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- PDB-7dc6: Giant panda MHC class I complexes -

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Basic information

Entry
Database: PDB / ID: 7dc6
TitleGiant panda MHC class I complexes
Components
  • Beta-2-microglobulin
  • CCV-NGY9 peptide from Spike protein
  • MHC class I antigen
KeywordsIMMUNE SYSTEM / Giant panda / MHC class I / Aime-128
Function / homology
Function and homology information


antigen processing and presentation of peptide antigen via MHC class I / antigen processing and presentation / : / endocytosis involved in viral entry into host cell / MHC class I protein complex / membrane => GO:0016020 / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / immune response / fusion of virus membrane with host plasma membrane ...antigen processing and presentation of peptide antigen via MHC class I / antigen processing and presentation / : / endocytosis involved in viral entry into host cell / MHC class I protein complex / membrane => GO:0016020 / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / immune response / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion membrane / extracellular region
Similarity search - Function
Spike glycoprotein, Alphacoronavirus / Spike glycoprotein S1, coronavirus / Coronavirus spike glycoprotein S1 / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin ...Spike glycoprotein, Alphacoronavirus / Spike glycoprotein S1, coronavirus / Coronavirus spike glycoprotein S1 / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / 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 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
MHC class I antigen / Beta-2-microglobulin / Spike glycoprotein
Similarity search - Component
Biological speciesAiluropoda melanoleuca (giant panda)
Canine coronavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.68 Å
AuthorsYuan, H. / Xia, C.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31572493 China
National Natural Science Foundation of China (NSFC)31972683 China
CitationJournal: Protein Sci. / Year: 2020
Title: Crystal structure of the giant panda MHC class I complex: First insights into the viral peptide presentation profile in the bear family.
Authors: Yuan, H. / Ma, L. / Zhang, L. / Li, X. / Xia, C.
History
DepositionOct 23, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 16, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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: MHC class I antigen
B: Beta-2-microglobulin
C: MHC class I antigen
D: Beta-2-microglobulin
E: CCV-NGY9 peptide from Spike protein
F: CCV-NGY9 peptide from Spike protein


Theoretical massNumber of molelcules
Total (without water)88,9026
Polymers88,9026
Non-polymers00
Water57632
1
A: MHC class I antigen
B: Beta-2-microglobulin
E: CCV-NGY9 peptide from Spike protein


Theoretical massNumber of molelcules
Total (without water)44,4513
Polymers44,4513
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4460 Å2
ΔGint-15 kcal/mol
Surface area18880 Å2
MethodPISA
2
C: MHC class I antigen
D: Beta-2-microglobulin
F: CCV-NGY9 peptide from Spike protein


Theoretical massNumber of molelcules
Total (without water)44,4513
Polymers44,4513
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4430 Å2
ΔGint-19 kcal/mol
Surface area18970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)173.677, 173.677, 84.346
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11C-303-

HOH

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Components

#1: Protein MHC class I antigen / MHC I heavy chain


Mass: 31776.852 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ailuropoda melanoleuca (giant panda) / Gene: Aime-128 / Production host: Escherichia coli (E. coli) / References: UniProt: B2KT53
#2: Protein Beta-2-microglobulin / MHC I light chain


Mass: 11578.034 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ailuropoda melanoleuca (giant panda) / Gene: B2M, PANDA_000996 / Production host: Escherichia coli (E. coli) / References: UniProt: D2GW37
#3: Protein/peptide CCV-NGY9 peptide from Spike protein


Mass: 1096.149 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Canine coronavirus / Production host: Escherichia coli (E. coli) / References: UniProt: Q65984
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.58 Å3/Da / Density % sol: 65.67 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 30% (w/v) polyethylene glycol 3350, 0.05M magnesium chloride hexahydrate, 0.1M HEPES (pH 7.5)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97892 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97892 Å / Relative weight: 1
ReflectionResolution: 2.68→50 Å / Num. obs: 34668 / % possible obs: 99.1 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 18.2
Reflection shellResolution: 2.68→2.75 Å / Rmerge(I) obs: 0.094 / Num. unique obs: 34668

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Starting model: 1.0E+27 / Resolution: 2.68→50 Å / Cor.coef. Fo:Fc: 0.895 / Cor.coef. Fo:Fc free: 0.863 / SU B: 39.385 / SU ML: 0.355 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.593 / ESU R Free: 0.339 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2911 1788 4.9 %RANDOM
Rwork0.2662 ---
obs0.2675 34668 99.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 92.23 Å2 / Biso mean: 55.72 Å2 / Biso min: 19.89 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20 Å20 Å2
2---0.11 Å2-0 Å2
3---0.22 Å2
Refinement stepCycle: final / Resolution: 2.68→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6266 0 0 32 6298
Biso mean---33.89 -
Num. residues----765
LS refinement shellResolution: 2.68→2.749 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.47 119 -
Rwork0.422 2497 -
all-2616 -
obs--97.94 %
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)
10.4983-0.0672-0.28710.32540.14510.5013-0.1602-0.2146-0.0015-0.05820.05360.0213-0.00770.20110.10660.2269-0.0111-0.02280.3550.0720.0439-22.1183-36.03419.517
21.991-0.5992-0.46220.51490.84371.9565-0.0995-0.1377-0.14-0.07220.03750.0783-0.02460.28020.06190.20490.0451-0.0170.31750.08730.0928-21.8455-47.6169-5.2005
31.7341-0.18620.34910.28570.04830.47350.07530.11390.1728-0.0725-0.098-0.0610.10840.05470.02270.2313-0.05980.0230.27880.02880.024415.5762-49.9339-20.6866
43.0681.04061.38011.34470.59012.34430.0874-0.3094-0.2389-0.1061-0.0248-0.01930.1879-0.143-0.06260.1506-0.06950.00020.31870.07350.05491.6629-62.6592-17.2527
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 276
2X-RAY DIFFRACTION2B1 - 99
3X-RAY DIFFRACTION3C2 - 276
4X-RAY DIFFRACTION4D2 - 99

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