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

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Basic information

Entry
Database: PDB / ID: 4zuu
TitleCrystal structure of Equine MHC I(Eqca-N*00602) in complexed with equine infectious anaemia virus (EIAV) derived peptide Gag-CF9
Components
  • Beta-2-microglobulin
  • CYS-THR-SER-GLU-GLU-MET-ASN-ALA-PHE
  • Classical MHC class I antigen
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 / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / phagocytic vesicle membrane / positive regulation of cellular senescence / peptide antigen binding / negative regulation of epithelial cell proliferation / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / 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 / 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 / lysosomal membrane / external side of plasma 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 / Beta-2-Microglobulin / MHC class I-like antigen recognition-like ...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: 2.2 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: CYS-THR-SER-GLU-GLU-MET-ASN-ALA-PHE


Theoretical massNumber of molelcules
Total (without water)44,3353
Polymers44,3353
Non-polymers00
Water2,342130
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4030 Å2
ΔGint-16 kcal/mol
Surface area19020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.470, 69.470, 206.458
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-311-

HOH

21A-353-

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 CYS-THR-SER-GLU-GLU-MET-ASN-ALA-PHE


Mass: 1031.117 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.: 130 / 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: 2.81 Å3/Da / Density % sol: 56.22 %
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: 2.2→50 Å / Num. obs: 26541 / % possible obs: 98.7 % / Redundancy: 8.8 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 32.714
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.538 / Mean I/σ(I) obs: 4.867 / % possible all: 99.5

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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: 2.2→31.608 Å / SU ML: 0.31 / Cross valid method: NONE / σ(F): 0.18 / Phase error: 29.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2664 1246 5.04 %
Rwork0.2279 --
obs0.2299 24712 92.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.405 Å2 / ksol: 0.341 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-7.894 Å20 Å2-0 Å2
2--7.894 Å20 Å2
3----15.7879 Å2
Refinement stepCycle: LAST / Resolution: 2.2→31.608 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3116 0 0 130 3246
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083204
X-RAY DIFFRACTIONf_angle_d0.8534345
X-RAY DIFFRACTIONf_dihedral_angle_d19.1221168
X-RAY DIFFRACTIONf_chiral_restr0.068440
X-RAY DIFFRACTIONf_plane_restr0.004580
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1952-2.28310.34721060.3082230X-RAY DIFFRACTION80
2.2831-2.3870.36581260.2962442X-RAY DIFFRACTION88
2.387-2.51280.3421350.2752481X-RAY DIFFRACTION90
2.5128-2.67010.29861530.28952549X-RAY DIFFRACTION92
2.6701-2.87610.30871260.28062650X-RAY DIFFRACTION95
2.8761-3.16530.35951480.26312697X-RAY DIFFRACTION96
3.1653-3.62280.25691410.22742774X-RAY DIFFRACTION98
3.6228-4.56220.21781610.18642761X-RAY DIFFRACTION96
4.5622-31.61140.22231500.1922882X-RAY DIFFRACTION94
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)
11.24560.39940.27752.1590.22352.28930.0677-0.0990.00540.497-0.19070.19150.094-0.47910.04550.4248-0.04060.1150.3616-0.05660.3321-7.26324.396416.3251
21.6774-0.29420.51780.2711-0.47220.75860.0166-0.35860.20040.3111-0.1121-0.10430.0323-0.12830.11670.6632-0.05730.0150.2763-0.01610.400719.6958-3.799438.485
30.6058-0.170.34320.0501-0.03351.1943-0.1473-0.00870.15020.5353-0.2901-0.4836-0.40880.5230.19290.4893-0.02620.03180.2310.01330.434617.0416.626519.6321
41.1805-0.32070.39570.1850.09051.1150.0389-0.00670.0343-0.1856-0.13540.37640.46630.34530.02630.7280.12520.07360.35390.10790.588924.6614-15.011224.0175
50.719-0.18450.50780.0501-0.19211.2906-0.0953-0.09320.0356-0.16980.13950.2456-0.0065-0.06140.11490.57360.01850.02560.26350.01360.433917.029-2.324819.2978
61.0825-0.17270.40920.0450.0610.9832-0.32020.36410.26590.1341-0.1581-0.2086-0.1444-0.21660.16620.45270.06130.04110.33040.04420.462216.65643.546910.3218
71.9802-0.681.2750.2937-0.31151.48440.03810.3727-0.2081-0.4105-0.5706-0.09590.31270.09320.08520.73570.1010.18740.63250.11610.686527.8673-5.30457.3478
81.3521-0.26550.02950.06520.13191.38610.0229-0.2683-0.49890.5273-0.23530.63420.5703-0.28140.09921.1192-0.0182-0.11960.26030.02350.634816.4311-8.10069.2837
90.5792-0.29070.19270.1473-0.05730.57710.31040.3945-0.65730.22660.4482-0.45490.27380.01030.03210.5522-0.0355-0.04080.4041-0.13790.64775.47361.293515.9187
100.0716-0.05280.06080.7278-0.99491.3615-0.0324-0.36890.01170.56280.1332-0.53240.0777-0.16730.12290.86460.15030.04410.5066-0.05270.42353.593410.014122.7433
110.7709-0.32150.80650.1978-0.32940.8371-0.22770.2936-0.27640.2471-0.17870.16970.3608-0.16840.05860.56230.0190.050.24350.02890.507815.8986-5.354216.2727
121.3213-0.56611.49251.5017-0.52621.72150.0052-0.14840.28670.2239-0.58420.35370.27330.7001-0.00530.68820.1870.12060.59760.14880.432633.9211-10.534817.6104
130.0461-0.07080.29940.148-0.44461.9112-0.18650.2205-0.010.2146-0.20340.2444-0.14860.48870.11970.45510.07180.02560.42550.11180.48323.87521.094812.2082
140.6252-0.23340.21530.13860.01420.2465-0.45140.44270.18140.2908-0.0354-0.1686-0.4066-0.11230.21320.5181-0.0405-0.04580.36160.14310.402319.884712.797810.6275
150.36960.11610.30110.03520.10341.7038-0.07350.00410.39720.5301-0.12590.1673-0.24880.47460.10960.56030.0402-0.02850.57420.11150.553127.8762-1.239421.5546
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 1:174)
2X-RAY DIFFRACTION2chain 'A' and (resseq 175:274)
3X-RAY DIFFRACTION3chain 'B' and (resseq 1:11)
4X-RAY DIFFRACTION4chain 'B' and (resseq 12:19)
5X-RAY DIFFRACTION5chain 'B' and (resseq 20:30)
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 52:56)
10X-RAY DIFFRACTION10chain 'B' and (resseq 57:61)
11X-RAY DIFFRACTION11chain 'B' and (resseq 62:71)
12X-RAY DIFFRACTION12chain 'B' and (resseq 72:77)
13X-RAY DIFFRACTION13chain 'B' and (resseq 78:83)
14X-RAY DIFFRACTION14chain 'B' and (resseq 84:90)
15X-RAY DIFFRACTION15chain 'B' and (resseq 91:99)

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