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- PDB-4zuw: Crystal structure of Equine MHC I(Eqca-N*00601) in complexed with... -

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Basic information

Entry
Database: PDB / ID: 4zuw
TitleCrystal structure of Equine MHC I(Eqca-N*00601) 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 / 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: 2.6 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)44,5833
Polymers44,5833
Non-polymers00
Water70339
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4260 Å2
ΔGint-14 kcal/mol
Surface area19070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.566, 69.566, 206.612
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-319-

HOH

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Components

#1: Protein Classical MHC class I antigen


Mass: 31569.674 Da / Num. of mol.: 1 / Fragment: UNP residues 22-295 / Mutation: E152V
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 resides 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.: 39 / 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: 2.8 Å3/Da / Density % sol: 56.12 %
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: 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: 16362 / % possible obs: 99.2 % / Redundancy: 11.3 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 38.407
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 11.9 % / Rmerge(I) obs: 0.408 / Mean I/σ(I) obs: 7 / % possible all: 99.6

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Processing

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

1q94


Resolution: 2.6→31.64 Å / SU ML: 0.39 / Cross valid method: NONE / σ(F): 0.12 / Phase error: 26.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2763 752 5.12 %
Rwork0.2108 --
obs0.2138 14688 89.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.024 Å2 / ksol: 0.313 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-6.6744 Å20 Å2-0 Å2
2--6.6744 Å20 Å2
3----13.3489 Å2
Refinement stepCycle: LAST / Resolution: 2.6→31.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3135 0 0 39 3174
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083224
X-RAY DIFFRACTIONf_angle_d0.8314374
X-RAY DIFFRACTIONf_dihedral_angle_d19.8941172
X-RAY DIFFRACTIONf_chiral_restr0.058444
X-RAY DIFFRACTIONf_plane_restr0.003582
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.599-2.79950.4121410.32262365X-RAY DIFFRACTION79
2.7995-3.0810.34541510.29192556X-RAY DIFFRACTION84
3.081-3.52640.31891470.24912781X-RAY DIFFRACTION90
3.5264-4.44090.27241570.18632998X-RAY DIFFRACTION96
4.4409-31.64240.21041560.17283236X-RAY DIFFRACTION97
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)
10.8128-0.0319-0.23691.49870.22171.8029-0.04610.0244-0.0139-0.2815-0.08450.0413-0.0446-0.26850.09090.41090.0146-0.060.3119-0.02080.3364-5.1301-3.818336.4306
20.6246-0.14370.07610.9995-0.02371.6550.00710.26050.0732-0.352-0.14340.2299-0.2459-0.63990.11270.59020.0344-0.15130.438-0.06460.4604-11.6803-1.047928.3905
31.33050.4092-0.38440.3696-0.38610.6364-0.0690.187-0.4058-0.2682-0.03440.04270.1557-0.16950.11760.68160.00320.00420.3225-0.03060.447621.77592.792312.5957
40.76760.0276-0.30530.14440.18851.16730.0548-0.0031-0.2603-0.4425-0.31720.11050.01360.29730.17020.5925-0.0343-0.0580.27710.05250.576117.1351-6.537131.8937
51.1310.2708-0.26150.27580.2990.8799-0.2531-0.2058-0.07470.3333-0.1580.3018-0.31630.3780.00960.7755-0.1088-0.1080.2550.0690.536424.80715.213227.7862
60.90080.0617-0.57460.4080.11411.0685-0.007-0.4019-0.21430.2281-0.441-0.1063-0.03560.05260.11410.5162-0.0513-0.05450.32050.0490.415118.85790.430538.2522
70.88420.4652-0.15120.34070.18041.07570.2557-0.28670.0848-0.24620.1549-0.0335-0.60650.3720.06150.9315-0.12760.08410.5279-0.02010.659716.4428.054342.6425
80.53250.1654-0.37530.1772-0.35451.03910.02670.16650.2806-0.4020.58390.19940.3489-1.04870.10040.5461-0.04010.03040.3487-0.02230.41844.6372-5.626532.1961
90.58650.2806-0.55820.2502-0.39360.6534-0.3092-0.352-0.2601-0.1019-0.0728-0.0444-0.03420.21780.05990.6481-0.057-0.08840.31220.04380.563815.94545.440235.5565
100.45880.1661-0.53550.0785-0.06041.2451-0.0347-0.2187-0.37-0.041-0.0237-0.21110.28780.27760.12290.4766-0.0777-0.04270.37940.11790.465825.712-1.70738.4645
110.2047-0.0641-0.18310.02140.1331.3891-0.1428-0.0367-0.3837-0.65060.10530.10260.30630.54360.07090.6362-0.02440.04720.65320.0860.603828.05991.375530.2254
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 1:137)
2X-RAY DIFFRACTION2chain 'A' and (resseq 138:185)
3X-RAY DIFFRACTION3chain 'A' and (resseq 186:274)
4X-RAY DIFFRACTION4chain 'B' and (resseq 1:11)
5X-RAY DIFFRACTION5chain 'B' and (resseq 12:19)
6X-RAY DIFFRACTION6chain 'B' and (resseq 20:46)
7X-RAY DIFFRACTION7chain 'B' and (resseq 47:51)
8X-RAY DIFFRACTION8chain 'B' and (resseq 52:61)
9X-RAY DIFFRACTION9chain 'B' and (resseq 62:71)
10X-RAY DIFFRACTION10chain 'B' and (resseq 72:90)
11X-RAY DIFFRACTION11chain 'B' and (resseq 91:99)

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