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- PDB-7xqu: The structure of FLA-E*00301/EM-FECV-10 -

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Basic information

Entry
Database: PDB / ID: 7xqu
TitleThe structure of FLA-E*00301/EM-FECV-10
Components
  • Beta-2-microglobulin
  • MHC class I antigen
  • peptide from Nucleoprotein
KeywordsIMMUNE SYSTEM / Complex / Peptide prensentation / STRUCTURAL PROTEIN
Function / homology
Function and homology information


antigen processing and presentation of peptide antigen via MHC class I / 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 / 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 / MHC class I protein complex / positive regulation of immune response / peptide antigen binding ...antigen processing and presentation of peptide antigen via MHC class I / 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 / 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 / MHC class I protein complex / positive regulation of immune response / peptide antigen binding / positive regulation of T cell mediated cytotoxicity / positive regulation of T cell activation / phagocytic vesicle membrane / MHC class II protein complex binding / late endosome membrane / host cell endoplasmic reticulum-Golgi intermediate compartment / viral nucleocapsid / host cell Golgi apparatus / immune response / ribonucleoprotein complex / external side of plasma membrane / signaling receptor binding / lysosomal membrane / extracellular space / RNA binding / extracellular region
Similarity search - Function
Nucleocapsid protein, alphacoronavirus / Nucleocapsid protein, coronavirus / Nucleocapsid protein, C-terminal / Nucleocapsid protein, N-terminal / Nucleocapsid (N) protein, C-terminal domain, coronavirus / Nucleocapsid (N) protein, N-terminal domain, coronavirus / Coronavirus nucleocapsid / Coronavirus nucleocapsid (CoV N) protein N-terminal (NTD) domain profile. / Coronavirus nucleocapsid (CoV N) protein C-terminal (CTD) domain profile. / MHC class I, alpha chain, C-terminal ...Nucleocapsid protein, alphacoronavirus / Nucleocapsid protein, coronavirus / Nucleocapsid protein, C-terminal / Nucleocapsid protein, N-terminal / Nucleocapsid (N) protein, C-terminal domain, coronavirus / Nucleocapsid (N) protein, N-terminal domain, coronavirus / Coronavirus nucleocapsid / Coronavirus nucleocapsid (CoV N) protein N-terminal (NTD) domain profile. / Coronavirus nucleocapsid (CoV N) protein C-terminal (CTD) domain profile. / 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 / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Nucleoprotein / Beta-2-microglobulin / MHC class I antigen
Similarity search - Component
Biological speciesFelis catus (domestic cat)
Feline coronavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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 20, 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
B: Beta-2-microglobulin
C: peptide from Nucleoprotein
D: MHC class I antigen
E: Beta-2-microglobulin
F: peptide from Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)89,2476
Polymers89,2476
Non-polymers00
Water1,47782
1
A: MHC class I antigen
B: Beta-2-microglobulin
C: peptide from Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)44,6243
Polymers44,6243
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4680 Å2
ΔGint-20 kcal/mol
Surface area18740 Å2
MethodPISA
2
D: MHC class I antigen
E: Beta-2-microglobulin
F: peptide from Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)44,6243
Polymers44,6243
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4720 Å2
ΔGint-18 kcal/mol
Surface area18670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.221, 132.221, 130.846
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number90
Space group name H-MP4212
Space group name HallP4ab2ab
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z
#3: y+1/2,-x+1/2,z
#4: x+1/2,-y+1/2,-z
#5: -x+1/2,y+1/2,-z
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z

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Components

#1: Protein MHC class I antigen


Mass: 31878.260 Da / Num. of mol.: 2
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: Q95482
#2: Protein Beta-2-microglobulin


Mass: 11618.078 Da / Num. of mol.: 2
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 Nucleoprotein / Nucleocapsid protein / NC / Protein N


Mass: 1127.266 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Feline coronavirus / References: UniProt: P25909
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 3.21 Å3/Da / Density % sol: 61.64 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES sodium, 2% VL Polyethylene glycol 400, 2.0M Ammonium sulfate

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Data collection

DiffractionMean temperature: 291 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 35453 / % possible obs: 97.9 % / Redundancy: 14.4 % / Biso Wilson estimate: 45.86 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 5.909
Reflection shellResolution: 2.6→2.64 Å / Rmerge(I) obs: 0.669 / Num. unique obs: 35453

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XMF

5xmf


Resolution: 2.6→38.04 Å / SU ML: 0.3884 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.0358
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2757 1741 4.97 %
Rwork0.2191 33314 -
obs0.2219 35055 96.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.7 Å2
Refinement stepCycle: LAST / Resolution: 2.6→38.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6275 0 0 82 6357
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00856444
X-RAY DIFFRACTIONf_angle_d1.03348755
X-RAY DIFFRACTIONf_chiral_restr0.0547903
X-RAY DIFFRACTIONf_plane_restr0.01011155
X-RAY DIFFRACTIONf_dihedral_angle_d6.252857
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.680.41721600.36662523X-RAY DIFFRACTION90.37
2.68-2.770.32931470.29712778X-RAY DIFFRACTION98.85
2.77-2.860.28631280.23322826X-RAY DIFFRACTION99.19
2.86-2.980.32861510.22632803X-RAY DIFFRACTION99.66
2.98-3.110.29891560.24362805X-RAY DIFFRACTION99.6
3.11-3.280.36651580.28742807X-RAY DIFFRACTION99.5
3.28-3.480.35861560.29992644X-RAY DIFFRACTION93.4
3.48-3.750.29751390.27232583X-RAY DIFFRACTION90.73
3.75-4.130.26041410.21982603X-RAY DIFFRACTION90.62
4.13-4.730.19711210.14822909X-RAY DIFFRACTION100
4.73-5.950.19931410.15612935X-RAY DIFFRACTION99.9
5.95-38.040.20971430.16823098X-RAY DIFFRACTION99.51

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