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- PDB-8zfh: Structure of the C-terminal domain of nsp4 from PDCOV -

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Basic information

Entry
Database: PDB / ID: 8zfh
TitleStructure of the C-terminal domain of nsp4 from PDCOV
ComponentsORF1ab polyprotein
KeywordsVIRAL PROTEIN / Coronavirus / PDCOV / nsp4
Function / homology
Function and homology information


host cell membrane / host cell endoplasmic reticulum-Golgi intermediate compartment / 3'-5'-RNA exonuclease activity / 5'-3' DNA helicase activity / omega peptidase activity / endonuclease activity / methyltransferase cap1 activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / regulation of autophagy / host cell perinuclear region of cytoplasm ...host cell membrane / host cell endoplasmic reticulum-Golgi intermediate compartment / 3'-5'-RNA exonuclease activity / 5'-3' DNA helicase activity / omega peptidase activity / endonuclease activity / methyltransferase cap1 activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / regulation of autophagy / host cell perinuclear region of cytoplasm / viral protein processing / lyase activity / viral translational frameshifting / symbiont-mediated activation of host autophagy / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane
Similarity search - Function
Non-structural protein 5, deltacoronavirus / Nonstructural protein 14, deltacoronavirus / Nonstructural protein 15, middle domain, deltacoronavirus / Nonstructural protein 15, N-terminal, deltacoronavirus / RNA-dependent RNA polymerase, deltacoronavirus / Non-structural protein 6, deltacoronavirus / Non-structural protein 2, IBV-like / AAA domain / NSP15, NendoU domain, coronavirus / NSP14, guanine-N7-methyltransferase domain, coronavirus ...Non-structural protein 5, deltacoronavirus / Nonstructural protein 14, deltacoronavirus / Nonstructural protein 15, middle domain, deltacoronavirus / Nonstructural protein 15, N-terminal, deltacoronavirus / RNA-dependent RNA polymerase, deltacoronavirus / Non-structural protein 6, deltacoronavirus / Non-structural protein 2, IBV-like / AAA domain / NSP15, NendoU domain, coronavirus / NSP14, guanine-N7-methyltransferase domain, coronavirus / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / NSP12 RNA-dependent RNA polymerase, coronavirus / : / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Coronavirus Nsp12 Interface domain profile. / : / : / Coronavirus Nonstructural protein 13, 1B domain / Coronavirus Non-structural protein 13, zinc-binding domain / Coronavirus Nonstructural protein 13, stalk domain / Nidovirus 2-O-methyltransferase / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / Non-structural protein NSP15, N-terminal domain superfamily, coronavirus / Non-structural protein NSP15, middle domain superfamily / Coronavirus replicase NSP15, N-terminal oligomerization / Nonstructural protein 15, middle domain, coronavirus / Nonstructural protein 13, 1B domain, coronavirus / Coronavirus replicase NSP15, middle domain / Coronavirus replicase NSP15, N-terminal oligomerisation / Nidovirus 3'-5' exoribonuclease domain / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / Non-structural protein NSP16, coronavirus-like / Non-structural protein 14, coronavirus / RNA polymerase, N-terminal, coronavirus / Coronavirus 2'-O-methyltransferase / Coronavirus proofreading exoribonuclease / Coronavirus RNA-dependent RNA polymerase, N-terminal / Nonstructural protein 13, zinc-binding domain, coronavirus-like / Coronaviridae zinc-binding (CV ZBD) domain profile. / Arterivirus Nsp11 N-terminal/Coronavirus NSP15 middle domain / Arterivirus Nsp11 N-terminal/coronavirus NSP15 middle (AV-Nsp11N/CoV-Nsp15M) domain profile. / Nidoviral uridylate-specific endoribonuclease (NendoU) domain profile. / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain profile. / Endoribonuclease EndoU-like / NendoU domain, nidovirus / Coronavirus replicase NSP15, uridylate-specific endoribonuclease / : / DNA2/NAM7 helicase-like, C-terminal / AAA domain / (+) RNA virus helicase core domain / (+)RNA virus helicase core domain profile. / : / : / Coronavirus 3Ecto domain profile. / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp7 cofactor domain profile. / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp8 cofactor domain profile. / Coronavirus Nsp9 single-stranded RNA (ssRNA)-binding domain profile. / Coronavirus (CoV) ExoN/MTase coactivator domain profile. / Coronavirus (CoV) Nsp3 Y domain profile. / Coronavirus Nsp4 C-terminal (Nsp4C) domain profile. / Coronavirus main protease (M-pro) domain profile. / Peptidase C30, coronavirus / Peptidase C16, coronavirus / Non-structural protein NSP9, coronavirus / Non-structural protein NSP7, coronavirus / Non-structural protein NSP8, coronavirus / RNA synthesis protein NSP10, coronavirus / Non-structural protein NSP4, C-terminal, coronavirus / RNA synthesis protein NSP10 superfamily, coronavirus / Non-structural protein NSP9 superfamily, coronavirus / Non-structural protein NSP7 superfamily, coronavirus / Non-structural protein NSP8 superfamily, coronavirus / Non-structural protein NSP4, C-terminal superfamily, coronavirus / Papain-like protease, thumb domain superfamily, coronavirus / Peptidase C30, domain 3, coronavirus / Non-structural protein 6, coronavirus / Coronavirus replicase NSP3, C-terminal / Non-structural protein NSP4, N-terminal, coronavirus / Coronavirus endopeptidase C30 / Coronavirus papain-like peptidase / Coronavirus replicase NSP8 / Coronavirus RNA synthesis protein NSP10 / Coronavirus replicase NSP4, C-terminal / Coronavirus replicase NSP6 / Coronavirus replicase NSP4, N-terminal / Coronavirus replicase NSP3, C-terminal / Coronavirus replicase NSP9 / Non-structural protein 3, X-domain-like / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain / Macro domain-like / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
Biological speciesPorcine deltacoronavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.55 Å
AuthorsZhang, Z.T. / Liang, R. / Zhang, J.T. / Zhang, D. / Shi, Y.J. / Peng, G.Q.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Structure of the C-terminal domain of nsp4 from PDCOV
Authors: Zhang, Z.T. / Liang, R. / Zhang, J.T. / Zhang, D. / Shi, Y.J. / Peng, G.Q.
History
DepositionMay 7, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 21, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: ORF1ab polyprotein
A: ORF1ab polyprotein


Theoretical massNumber of molelcules
Total (without water)24,8202
Polymers24,8202
Non-polymers00
Water1,56787
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1610 Å2
ΔGint-9 kcal/mol
Surface area8550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.320, 88.320, 71.130
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein ORF1ab polyprotein


Mass: 12410.102 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porcine deltacoronavirus / Production host: Escherichia coli (E. coli) / References: UniProt: A0A8E8PIM9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 3.23 Å3/Da / Density % sol: 61.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 2.0 M Sodium chloride,10% w/v Polyethylene glycol 6,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Apr 1, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.55→32.25 Å / Num. obs: 10339 / % possible obs: 99.5 % / Redundancy: 19.1 % / Rmerge(I) obs: 0.108 / Net I/σ(I): 22.5
Reflection shellResolution: 2.55→2.66 Å / Rmerge(I) obs: 0.541 / Num. unique obs: 1250

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
autoPROCdata reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.55→32.25 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.41 / Phase error: 33.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.297 534 5.17 %
Rwork0.2312 --
obs0.2345 10324 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.55→32.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1274 0 0 87 1361
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081304
X-RAY DIFFRACTIONf_angle_d1.7211756
X-RAY DIFFRACTIONf_dihedral_angle_d17.635464
X-RAY DIFFRACTIONf_chiral_restr0.06184
X-RAY DIFFRACTIONf_plane_restr0.006224
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.810.35941590.29332386X-RAY DIFFRACTION99
2.81-3.210.36081300.23782436X-RAY DIFFRACTION99
3.21-4.040.27461130.24422472X-RAY DIFFRACTION100
4.05-8.30.27181320.2092496X-RAY DIFFRACTION100

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