[English] 日本語
Yorodumi
- EMDB-22160: Structure of SARS-CoV-2 replication-transcription complex bound t... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-22160
TitleStructure of SARS-CoV-2 replication-transcription complex bound to nsp13 helicase - nsp13(2)-RTC
Map data
SampleSARS-CoV-2 replication/transcription complex bound to nsp13 helicase - nsp13(2)-RTC:
nsp12 / nsp8 / nsp7 / nsp13 / (nucleic-acidNucleic acid) x 2 / (ligand) x 5
Function / homology
Function and homology information


SARS coronavirus main proteinase / induction by virus of catabolism of host mRNA / suppression by virus of host ISG15 activity / exonuclease activity / host cell endoplasmic reticulum-Golgi intermediate compartment / suppression by virus of host NF-kappaB transcription factor activity / modulation by virus of host protein ubiquitination / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / go:0036459: / ubiquitinyl hydrolase 1 ...SARS coronavirus main proteinase / induction by virus of catabolism of host mRNA / suppression by virus of host ISG15 activity / exonuclease activity / host cell endoplasmic reticulum-Golgi intermediate compartment / suppression by virus of host NF-kappaB transcription factor activity / modulation by virus of host protein ubiquitination / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / go:0036459: / ubiquitinyl hydrolase 1 / Transferases; Transferring one-carbon groups; Methyltransferases / DNA helicase / DNA helicase activity / methyltransferase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / host cell perinuclear region of cytoplasm / host cell membrane / suppression by virus of host type I interferon-mediated signaling pathway / RNA helicase / methylation / induction by virus of host autophagy / RNA-directed RNA polymerase / endonuclease activity / RNA helicase activity / RNA-directed 5'-3' RNA polymerase activity / Hydrolases; Acting on ester bonds / RNA binding / integral component of membrane / ATP binding / metal ion binding
Peptidase S1, PA clan / Non-structural protein NSP15, coronavirus / Non-structural protein NSP4, C-terminal, coronavirus / S-adenosyl-L-methionine-dependent methyltransferase / Macro domain / Peptidase C30, coronavirus / P-loop containing nucleoside triphosphate hydrolase / Non-structural protein NSP16, coronavirus-like / RNA polymerase, N-terminal, coronaviral / RNA synthesis protein NSP10 superfamily, coronavirus ...Peptidase S1, PA clan / Non-structural protein NSP15, coronavirus / Non-structural protein NSP4, C-terminal, coronavirus / S-adenosyl-L-methionine-dependent methyltransferase / Macro domain / Peptidase C30, coronavirus / P-loop containing nucleoside triphosphate hydrolase / Non-structural protein NSP16, coronavirus-like / RNA polymerase, N-terminal, coronaviral / RNA synthesis protein NSP10 superfamily, coronavirus / Non-structural protein NSP9, coronavirus / in:ipr014827: / Non-structural protein NSP7, coronavirus / Non-structural protein NSP8, coronavirus-like / RNA synthesis protein NSP10, coronavirus / Non-structural protein NSP1, betacoronavirus / DPUP/SUD, C-terminal, betacoronavirus / Non-structural protein NSP3, single-stranded poly(A) binding domain, betacoronavirus / Non-structural protein NSP3, nucleic acid-binding (NAR) domain, betacoronavirus / Non-structural protein NSP9 superfamily, coronavirus / Non-structural protein NSP4, C-terminal superfamily, coronavirus / Papain-like protease, thumb domain superfamily, coronavirus / Papain-like protease, N-terminal domain superfamily, coronavirus / Non-structural protein NSP15, middle domain superfamily / Replicase polyprotein, nucleic acid-binding domain superfamily / Non-structural protein NSP15, N-terminal domain superfamily, coronavirus / Non-structural protein NSP3, SUD-M domain superfamily, betacoronavirus / Polyprotein cleavage domain PL2pro superfamily, coronavirus / Non-structural protein NSP3A domain-like superfamily / Non-structural protein NSP1 superfamily, betacoronavirus / Non-structural protein NSP8 superfamily, coronavirus / Endoribonuclease EndoU-like / Non-structural protein NSP7 superfamily, coronavirus / Non-structural protein NSP3, N-terminal, betacoronavirus
Replicase polyprotein 1ab
Biological speciesSevere acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsChen J / Malone B / Llewellyn EC / Campbell EA / Darst SA
Funding support United States, 1 items
OrganizationGrant numberCountry
Other private United States
Citation
Journal: bioRxiv / Year: 2020
Title: Structural basis for helicase-polymerase coupling in the SARS-CoV-2 replication-transcription complex.
Authors: James Chen / Brandon Malone / Eliza Llewellyn / Michael Grasso / Patrick M M Shelton / Paul Dominic B Olinares / Kashyap Maruthi / Edward T Eng / Hasan Vatandaslar / Brian Chait / Tarun ...Authors: James Chen / Brandon Malone / Eliza Llewellyn / Michael Grasso / Patrick M M Shelton / Paul Dominic B Olinares / Kashyap Maruthi / Edward T Eng / Hasan Vatandaslar / Brian Chait / Tarun Kapoor / Seth A Darst / Elizabeth A Campbell
Abstract: SARS-CoV-2 is the causative agent of the 2019-2020 pandemic. The SARS-CoV-2 genome is replicated-transcribed by the RNA-dependent RNA polymerase holoenzyme (subunits nsp7/nsp82/nsp12) along with a ...SARS-CoV-2 is the causative agent of the 2019-2020 pandemic. The SARS-CoV-2 genome is replicated-transcribed by the RNA-dependent RNA polymerase holoenzyme (subunits nsp7/nsp82/nsp12) along with a cast of accessory factors. One of these factors is the nsp13 helicase. Both the holo-RdRp and nsp13 are essential for viral replication and are targets for treating the disease COVID-19. Here we present cryo-electron microscopic structures of the SARS-CoV-2 holo-RdRp with an RNA template-product in complex with two molecules of the nsp13 helicase. The Nidovirus-order-specific N-terminal domains of each nsp13 interact with the N-terminal extension of each copy of nsp8. One nsp13 also contacts the nsp12-thumb. The structure places the nucleic acid-binding ATPase domains of the helicase directly in front of the replicating-transcribing holo-RdRp, constraining models for nsp13 function. We also observe ADP-Mg2+ bound in the nsp12 N-terminal nidovirus RdRp-associated nucleotidyltransferase domain, detailing a new pocket for anti-viral therapeutic development.
#1: Journal: bioRxiv / Year: 2020
Title: Structural basis for helicase-polymerase coupling in the SARS-CoV-2 replication-transcription complex.
Authors: James Chen / Brandon Malone / Eliza Llewellyn / Michael Grasso / Patrick M M Shelton / Paul Dominic B Olinares / Kashyap Maruthi / Edward T Eng / Hasan Vatandaslar / Brian Chait / Tarun ...Authors: James Chen / Brandon Malone / Eliza Llewellyn / Michael Grasso / Patrick M M Shelton / Paul Dominic B Olinares / Kashyap Maruthi / Edward T Eng / Hasan Vatandaslar / Brian Chait / Tarun Kapoor / Seth A Darst / Elizabeth A Campbell
Abstract: SARS-CoV-2 is the causative agent of the 2019-2020 pandemic. The SARS-CoV-2 genome is replicated-transcribed by the RNA-dependent RNA polymerase holoenzyme (subunits nsp7/nsp82/nsp12) along with a ...SARS-CoV-2 is the causative agent of the 2019-2020 pandemic. The SARS-CoV-2 genome is replicated-transcribed by the RNA-dependent RNA polymerase holoenzyme (subunits nsp7/nsp82/nsp12) along with a cast of accessory factors. One of these factors is the nsp13 helicase. Both the holo-RdRp and nsp13 are essential for viral replication and are targets for treating the disease COVID-19. Here we present cryo-electron microscopic structures of the SARS-CoV-2 holo-RdRp with an RNA template-product in complex with two molecules of the nsp13 helicase. The Nidovirus-order-specific N-terminal domains of each nsp13 interact with the N-terminal extension of each copy of nsp8. One nsp13 also contacts the nsp12-thumb. The structure places the nucleic acid-binding ATPase domains of the helicase directly in front of the replicating-transcribing holo-RdRp, constraining models for nsp13 function. We also observe ADP-Mg2+ bound in the nsp12 N-terminal nidovirus RdRp-associated nucleotidyltransferase domain, detailing a new pocket for anti-viral therapeutic development.
Validation ReportPDB-ID: 6xez

SummaryFull reportAbout validation report
History
DepositionJun 14, 2020-
Header (metadata) releaseJul 29, 2020-
Map releaseJul 29, 2020-
UpdateAug 5, 2020-
Current statusAug 5, 2020Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.25
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.25
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6xez
  • Surface level: 0.3
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

FileDownload / File: emd_22160.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 320 pix.
= 352. Å
1.1 Å/pix.
x 320 pix.
= 352. Å
1.1 Å/pix.
x 320 pix.
= 352. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density
Contour LevelBy AUTHOR: 0.25 / Movie #1: 0.25
Minimum - Maximum-1.3423268 - 2.3366559
Average (Standard dev.)0.0024131667 (±0.05811289)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 352.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.11.11.1
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z352.000352.000352.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ352352352
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-1.3422.3370.002

-
Supplemental data

-
Additional map: map filtered by local resolution

Fileemd_22160_additional.map
Annotationmap filtered by local resolution
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

-
Sample components

+
Entire SARS-CoV-2 replication/transcription complex bound to nsp13 helic...

EntireName: SARS-CoV-2 replication/transcription complex bound to nsp13 helicase - nsp13(2)-RTC
Number of components: 12

+
Component #1: protein, SARS-CoV-2 replication/transcription complex bound to ns...

ProteinName: SARS-CoV-2 replication/transcription complex bound to nsp13 helicase - nsp13(2)-RTC
Recombinant expression: No
SourceSpecies: Severe acute respiratory syndrome coronavirus 2
Source (engineered)Expression System: Escherichia coli BL21(DE3) (bacteria)

+
Component #2: protein, nsp12

ProteinName: nsp12 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 106.780977 kDa
SourceSpecies: Severe acute respiratory syndrome coronavirus 2
Source (engineered)Expression System: Escherichia coli BL21(DE3) (bacteria)

+
Component #3: protein, nsp8

ProteinName: nsp8 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 22.034242 kDa
SourceSpecies: Severe acute respiratory syndrome coronavirus 2
Source (engineered)Expression System: Escherichia coli BL21(DE3) (bacteria)

+
Component #4: protein, nsp7

ProteinName: nsp7 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.748385 kDa
SourceSpecies: Severe acute respiratory syndrome coronavirus 2
Source (engineered)Expression System: Escherichia coli BL21(DE3) (bacteria)

+
Component #5: protein, nsp13

ProteinName: nsp13 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 67.354039 kDa
SourceSpecies: Severe acute respiratory syndrome coronavirus 2
Source (engineered)Expression System: Escherichia coli BL21(DE3) (bacteria)

+
Component #6: nucleic-acid, Product RNA

nucleic acidName: Product RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
CGCGUAGCAU GCUACGUCAU UCUCCUAAGA AGCUA
MassTheoretical: 11.141644 kDa
SourceSpecies: Severe acute respiratory syndrome coronavirus 2

+
Component #7: nucleic-acid, Template RNA

nucleic acidName: Template RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
CUAUCCCCAU GUGAUUUUAA UAGCUUCUUA GGAGAAUGAC GUAGCAUGCU ACGCG
MassTheoretical: 17.573391 kDa
SourceSpecies: Severe acute respiratory syndrome coronavirus 2

+
Component #8: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 8 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

+
Component #9: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

+
Component #10: ligand, ADENOSINE-5'-DIPHOSPHATE

LigandName: ADENOSINE-5'-DIPHOSPHATE / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 0.427201 kDa

+
Component #11: ligand, CHAPSO

LigandName: CHAPSOCHAPS detergent / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 0.631884 kDa

+
Component #12: ligand, ALUMINUM FLUORIDE

LigandName: ALUMINUM FLUORIDEAluminium fluoride / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 8.397705 MDa

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 8
Support filmunspecified
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 65 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: OTHER

-
Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 58942
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

-
Atomic model buiding

Output model

+
About Yorodumi

-
News

-
Aug 12, 2020. New: Covid-19 info

New: Covid-19 info

  • 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. New: 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. (see PDBe EMDB page)
  • 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 at PDBe / 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. See below links for details.
  • 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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search

Read more

-
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.

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