein / 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
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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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: GLY-SER-GLN-LYS-LEU-THR-THR-GLY-ASN-CYS-ASN-TRP


Theoretical massNumber of molelcules
Total (without water)44,6133
Polymers44,6133
Non-polymers00
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4210 Å2
ΔGint-13 kcal/mol
Surface area18990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.793, 69.793, 207.130
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-325-

HOH

21A-343-

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


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 GLY-SER-GLN-LYS-LEU-THR-THR-GLY-ASN-CYS-ASN-TRP


Mass: 1309.429 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Equine infectious anemia virus / References: UniProt: P69732*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 2.83 Å3/Da / Density % sol: 56.49 %
Crystal growTemperature: 295 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: 16706 / % possible obs: 99.2 % / Redundancy: 11.3 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 38.407
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 11.7 % / Rmerge(I) obs: 0.587 / Mean I/σ(I) obs: 5.314 / % possible all: 99.8

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Processing

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

1q94


Resolution: 2.6→35.623 Å / SU ML: 0.37 / Cross valid method: NONE / σ(F): 0.15 / Phase error: 28.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2651 836 5 %
Rwork0.2213 --
obs0.2235 16362 91.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.034 Å2 / ksol: 0.315 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-8.1082 Å20 Å2-0 Å2
2--8.1082 Å20 Å2
3----16.2164 Å2
Refinement stepCycle: LAST / Resolution: 2.6→35.623 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3137 0 0 60 3197
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053226
X-RAY DIFFRACTIONf_angle_d0.7594376
X-RAY DIFFRACTIONf_dihedral_angle_d18.6171174
X-RAY DIFFRACTIONf_chiral_restr0.055443
X-RAY DIFFRACTIONf_plane_restr0.002583
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5123-2.66960.41411350.31212259X-RAY DIFFRACTION81
2.6696-2.87570.36921310.29942479X-RAY DIFFRACTION88
2.8757-3.16490.31821540.28172603X-RAY DIFFRACTION92
3.1649-3.62250.29791370.24922712X-RAY DIFFRACTION95
3.6225-4.56250.23281570.19392810X-RAY DIFFRACTION96
4.5625-35.6270.20431220.17793007X-RAY DIFFRACTION96
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.02930.13150.37021.83860.87982.11580.0153-0.1079-0.02890.2929-0.16520.18170.222-0.49410.07210.4496-0.04680.09640.4654-0.02040.4092-5.05534.053815.2015
20.74810.6650.68580.56480.08011.6460.3878-0.2302-0.04850.5659-0.61011.25060.1618-0.94070.01310.62-0.0150.22390.7361-0.08670.5749-15.24895.651620.7929
31.7057-0.06350.96550.0372-0.36170.663-0.01-0.25620.28130.2387-0.08380.0223-0.1035-0.19770.11770.68-0.05610.05280.3657-0.02810.478419.8327-3.846638.5446
40.2133-0.2671-0.27480.0640.03880.90080.25610.00310.28550.596-0.55590.4497-0.3421.03860.17530.58590.03080.04170.34880.01020.54817.16886.636219.761
50.5774-0.18250.62390.1988-0.40531.0252-0.09940.0446-0.3705-0.1693-0.11570.55790.02360.05020.07870.54140.020.13060.23130.07080.5220.2958-7.685321.2438
60.9406-0.09090.3942-0.012-0.05510.6673-0.43320.07150.60240.4424-0.0813-0.22590.2566-0.11280.15040.64160.05280.02160.42240.05870.511416.8413.611310.312
70.8827-0.41590.86160.29-0.27821.1856-0.49180.19660.1051-0.62320.05450.36820.4461-0.01320.10780.82340.09450.34510.47380.14870.732627.8771-5.38657.3424
80.4556-0.03920.24640.05510.17310.93410.0397-0.0099-0.66240.36460.12020.93450.7034-0.18650.09511.0560.07110.02290.45760.00730.737216.4565-8.0439.1117
90.2012-0.12030.24780.1589-0.3750.7721-0.0061-0.2692-0.48560.6030.7360.043-0.2736-0.52250.09480.71020.03080.02450.5598-0.00550.54634.60675.778619.4795
100.321-0.15850.47920.1212-0.15170.644-0.43160.621-0.45560.7786-0.25080.79250.3868-0.25010.07660.58730.02630.09440.3720.020.544715.96-5.384316.1867
110.392-0.44060.66350.7738-0.97691.3149-0.1079-0.05790.03080.7029-0.16970.27870.70110.61840.09740.86360.22740.07040.65210.05060.620834.1077-10.68417.5705
120.8092-1.02930.89241.3631-0.87241.7220.00620.09760.0259-0.2416-0.2792-0.26920.17720.08850.13520.50190.08380.07970.5310.15740.654324.10051.00812.1831
130.1218-0.06370.13990.05250.00370.28980.23340.2820.1636-0.13660.4597-0.0562-0.5396-0.10590.19960.7367-0.08090.01790.67430.07080.501620.071912.889610.7164
140.19510.00930.2244-0.0129-0.05541.411-0.25570.34030.49640.3928-0.6666-0.7737-0.34381.25140.1230.51820.07090.04210.60820.13780.611128.031-1.314721.6062
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 1:137)
2X-RAY DIFFRACTION2chain 'A' and (resseq 138:174)
3X-RAY DIFFRACTION3chain 'A' and (resseq 175:274)
4X-RAY DIFFRACTION4chain 'B' and (resseq 1:11)
5X-RAY DIFFRACTION5chain 'B' and (resseq 12:30)
6X-RAY DIFFRACTION6chain 'B' and (resseq 31:41)
7X-RAY DIFFRACTION7chain 'B' and (resseq 42:46)
8X-RAY DIFFRACTION8chain 'B' and (resseq 47:51)
9X-RAY DIFFRACTION9chain 'B' and (resseq 52:61)
10X-RAY DIFFRACTION10chain 'B' and (resseq 62:71)
11X-RAY DIFFRACTION11chain 'B' and (resseq 72:77)
12X-RAY DIFFRACTION12chain 'B' and (resseq 78:83)
13X-RAY DIFFRACTION13chain 'B' and (resseq 84:90)
14X-RAY DIFFRACTION14chain 'B' and (resseq 91:99)

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