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- PDB-5xbc: Crystal Structure Basis for PEDV nsp1 -

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Basic information

Entry
Database: PDB / ID: 5xbc
TitleCrystal Structure Basis for PEDV nsp1
Componentsnsp1 protein
KeywordsHYDROLASE / Porcine epidemic diarrhea virus / nsp1
Function / homology
Function and homology information


exonuclease activity / endoplasmic reticulum-Golgi intermediate compartment / host cell membrane / DNA helicase activity / viral genome replication / methyltransferase activity / 5'-3' DNA helicase activity / host cell endoplasmic reticulum-Golgi intermediate compartment / 3'-5'-RNA exonuclease activity / omega peptidase activity ...exonuclease activity / endoplasmic reticulum-Golgi intermediate compartment / host cell membrane / DNA helicase activity / viral genome replication / methyltransferase activity / 5'-3' DNA helicase activity / host cell endoplasmic reticulum-Golgi intermediate compartment / 3'-5'-RNA exonuclease activity / omega peptidase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / methylation / symbiont-mediated perturbation of host ubiquitin-like protein modification / endonuclease activity / mRNA (nucleoside-2'-O-)-methyltransferase activity / DNA helicase / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / membrane => GO:0016020 / RNA helicase activity / host cell perinuclear region of cytoplasm / viral protein processing / lyase activity / RNA helicase / induction by virus of host autophagy / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / DNA-templated transcription / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane
Similarity search - Function
: / Nonstructural protein 14, alphacoronavirus / RNA-dependent RNA polymerase, alphacoronavirus / Non-structural protein 5, alphacoronavirus / Non-structural protein 6, alphacoronavirus / Nonstructural protein 2, HCoV-229E-like / AAA domain / Pectin lyase fold/virulence factor / NSP15, NendoU domain, coronavirus / : ...: / Nonstructural protein 14, alphacoronavirus / RNA-dependent RNA polymerase, alphacoronavirus / Non-structural protein 5, alphacoronavirus / Non-structural protein 6, alphacoronavirus / Nonstructural protein 2, HCoV-229E-like / AAA domain / Pectin lyase fold/virulence factor / NSP15, NendoU domain, coronavirus / : / : / Coronavirus Nonstructural protein 13, 1B domain / Coronavirus Non-structural protein 13, zinc-binding domain / Coronavirus Nonstructural protein 13, stalk domain / : / Coronavirus Nsp12 Interface domain profile. / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Nonstructural protein 15, N-terminal domain, alpha/beta-coronavirus / NSP14, guanine-N7-methyltransferase domain, coronavirus / NSP12 RNA-dependent RNA polymerase, coronavirus / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / Nidovirus 2-O-methyltransferase / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Nidovirus 3'-5' exoribonuclease domain / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / Nonstructural protein 13, 1B domain, coronavirus / Arterivirus Nsp11 N-terminal/Coronavirus NSP15 middle domain / 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 / Coronavirus replicase NSP15, middle domain / Coronavirus replicase NSP15, N-terminal oligomerisation / Arterivirus Nsp11 N-terminal/coronavirus NSP15 middle (AV-Nsp11N/CoV-Nsp15M) 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 / Nidoviral uridylate-specific endoribonuclease (NendoU) domain profile. / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain / Nonstructural protein 13, zinc-binding domain, coronavirus-like / Coronaviridae zinc-binding (CV ZBD) domain profile. / 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. / Papain-like viral protease, palm and finger domains, coronavirus / : / Coronavirus 3Ecto domain profile. / : / Coronavirus (CoV) Nsp2 middle domain profile. / Coronavirus (CoV) Nsp2 N-terminal domain profile. / Coronavirus (CoV) Nsp2 C-terminal domain profile. / NSP1, globular domain, alpha/betacoronavirus / : / Coronavirus (CoV) Nsp3 Y domain profile. / Coronavirus (CoV) Nsp1 globular domain profile. / Coronavirus replicase NSP2, N-terminal / Nonstructural protein 2, N-terminal domain, coronavirus / Coronavirus replicase NSP2, C-terminal / Non-structural protein 2, C-terminal domain, coronavirus / Coronavirus Nsp3a Ubl domain profile. / Coronavirus Nsp3d Ubl 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. / NSP3, first ubiquitin-like (Ubl) domain, coronavirus / NSP3, second ubiquitin-like (Ubl) domain, coronavirus / Coronavirus Nsp4 C-terminal (Nsp4C) domain profile. / Papain-like protease, thumb domain superfamily, coronavirus / Coronavirus replicase NSP7 / Peptidase family C16 domain profile. / Non-structural protein NSP7, coronavirus / Peptidase C30, coronavirus / Peptidase C16, coronavirus / Non-structural protein NSP9, 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 / 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
Similarity search - Domain/homology
3C-like proteinase / ORF1ab polyprotein
Similarity search - Component
Biological speciesPorcine epidemic diarrhea virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.249 Å
AuthorsShen, Z. / Peng, G.Q.
CitationJournal: To Be Published
Title: Crystal Structure Basis for PEDV nsp1
Authors: Shen, Z. / Peng, G.Q.
History
DepositionMar 16, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 13, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: nsp1 protein
B: nsp1 protein


Theoretical massNumber of molelcules
Total (without water)26,2312
Polymers26,2312
Non-polymers00
Water6,269348
1
A: nsp1 protein


Theoretical massNumber of molelcules
Total (without water)13,1161
Polymers13,1161
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: nsp1 protein


Theoretical massNumber of molelcules
Total (without water)13,1161
Polymers13,1161
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.709, 75.053, 37.363
Angle α, β, γ (deg.)90.00, 89.96, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein nsp1 protein


Mass: 13115.570 Da / Num. of mol.: 2 / Fragment: UNP residues 2-110
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porcine epidemic diarrhea virus / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: A0A1N7TG28, UniProt: K4L9I6*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 348 / Source method: isolated from a natural source / Formula: H2O

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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: 1.86 Å3/Da / Density % sol: 33.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M Lithium sulfate monohydrate, 0.1 M Sodium citrate tribasic dihydrate pH 5.5, 18% w/v Polyethylene glycol 1,000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97917 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97917 Å / Relative weight: 1
ReflectionResolution: 1.25→37.53 Å / Num. obs: 52517 / % possible obs: 99.3 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.029 / Rrim(I) all: 0.057 / Χ2: 1.379 / Net I/σ(I): 13.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.25-1.293.80.4360.8750.2580.5091.1699.2
1.29-1.353.90.3520.9230.2070.411.20299.4
1.35-1.413.90.2650.9470.1560.3081.30899.7
1.41-1.483.90.1860.9750.1090.2161.40999.7
1.48-1.573.90.1380.9830.0810.1611.44799.7
1.57-1.740.0950.9920.0550.111.4699.7
1.7-1.8740.0680.9950.0390.0791.33699.8
1.87-2.1440.0580.9950.0330.0671.48599.5
2.14-2.6940.050.9960.0290.0571.44199.6
2.69-5040.0330.9980.0180.0381.51496.2

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data scaling
PDB_EXTRACT3.22data extraction
HKLdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.249→26.477 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.193 2681 5.11 %RANDOM
Rwork0.1708 ---
obs0.1719 52517 99.22 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.249→26.477 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1836 0 0 348 2184
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061885
X-RAY DIFFRACTIONf_angle_d0.9912557
X-RAY DIFFRACTIONf_dihedral_angle_d14.161633
X-RAY DIFFRACTIONf_chiral_restr0.041275
X-RAY DIFFRACTIONf_plane_restr0.005334
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.249-1.27170.25681410.24542556X-RAY DIFFRACTION99
1.2717-1.29620.25511720.23672615X-RAY DIFFRACTION99
1.2962-1.32260.24651510.22352571X-RAY DIFFRACTION100
1.3226-1.35140.22731680.20842612X-RAY DIFFRACTION99
1.3514-1.38280.24881550.19852632X-RAY DIFFRACTION100
1.3828-1.41740.21691060.1822649X-RAY DIFFRACTION100
1.4174-1.45570.21891290.17822645X-RAY DIFFRACTION100
1.4557-1.49860.23571130.17262678X-RAY DIFFRACTION100
1.4986-1.54690.23551250.16912633X-RAY DIFFRACTION100
1.5469-1.60220.1741270.16452645X-RAY DIFFRACTION100
1.6022-1.66630.19821350.16352614X-RAY DIFFRACTION100
1.6663-1.74220.19221380.15692662X-RAY DIFFRACTION100
1.7422-1.8340.17791760.16192611X-RAY DIFFRACTION100
1.834-1.94890.18571410.15582623X-RAY DIFFRACTION100
1.9489-2.09930.16851290.15882636X-RAY DIFFRACTION99
2.0993-2.31040.1681350.16682669X-RAY DIFFRACTION100
2.3104-2.64450.19351370.18232645X-RAY DIFFRACTION100
2.6445-3.33070.19061620.16662618X-RAY DIFFRACTION100
3.3307-26.48320.18651410.16352522X-RAY DIFFRACTION93

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