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- PDB-7vpq: Structures of a deltacoronavirus spike protein bound to porcine a... -

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Basic information

Entry
Database: PDB / ID: 7vpq
TitleStructures of a deltacoronavirus spike protein bound to porcine and human receptors indicate the risk of virus adaptation to humans
Components
  • Aminopeptidase N
  • Spike protein
KeywordsHYDROLASE/VIRAL PROTEIN / Porcine Deltacoronavirus / receptor / cross-species transmission / VIRAL PROTEIN / HYDROLASE-VIRAL PROTEIN complex
Function / homology
Function and homology information


alanyl aminopeptidase activity / membrane alanyl aminopeptidase / peptide catabolic process / endoplasmic reticulum-Golgi intermediate compartment / metalloaminopeptidase activity / aminopeptidase activity / Metabolism of Angiotensinogen to Angiotensins / angiotensin maturation / peptide binding / secretory granule membrane ...alanyl aminopeptidase activity / membrane alanyl aminopeptidase / peptide catabolic process / endoplasmic reticulum-Golgi intermediate compartment / metalloaminopeptidase activity / aminopeptidase activity / Metabolism of Angiotensinogen to Angiotensins / angiotensin maturation / peptide binding / secretory granule membrane / metallopeptidase activity / signaling receptor activity / virus receptor activity / angiogenesis / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / cell differentiation / receptor-mediated virion attachment to host cell / endocytosis involved in viral entry into host cell / fusion of virus membrane with host plasma membrane / lysosomal membrane / external side of plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / Neutrophil degranulation / virion membrane / proteolysis / extracellular space / extracellular exosome / zinc ion binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
Coronavirus S1 glycoprotein, central receptor binding domain (RBD) / Spike glycoprotein S1, coronavirus / Coronavirus spike glycoprotein S1 / Aminopeptidase N-type / ERAP1-like C-terminal domain / : / ERAP1-like C-terminal domain / Peptidase M1, alanine aminopeptidase/leukotriene A4 hydrolase / Peptidase M1, membrane alanine aminopeptidase / Aminopeptidase N-like , N-terminal domain ...Coronavirus S1 glycoprotein, central receptor binding domain (RBD) / Spike glycoprotein S1, coronavirus / Coronavirus spike glycoprotein S1 / Aminopeptidase N-type / ERAP1-like C-terminal domain / : / ERAP1-like C-terminal domain / Peptidase M1, alanine aminopeptidase/leukotriene A4 hydrolase / Peptidase M1, membrane alanine aminopeptidase / Aminopeptidase N-like , N-terminal domain / Peptidase family M1 domain / Peptidase M1 N-terminal domain / Aminopeptidase N-like , N-terminal domain superfamliy / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / Peptidase M4/M1, CTD superfamily / Neutral zinc metallopeptidases, zinc-binding region signature. / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-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 / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Spike protein / Aminopeptidase N
Similarity search - Component
Biological speciesHomo sapiens (human)
Porcine deltacoronavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsJi, W. / Xu, Y. / Zhang, S.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32000659 China
CitationJournal: Nat Commun / Year: 2022
Title: Structures of a deltacoronavirus spike protein bound to porcine and human receptors.
Authors: Ji, W. / Peng, Q. / Fang, X. / Li, Z. / Li, Y. / Xu, C. / Zhao, S. / Li, J. / Chen, R. / Mo, G. / Wei, Z. / Xu, Y. / Li, B. / Zhang, S.
History
DepositionOct 17, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 16, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aminopeptidase N
B: Spike protein
C: Aminopeptidase N
D: Spike protein
E: Aminopeptidase N
F: Spike protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)361,87936
Polymers354,8786
Non-polymers7,00130
Water00
1
A: Aminopeptidase N
B: Spike protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,62612
Polymers118,2932
Non-polymers2,33410
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Aminopeptidase N
D: Spike protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,62612
Polymers118,2932
Non-polymers2,33410
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Aminopeptidase N
F: Spike protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,62612
Polymers118,2932
Non-polymers2,33410
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)201.225, 347.690, 255.114
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number21
Space group name H-MC222

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Components

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Protein , 2 types, 6 molecules ACEBDF

#1: Protein Aminopeptidase N / AP-N / hAPN / Alanyl aminopeptidase / Aminopeptidase M / AP-M / Microsomal aminopeptidase / Myeloid ...AP-N / hAPN / Alanyl aminopeptidase / Aminopeptidase M / AP-M / Microsomal aminopeptidase / Myeloid plasma membrane glycoprotein CD13 / gp150


Mass: 103966.531 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ANPEP, APN, CD13, PEPN / Production host: Baculovirus expression vector pFastBac1-HM / References: UniProt: P15144, membrane alanyl aminopeptidase
#2: Protein Spike protein


Mass: 14326.173 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porcine deltacoronavirus / Production host: Baculovirus expression vector pFastBac1-HM / References: UniProt: A0A4P8D758

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Sugars , 3 types, 24 molecules

#3: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-3DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a3-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(3+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#6: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 6 molecules

#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
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: 6.29 Å3/Da / Density % sol: 80.44 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: solution containing 25% w/v Polyethylene glycol 1500, 0.1 M BIS-TRIS propane pH9.0, 0.1 M Sodium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 6, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 160248 / % possible obs: 99.4 % / Redundancy: 6.1 % / CC1/2: 0.964 / Net I/σ(I): 5.28
Reflection shellResolution: 3.1→3.29 Å / Num. unique obs: 25301 / CC1/2: 0.583

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6atk

6atk


Resolution: 3.1→49.36 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2784 8136 5.08 %
Rwork0.2591 152046 -
obs0.2601 160182 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 137.76 Å2 / Biso mean: 37.0786 Å2 / Biso min: 11.91 Å2
Refinement stepCycle: final / Resolution: 3.1→49.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24096 0 441 0 24537
Biso mean--63.11 --
Num. residues----2991
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.1-3.130.36462620.33824640490292
3.13-3.170.29552920.309149855277100
3.17-3.210.35772580.306250605318100
3.21-3.250.36593120.29750155327100
3.25-3.290.3152400.282650855325100
3.29-3.340.32482530.277950345287100
3.34-3.390.33522380.272451025340100
3.39-3.440.32482870.276249865273100
3.44-3.490.29532540.282251485402100
3.49-3.550.31552450.283150675312100
3.55-3.610.33332680.28250925360100
3.61-3.670.29252730.26364975524899
3.67-3.750.3012820.25815048533099
3.75-3.820.28312770.24550715348100
3.82-3.90.25223520.246549655317100
3.9-40.26962870.242550755362100
4-4.10.24732560.240251245380100
4.1-4.210.25352640.2450585322100
4.21-4.330.23712710.228950885359100
4.33-4.470.23272760.229951195395100
4.47-4.630.27752460.233150695315100
4.63-4.810.242530.229651085361100
4.81-5.030.24352370.236751385375100
5.03-5.30.2363100.244350595369100
5.3-5.630.26612620.25495022528498
5.63-6.060.26792690.262751545423100
6.06-6.670.27292700.264551585428100
6.67-7.630.2542860.258451525438100
7.64-9.610.22382520.242952375489100
9.61-49.360.31983040.29555212551697

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