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- PDB-6l5t: The crystal structure of SADS-CoV Papain Like protease -

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Basic information

Entry
Database: PDB / ID: 6l5t
TitleThe crystal structure of SADS-CoV Papain Like protease
ComponentsPeptidase C16
KeywordsHYDROLASE / Protease
Function / homology
Function and homology information


RNA exonuclease activity / host cell membrane / endoplasmic reticulum-Golgi intermediate compartment / DNA helicase activity / methyltransferase activity / methylation / 3'-5'-RNA exonuclease activity / host cell endoplasmic reticulum-Golgi intermediate compartment / omega peptidase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity ...RNA exonuclease activity / host cell membrane / endoplasmic reticulum-Golgi intermediate compartment / DNA helicase activity / methyltransferase activity / methylation / 3'-5'-RNA exonuclease activity / host cell endoplasmic reticulum-Golgi intermediate compartment / omega peptidase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / symbiont-mediated perturbation of host ubiquitin-like protein modification / mRNA (nucleoside-2'-O-)-methyltransferase activity / endonuclease activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / DNA helicase / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / RNA helicase activity / membrane => GO:0016020 / host cell perinuclear region of cytoplasm / viral protein processing / lyase activity / RNA helicase / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane / identical protein binding
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 / NSP15, NendoU domain, coronavirus / 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 ...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 / NSP15, NendoU domain, coronavirus / 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 / (+) RNA virus helicase core domain / (+)RNA virus helicase core domain profile. / Papain-like viral protease, palm and finger domains, coronavirus / NSP1, globular domain, alpha/betacoronavirus / 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 / Coronavirus RNA synthesis protein NSP10 / Coronavirus replicase NSP4, C-terminal / Coronavirus replicase NSP6 / Coronavirus replicase NSP4, N-terminal / Coronavirus replicase NSP3, C-terminal / Coronavirus main protease (M-pro) domain profile. / Coronavirus replicase NSP9 / Non-structural protein 3, X-domain-like / Macro domain / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / 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 / ATPases associated with a variety of cellular activities / AAA+ ATPase domain
Similarity search - Domain/homology
Replicase polyprotein 1ab / 3C-like proteinase
Similarity search - Component
Biological speciesSwine acute diarrhea syndrome coronavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.72 Å
AuthorsFan, C.P.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31500150 China
CitationJournal: Protein Sci. / Year: 2020
Title: Structural and biochemical characterization of SADS-CoV papain-like protease 2.
Authors: Wang, L. / Hu, W. / Fan, C.
History
DepositionOct 24, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 8, 2020Provider: repository / Type: Initial release
Revision 1.1May 13, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Mar 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: Peptidase C16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6172
Polymers31,5511
Non-polymers651
Water3,603200
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11560 Å2
Unit cell
Length a, b, c (Å)34.231, 68.511, 104.350
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 Peptidase C16 / Papain Like protease


Mass: 31551.348 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Swine acute diarrhea syndrome coronavirus
Gene: orf1ab, ORF1ab / Plasmid: pET28a-SUMO / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2P1G738, UniProt: A0A385H8D7*PLUS
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 200 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.94 Å3/Da / Density % sol: 36.57 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1M MES (PH6.5), 0.1M CaCl2, 16% PEG 20000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.72→41.51 Å / Num. obs: 26961 / % possible obs: 100 % / Redundancy: 12.8 % / Biso Wilson estimate: 21.82 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.034 / Rrim(I) all: 0.121 / Rsym value: 0.116 / Net I/σ(I): 16.7
Reflection shellResolution: 1.72→1.72 Å / Redundancy: 12.5 % / Rmerge(I) obs: 1.636 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1362 / CC1/2: 0.623 / Rpim(I) all: 0.663 / Rrim(I) all: 1.705 / Rsym value: 1.636 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
XDSdata reduction
Aimlessdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.72→34.26 Å / SU ML: 0.1817 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.2846
RfactorNum. reflection% reflection
Rfree0.2116 1345 5 %
Rwork0.1793 --
obs0.1809 26899 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 27.11 Å2
Refinement stepCycle: LAST / Resolution: 1.72→34.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1799 0 1 200 2000
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01271840
X-RAY DIFFRACTIONf_angle_d1.13012500
X-RAY DIFFRACTIONf_chiral_restr0.0778285
X-RAY DIFFRACTIONf_plane_restr0.0076315
X-RAY DIFFRACTIONf_dihedral_angle_d3.60181054
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.72-1.780.31751310.25392493X-RAY DIFFRACTION99.66
1.78-1.850.24161320.22882489X-RAY DIFFRACTION100
1.85-1.940.27111320.21772518X-RAY DIFFRACTION100
1.94-2.040.24361320.19562528X-RAY DIFFRACTION100
2.04-2.170.22041340.18692528X-RAY DIFFRACTION99.96
2.17-2.330.22071340.17662536X-RAY DIFFRACTION100
2.33-2.570.22821340.18822553X-RAY DIFFRACTION100
2.57-2.940.22861350.18142574X-RAY DIFFRACTION100
2.94-3.70.1821370.16242588X-RAY DIFFRACTION100
3.7-34.260.18491440.16312747X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 28.9797185354 Å / Origin y: 38.6282965119 Å / Origin z: 35.8902317801 Å
111213212223313233
T0.14689788147 Å20.00233483280092 Å20.00692531415688 Å2-0.182598228958 Å2-0.0317975909633 Å2--0.150952116393 Å2
L0.605072406305 °20.334502110905 °20.192672938422 °2-0.767937586426 °2-0.0798804438307 °2--0.355079221131 °2
S0.0530115952645 Å °-0.110554204625 Å °0.0279530313623 Å °0.0835981032732 Å °-0.111812560845 Å °0.0331181053259 Å °-0.0450296039487 Å °-0.0391741648642 Å °0.0669734176709 Å °
Refinement TLS groupSelection details: all

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