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- PDB-7xqt: The structure of FLA-K*00701/KP-FECV-11 -

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Basic information

Entry
Database: PDB / ID: 7xqt
TitleThe structure of FLA-K*00701/KP-FECV-11
Components
  • Beta-2-microglobulin
  • MHC class I antigen alpha chain
  • peptide from Spike glycoprotein
KeywordsIMMUNE SYSTEM / Complex / Peptide prensentation / STRUCTURAL PROTEIN
Function / homology
Function and homology information


antigen processing and presentation of peptide antigen via MHC class I / lumenal side of endoplasmic reticulum membrane / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / positive regulation of T cell activation / peptide antigen binding / phagocytic vesicle membrane ...antigen processing and presentation of peptide antigen via MHC class I / lumenal side of endoplasmic reticulum membrane / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / positive regulation of T cell activation / peptide antigen binding / phagocytic vesicle membrane / MHC class II protein complex binding / late endosome membrane / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / immune response / endocytosis involved in viral entry into host cell / lysosomal membrane / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion membrane / extracellular region / membrane
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 glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Spike glycoprotein / MHC class I antigen alpha chain / Beta-2-microglobulin
Similarity search - Component
Biological speciesFelis catus (domestic cat)
Feline coronavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsQiao, P.W. / Yue, C. / Peng, W.Y. / Liu, K.F. / Huo, S.T. / Zhang, D. / Chai, Y. / Qi, J.X. / Sun, Z.Y. / Gao, G.F. ...Qiao, P.W. / Yue, C. / Peng, W.Y. / Liu, K.F. / Huo, S.T. / Zhang, D. / Chai, Y. / Qi, J.X. / Sun, Z.Y. / Gao, G.F. / Liu, W.J. / Wu, G.Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Analysis of the characteristics of feline major histocompatibility complex class I molecules cross-presenting coronavirus peptides
Authors: Qiao, P.W. / Yue, C. / Peng, W.Y. / Liu, K.F. / Huo, S.T. / Zhang, D. / Chai, Y. / Qi, J.X. / Sun, Z.Y. / Gao, G.F. / Liu, W.J. / Wu, G.Z.
History
DepositionMay 8, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 8, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MHC class I antigen alpha chain
B: Beta-2-microglobulin
C: peptide from Spike glycoprotein


Theoretical massNumber of molelcules
Total (without water)44,1363
Polymers44,1363
Non-polymers00
Water43224
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Denaturation and renaturation experiments
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4630 Å2
ΔGint-16 kcal/mol
Surface area18960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.503, 70.758, 119.150
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein MHC class I antigen alpha chain / FLA class I histocompatibility antigen / alpha chain


Mass: 31467.830 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Felis catus (domestic cat) / Gene: FLA-I / Production host: Escherichia coli (E. coli) / References: UniProt: C6ZK69
#2: Protein Beta-2-microglobulin


Mass: 11618.078 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Felis catus (domestic cat) / Gene: B2M / Production host: Escherichia coli (E. coli) / References: UniProt: Q5MGS7
#3: Protein/peptide peptide from Spike glycoprotein / S glycoprotein / E2 / Peplomer protein


Mass: 1050.186 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Feline coronavirus / References: UniProt: A0A125R5A5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.56 Å3/Da / Density % sol: 51.86 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1M Sodium chloride, 0.1M HEPES PH 7, 25% (W/V) SOKALAN PA 25 CL

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 21, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.8→60.84 Å / Num. obs: 11706 / % possible obs: 99.9 % / Redundancy: 12.5 % / Biso Wilson estimate: 62.81 Å2 / Rmerge(I) obs: 0.277 / Net I/σ(I): 12.9
Reflection shellResolution: 2.8→2.95 Å / Rmerge(I) obs: 1.45 / Num. unique obs: 11706

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROCdata processing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XFM

5xfm


Resolution: 2.8→45.57 Å / SU ML: 0.5667 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.4969
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2933 562 4.83 %
Rwork0.2254 11071 -
obs0.2288 11633 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 63.21 Å2
Refinement stepCycle: LAST / Resolution: 2.8→45.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3104 0 0 24 3128
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00943187
X-RAY DIFFRACTIONf_angle_d1.14544331
X-RAY DIFFRACTIONf_chiral_restr0.058450
X-RAY DIFFRACTIONf_plane_restr0.0105572
X-RAY DIFFRACTIONf_dihedral_angle_d7.4607423
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-3.080.41231520.33682700X-RAY DIFFRACTION99.58
3.08-3.530.38531320.28092733X-RAY DIFFRACTION99.79
3.53-4.440.31231420.21342768X-RAY DIFFRACTION99.79
4.44-45.570.21841360.18422870X-RAY DIFFRACTION99.01

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