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- PDB-7wfc: X-ray structure of HKU1-PLP2(Cys109Ser) catalytic mutant in compl... -

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Basic information

Entry
Database: PDB / ID: 7wfc
TitleX-ray structure of HKU1-PLP2(Cys109Ser) catalytic mutant in complex with free ubiquitin
Components
  • 60S ribosomal protein L40
  • Papain-like protease
KeywordsHYDROLASE / HKU1-PLP2-Ub complex
Function / homology
Function and homology information


: / endoplasmic reticulum-Golgi intermediate compartment / host cell membrane / viral genome replication / symbiont-mediated suppression of host gene expression / host cell endoplasmic reticulum-Golgi intermediate compartment / 3'-5'-RNA exonuclease activity / symbiont-mediated degradation of host mRNA / symbiont-mediated suppression of host ISG15-protein conjugation / omega peptidase activity ...: / endoplasmic reticulum-Golgi intermediate compartment / host cell membrane / viral genome replication / symbiont-mediated suppression of host gene expression / host cell endoplasmic reticulum-Golgi intermediate compartment / 3'-5'-RNA exonuclease activity / symbiont-mediated degradation of host mRNA / symbiont-mediated suppression of host ISG15-protein conjugation / omega peptidase activity / symbiont-mediated perturbation of host ubiquitin-like protein modification / endonuclease activity / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / cysteine-type deubiquitinase activity / RNA helicase activity / single-stranded RNA binding / host cell perinuclear region of cytoplasm / viral protein processing / lyase activity / ribosome / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / structural constituent of ribosome / ribonucleoprotein complex / induction by virus of host autophagy / translation / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / proteolysis / zinc ion binding / ATP binding / membrane / nucleus / cytoplasm
Similarity search - Function
RNA-dependent RNA polymerase, coronavirus HKU1-like / Non-structural protein 2, MHV-like / Peptidase C30/C16, Betacoronavirus / Betacoronavirus, lineage A, NSP1 / Peptidase C16 family / Betacoronavirus, lineage A, NSP1 / Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily ...RNA-dependent RNA polymerase, coronavirus HKU1-like / Non-structural protein 2, MHV-like / Peptidase C30/C16, Betacoronavirus / Betacoronavirus, lineage A, NSP1 / Peptidase C16 family / Betacoronavirus, lineage A, NSP1 / Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Nonstructural protein 14, betacoronavirus / NSP15, NendoU domain, coronavirus / Nonstructural protein 15, middle domain, alpha/betacoronavirus / 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 / Ubiquitin homologues / DNA2/NAM7 helicase-like, C-terminal / AAA domain / Ubiquitin domain profile. / Ubiquitin-like domain / (+) RNA virus helicase core domain / (+)RNA virus helicase core domain profile. / NSP1, C-terminal domain, betacoronavirus / Betacoronavirus (BetaCoV) Nsp1 C-terminal domain profile. / Betacoronavirus Nsp3c-C domain profile. / Betacoronavirus Nsp3e nucleic acid-binding (NAB) domain profile. / DPUP/SUD, C-terminal, betacoronavirus / Non-structural protein NSP3, nucleic acid-binding domain superfamily, betacoronavirus / Non-structural protein 6, betacoronavirus / Betacoronavirus nucleic acid-binding (NAB) / Non-structural protein NSP3, nucleic acid-binding domain, betacoronavirus / Non-structural protein NSP3A domain-like superfamily / Papain-like protease, N-terminal domain superfamily, coronavirus / Papain-like viral protease, palm and finger domains, coronavirus / NSP1, globular domain, alpha/betacoronavirus / Coronavirus (CoV) Nsp1 globular domain profile. / 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
Similarity search - Domain/homology
Ubiquitin-60S ribosomal protein L40 / Replicase polyprotein 1ab
Similarity search - Component
Biological speciesHuman coronavirus HKU1
Homo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsXiong, Y.X. / Fu, Z.Y. / Huang, H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Sci.Signal. / Year: 2023
Title: The substrate selectivity of papain-like proteases from human-infecting coronaviruses correlates with innate immune suppression.
Authors: Xiong, Y. / Huang, B. / Yang, Y. / Fu, X. / Fu, Z. / Xu, H. / Liu, M. / Cao, D. / Zhang, M. / Yang, H. / Niu, X. / Yu, C. / Huang, H.
History
DepositionDec 26, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 28, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 12, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Papain-like protease
B: 60S ribosomal protein L40
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7274
Polymers43,5992
Non-polymers1272
Water3,513195
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2520 Å2
ΔGint-0 kcal/mol
Surface area17540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.342, 73.659, 96.756
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
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 Papain-like protease


Mass: 34550.734 Da / Num. of mol.: 1 / Mutation: C109S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human coronavirus HKU1 / Gene: 1a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: U3N841
#2: Protein 60S ribosomal protein L40 / CEP52 / Ubiquitin / Ubiquitin A-52 residue ribosomal protein fusion product 1 / Ubiquitin-60S ...CEP52 / Ubiquitin / Ubiquitin A-52 residue ribosomal protein fusion product 1 / Ubiquitin-60S ribosomal protein L40


Mass: 9048.358 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TREES_T100014679 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: L9KW39
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / 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: 2.92 Å3/Da / Density % sol: 57.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 1.1 M Ammonium tartrate dibasic, pH 7.0 / PH range: 6.5-7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Dec 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.6→22.75 Å / Num. obs: 16147 / % possible obs: 99.31 % / Redundancy: 3.7 % / Biso Wilson estimate: 23.11 Å2 / CC1/2: 0.993 / CC star: 0.998 / Rmerge(I) obs: 0.09198 / Rpim(I) all: 0.05386 / Rrim(I) all: 0.1073 / Net I/σ(I): 11.77
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.288 / Mean I/σ(I) obs: 4.2 / Num. unique obs: 8987 / CC1/2: 0.931 / Rpim(I) all: 0.166 / Rrim(I) all: 0.334 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
SCALAdata scaling
PDB_EXTRACT3.27data extraction
CrysalisProdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5WFI

5wfi


Resolution: 2.6→22.75 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2511 782 4.85 %
Rwork0.1711 15357 -
obs0.1749 16139 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 105.47 Å2 / Biso mean: 22.6006 Å2 / Biso min: 3.38 Å2
Refinement stepCycle: final / Resolution: 2.6→22.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3057 0 5 195 3257
Biso mean--21 22.09 -
Num. residues----390
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6-2.760.31841510.2092507265899
2.76-2.980.28951230.206225092632100
2.98-3.270.26741170.183625542671100
3.27-3.750.29311170.168325702687100
3.75-4.710.21531490.148425492698100
4.71-22.750.19551250.1552668279398

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