[English] 日本語
Yorodumi
- PDB-5nfy: SARS-CoV nsp10/nsp14 dynamic complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5nfy
TitleSARS-CoV nsp10/nsp14 dynamic complex
Components(Polyprotein 1ab) x 2
KeywordsTRANSFERASE / exonuclease / methyltransferase / dynamic / RNA-proofreading
Function / homology
Function and homology information


RNA exonuclease activity / : / Assembly of the SARS-CoV-1 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / Transcription of SARS-CoV-1 sgRNAs / Translation of Replicase and Assembly of the Replication Transcription Complex / K48-linked deubiquitinase activity / Replication of the SARS-CoV-1 genome / host cell endoplasmic reticulum / K63-linked deubiquitinase activity ...RNA exonuclease activity / : / Assembly of the SARS-CoV-1 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / Transcription of SARS-CoV-1 sgRNAs / Translation of Replicase and Assembly of the Replication Transcription Complex / K48-linked deubiquitinase activity / Replication of the SARS-CoV-1 genome / host cell endoplasmic reticulum / K63-linked deubiquitinase activity / SARS-CoV-1 modulates host translation machinery / viral transcription / endoplasmic reticulum-Golgi intermediate compartment / host cell membrane / DNA helicase activity / Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity / SARS-CoV-1 activates/modulates innate immune responses / 5'-3' RNA helicase activity / Lyases; Phosphorus-oxygen lyases / double membrane vesicle viral factory outer membrane / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 5'-3' DNA helicase activity / SARS coronavirus main proteinase / host cell endosome / host cell endoplasmic reticulum-Golgi intermediate compartment / 3'-5'-RNA exonuclease activity / symbiont-mediated degradation of host mRNA / mRNA guanylyltransferase / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / omega peptidase activity / methylation / mRNA (guanine-N7)-methyltransferase / host cell Golgi apparatus / methyltransferase cap1 / 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 / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / RNA helicase activity / single-stranded RNA binding / host cell perinuclear region of cytoplasm / viral protein processing / lyase activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / 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 / virus-mediated perturbation of host defense response / DNA-templated transcription / ATP hydrolysis activity / proteolysis / zinc ion binding / ATP binding / identical protein binding / membrane
Similarity search - Function
Non-structural protein 3, SUD-N macrodomain, SARS-CoV / Viral (Superfamily 1) RNA helicase / RNA-dependent RNA polymerase, SARS-CoV-like / Nonstructural protein 14, betacoronavirus / NSP15, NendoU domain, coronavirus / : / : / Coronavirus Nonstructural protein 13, 1B domain / Coronavirus Non-structural protein 13, zinc-binding domain / Coronavirus Nonstructural protein 13, stalk domain ...Non-structural protein 3, SUD-N macrodomain, SARS-CoV / Viral (Superfamily 1) RNA helicase / RNA-dependent RNA polymerase, SARS-CoV-like / Nonstructural protein 14, betacoronavirus / 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. / Non-structural protein NSP3, SUD-N (Mac2) domain, betacoronavirus / Sarbecovirus Nsp3c-N domain profile. / Non-structural protein NSP3, N-terminal, betacoronavirus / Polyprotein cleavage domain PL2pro superfamily, betacoronavirus / Non-structural protein NSP3, SUD-N (Mac2) domain superfamily, betacoronavirus / Betacoronavirus SUD-C domain / Betacoronavirus replicase NSP3, N-terminal / NSP1 globular domain superfamily, betacoronavirus / Non-structural protein 2, SARS-CoV-like / : / Betacoronavirus Nsp3e group 2-specific marker (G2M) domain profile. / NSP1, C-terminal domain, betacoronavirus / Betacoronavirus Nsp3c-M domain profile. / NSP1, globular domain, betacoronavirus / Non-structural protein NSP3, SUD-M domain, betacoronavirus / Non-structural protein NSP3, SUD-M domain superfamily, betacoronavirus / Betacoronavirus replicase NSP1 / Betacoronavirus single-stranded poly(A) binding domain / 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 / : / 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
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Replicase polyprotein 1ab / 2'-O-methyltransferase
Similarity search - Component
Biological speciesSARS coronavirus Frankfurt 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.382 Å
AuthorsFerron, F. / Gluais, L. / Vonrhein, C. / Bricogne, G. / Canard, B. / Imbert, I.
Funding support France, 1items
OrganizationGrant numberCountry
European Uniongrant agreement 260644 France
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Structural and molecular basis of mismatch correction and ribavirin excision from coronavirus RNA.
Authors: Ferron, F. / Subissi, L. / Silveira De Morais, A.T. / Le, N.T.T. / Sevajol, M. / Gluais, L. / Decroly, E. / Vonrhein, C. / Bricogne, G. / Canard, B. / Imbert, I.
History
DepositionMar 16, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 10, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Feb 20, 2019Group: Advisory / Data collection / Derived calculations
Category: pdbx_data_processing_status / pdbx_validate_close_contact ...pdbx_data_processing_status / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_conn / struct_conn_type

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Polyprotein 1ab
B: Polyprotein 1ab
C: Polyprotein 1ab
D: Polyprotein 1ab
M: Polyprotein 1ab
N: Polyprotein 1ab
O: Polyprotein 1ab
P: Polyprotein 1ab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)304,66431
Polymers303,0388
Non-polymers1,62723
Water4,396244
1
A: Polyprotein 1ab
M: Polyprotein 1ab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,2999
Polymers75,7592
Non-polymers5397
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4440 Å2
ΔGint-27 kcal/mol
Surface area29250 Å2
MethodPISA
2
B: Polyprotein 1ab
N: Polyprotein 1ab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,0867
Polymers75,7592
Non-polymers3275
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4540 Å2
ΔGint-28 kcal/mol
Surface area29990 Å2
MethodPISA
3
C: Polyprotein 1ab
P: Polyprotein 1ab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,1938
Polymers75,7592
Non-polymers4336
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5060 Å2
ΔGint-22 kcal/mol
Surface area29950 Å2
MethodPISA
4
D: Polyprotein 1ab
O: Polyprotein 1ab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,0867
Polymers75,7592
Non-polymers3275
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4710 Å2
ΔGint-104 kcal/mol
Surface area30160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)185.881, 189.786, 196.245
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein
Polyprotein 1ab


Mass: 60939.539 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SARS coronavirus Frankfurt 1 / Plasmid: pDEST14 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q1T6X8
#2: Protein
Polyprotein 1ab


Mass: 14819.863 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SARS coronavirus Frankfurt 1 / Plasmid: pDEST14 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q1T6X8, UniProt: P0C6X7*PLUS
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 244 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 5.94 Å3/Da / Density % sol: 79.29 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1M Sodium citrate tribasic pH5.5; 8%PEG 8000; 30% Hexandiol

-
Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.28348 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 4, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28348 Å / Relative weight: 1
ReflectionResolution: 3.382→94.893 Å / Num. obs: 97097 / % possible obs: 99.6 % / Redundancy: 9 % / CC1/2: 0.988 / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.046 / Net I/σ(I): 15.1
Reflection shellResolution: 3.382→3.393 Å / Redundancy: 9.3 % / Rmerge(I) obs: 1.139 / Mean I/σ(I) obs: 2 / Num. unique obs: 968 / CC1/2: 0.681 / Rpim(I) all: 0.395 / % possible all: 98.6

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
AutoPROC1.0.5data collection
autoSHARPphasing
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MAD / Resolution: 3.382→66.398 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2349 4907 5.06 %
Rwork0.1926 --
obs0.1947 96949 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.382→66.398 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20340 0 41 244 20625
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01620920
X-RAY DIFFRACTIONf_angle_d1.97828422
X-RAY DIFFRACTIONf_dihedral_angle_d11.3727448
X-RAY DIFFRACTIONf_chiral_restr0.13081
X-RAY DIFFRACTIONf_plane_restr0.0173658
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3816-3.420.36561750.31953013X-RAY DIFFRACTION100
3.42-3.46030.32841590.29223064X-RAY DIFFRACTION100
3.4603-3.50250.32161950.27013035X-RAY DIFFRACTION100
3.5025-3.54680.29891640.25022992X-RAY DIFFRACTION100
3.5468-3.59350.28381690.2423050X-RAY DIFFRACTION100
3.5935-3.64270.28031580.24213075X-RAY DIFFRACTION100
3.6427-3.69470.27071590.23843051X-RAY DIFFRACTION100
3.6947-3.74990.27131820.2363032X-RAY DIFFRACTION100
3.7499-3.80840.27931600.23293054X-RAY DIFFRACTION100
3.8084-3.87090.27641500.22813053X-RAY DIFFRACTION100
3.8709-3.93760.2671280.21412701X-RAY DIFFRACTION88
3.9376-4.00920.23381590.19823069X-RAY DIFFRACTION100
4.0092-4.08630.25141430.19433101X-RAY DIFFRACTION100
4.0863-4.16970.25091520.18823045X-RAY DIFFRACTION100
4.1697-4.26040.25681700.18543065X-RAY DIFFRACTION100
4.2604-4.35940.22811360.17543111X-RAY DIFFRACTION100
4.3594-4.46840.21811440.16653065X-RAY DIFFRACTION100
4.4684-4.58920.20521630.16623086X-RAY DIFFRACTION100
4.5892-4.72420.24431590.16783060X-RAY DIFFRACTION100
4.7242-4.87670.20181770.16383074X-RAY DIFFRACTION100
4.8767-5.05090.21251600.16183085X-RAY DIFFRACTION100
5.0509-5.25310.21241340.15653119X-RAY DIFFRACTION100
5.2531-5.4920.18961480.16343126X-RAY DIFFRACTION100
5.492-5.78140.22291840.16883080X-RAY DIFFRACTION100
5.7814-6.14340.22641740.1683087X-RAY DIFFRACTION100
6.1434-6.61740.21291840.16853092X-RAY DIFFRACTION100
6.6174-7.28250.21431650.17243127X-RAY DIFFRACTION100
7.2825-8.33460.22251570.17053152X-RAY DIFFRACTION100
8.3346-10.4940.18212130.16363134X-RAY DIFFRACTION100
10.494-66.41120.25511860.24833244X-RAY DIFFRACTION98

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more