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- EMDB-62625: nsp13-1 bound with RNA(local map of pre CI RTC) -

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Basic information

Entry
Database: EMDB / ID: EMD-62625
Titlensp13-1 bound with RNA(local map of pre CI RTC)
Map data
Sample
  • Complex: nsp13-1 bound with RNA(local map of SARS-CoV-2 pre-CI RTC)
Keywordshelicase / RNA / REPLICATION
Biological speciesSevere acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 3.51 Å
AuthorsLiming Yan LM / Yucen Huang YH / Yixiao Liu YL / Ji Ge JG / Shan Gao SG / Liping Tan LP / Lu Liu LL / Lan Zhu LZ / Zhiyong Lou ZL / Zihe Rao ZR
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Cell / Year: 2025
Title: Structural basis for the concurrence of template recycling and RNA capping in SARS-CoV-2.
Authors: Liming Yan / Yucen Huang / Yixiao Liu / Ji Ge / Shan Gao / Liping Tan / Lu Liu / Zhenyu Liu / Sihan Ye / Junbo Wang / Jiangran Xiong / Yu Zhou / Hesheng Zhao / Xiaoyue Zhao / Luke W Guddat / ...Authors: Liming Yan / Yucen Huang / Yixiao Liu / Ji Ge / Shan Gao / Liping Tan / Lu Liu / Zhenyu Liu / Sihan Ye / Junbo Wang / Jiangran Xiong / Yu Zhou / Hesheng Zhao / Xiaoyue Zhao / Luke W Guddat / Yan Gao / Lan Zhu / Zihe Rao / Zhiyong Lou /
Abstract: In the SARS-CoV-2 replication-transcription complex (RTC), the nascent template-product duplex is unwound into a template strand for recycling and a product strand that needs to be capped. Here, we ...In the SARS-CoV-2 replication-transcription complex (RTC), the nascent template-product duplex is unwound into a template strand for recycling and a product strand that needs to be capped. Here, we determined structures of the SARS-CoV-2 RTC in the pre- and post-capping initiation (CI) states. In the pre-CI state, the RTC has a dimer-of-dimeric architecture (ddRTC). The upstream RNA duplex in one RTC is reciprocally unwound by a helicase in a head-to-head-positioned RTC in the 3'-5' direction. The helicases bind either ADP or ADP⋅P in their ATP-binding pockets, suggesting a mechanism for ATP-hydrolysis-driven unwinding. In the post-CI state, the binding of nsp9 to the nsp12 nidovirus RdRp-associated nucleotidyltransferase (NiRAN) disrupts the ddRTC. The N terminus of nsp9 and the triphosphorylated 5' end of the product strand co-localize in NiRAN's catalytic site, exhibiting the state prior to nsp9 RNAylation for capping. These results provide an insight into the concurrence of template recycling and RNA capping in the SARS-CoV-2 RTC.
History
DepositionDec 7, 2024-
Header (metadata) releaseNov 12, 2025-
Map releaseNov 12, 2025-
UpdateNov 12, 2025-
Current statusNov 12, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_62625.png

Downloads & links

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Map

FileDownload / File: emd_62625.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 448 pix.
= 488.32 Å		1.09 Å/pix.
x 448 pix.
= 488.32 Å		1.09 Å/pix.
x 448 pix.
= 488.32 Å

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.09 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.060198694 - 3.850718
Average (Standard dev.)-0.00007249665 (±0.005323091)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 488.32 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_62625_half_map_1.map
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Half map: #2

Fileemd_62625_half_map_2.map
Projections & Slices
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Sample components

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Entire : nsp13-1 bound with RNA(local map of SARS-CoV-2 pre-CI RTC)

EntireName: nsp13-1 bound with RNA(local map of SARS-CoV-2 pre-CI RTC)
Components
  • Complex: nsp13-1 bound with RNA(local map of SARS-CoV-2 pre-CI RTC)

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Supramolecule #1: nsp13-1 bound with RNA(local map of SARS-CoV-2 pre-CI RTC)

SupramoleculeName: nsp13-1 bound with RNA(local map of SARS-CoV-2 pre-CI RTC)
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.51 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 155382
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD

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