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- PDB-7xqs: The structure of FLA-K*00701/KP-CoV-9 -

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Basic information

Entry
Database: PDB / ID: 7xqs
TitleThe structure of FLA-K*00701/KP-CoV-9
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 / symbiont-mediated disruption of host tissue / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / viral translation / host extracellular space / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / membrane fusion / entry receptor-mediated virion attachment to host cell / Attachment and Entry / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / host cell surface receptor binding / immune response / symbiont-mediated suppression of host innate immune response / receptor ligand activity / 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 / symbiont entry into host cell / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / extracellular region / identical protein binding / membrane / plasma membrane
Similarity search - Function
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 / : ...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 / Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2 superfamily, coronavirus / 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, coronavirus / Coronavirus spike glycoprotein S2 / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
MHC class I antigen alpha chain / Spike glycoprotein / Beta-2-microglobulin
Similarity search - Component
Biological speciesFelis catus (domestic cat)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.69 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 6, 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)46,3233
Polymers46,3233
Non-polymers00
Water543
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, de refolding
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4460 Å2
ΔGint-16 kcal/mol
Surface area18850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.292, 70.829, 121.347
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: 13714.637 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


Mass: 1140.309 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Severe acute respiratory syndrome coronavirus 2
References: UniProt: P0DTC2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 2.52 Å3/Da / Density % sol: 51.16 %
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: 2.69→61.17 Å / Num. obs: 13627 / % possible obs: 99.2 % / Redundancy: 12.8 % / Biso Wilson estimate: 79.62 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 22
Reflection shellResolution: 2.69→2.83 Å / Rmerge(I) obs: 0.857 / Num. unique obs: 13627

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Processing

Software
NameVersionClassification
autoPROCdata processing
PHENIX1.13_2998refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XMF

5xmf


Resolution: 2.69→27.89 Å / SU ML: 0.3939 / Cross valid method: NONE / σ(F): 1.36 / Phase error: 34.0884 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2921 636 4.69 %
Rwork0.2226 12919 -
obs0.2259 13555 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 80.42 Å2
Refinement stepCycle: LAST / Resolution: 2.69→27.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3103 0 0 3 3106
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00953190
X-RAY DIFFRACTIONf_angle_d1.1714337
X-RAY DIFFRACTIONf_chiral_restr0.0567449
X-RAY DIFFRACTIONf_plane_restr0.0076572
X-RAY DIFFRACTIONf_dihedral_angle_d10.16911892
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.69-2.890.40681250.3242515X-RAY DIFFRACTION99.29
2.89-3.190.37611170.30272564X-RAY DIFFRACTION100
3.19-3.650.36771200.27262556X-RAY DIFFRACTION100
3.65-4.590.28021410.21442583X-RAY DIFFRACTION100
4.59-27.890.24251330.18282701X-RAY DIFFRACTION99.33

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