7EGQ

Co-transcriptional capping machineries in SARS-CoV-2 RTC: Coupling of N7-methyltransferase and 3'-5' exoribonuclease with polymerase reveals mechanisms for capping and proofreading


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.35 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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Literature

Coupling of N7-methyltransferase and 3'-5' exoribonuclease with SARS-CoV-2 polymerase reveals mechanisms for capping and proofreading.

Yan, L.Yang, Y.Li, M.Zhang, Y.Zheng, L.Ge, J.Huang, Y.C.Liu, Z.Wang, T.Gao, S.Zhang, R.Huang, Y.Y.Guddat, L.W.Gao, Y.Rao, Z.Lou, Z.

(2021) Cell 184: 3474-3485.e11

  • DOI: 10.1016/j.cell.2021.05.033
  • Primary Citation of Related Structures:  
    7EGQ, 7EIZ

  • PubMed Abstract: 
  • The capping of mRNA and the proofreading play essential roles in SARS-CoV-2 replication and transcription. Here, we present the cryo-EM structure of the SARS-CoV-2 replication-transcription complex (RTC) in a form identified as Cap(0)-RTC, which couples a co-transcriptional capping complex (CCC) composed of nsp12 NiRAN, nsp9, the bifunctional nsp14 possessing an N-terminal exoribonuclease (ExoN) and a C-terminal N7-methyltransferase (N7-MTase), and nsp10 as a cofactor of nsp14 ...

    The capping of mRNA and the proofreading play essential roles in SARS-CoV-2 replication and transcription. Here, we present the cryo-EM structure of the SARS-CoV-2 replication-transcription complex (RTC) in a form identified as Cap(0)-RTC, which couples a co-transcriptional capping complex (CCC) composed of nsp12 NiRAN, nsp9, the bifunctional nsp14 possessing an N-terminal exoribonuclease (ExoN) and a C-terminal N7-methyltransferase (N7-MTase), and nsp10 as a cofactor of nsp14. Nsp9 and nsp12 NiRAN recruit nsp10/nsp14 into the Cap(0)-RTC, forming the N7-CCC to yield cap(0) ( 7Me GpppA) at 5' end of pre-mRNA. A dimeric form of Cap(0)-RTC observed by cryo-EM suggests an in trans backtracking mechanism for nsp14 ExoN to facilitate proofreading of the RNA in concert with polymerase nsp12. These results not only provide a structural basis for understanding co-transcriptional modification of SARS-CoV-2 mRNA but also shed light on how replication fidelity in SARS-CoV-2 is maintained.


    Organizational Affiliation

    MOE Key Laboratory of Protein Science, School of Medicine, Tsinghua University, Beijing, China; Guangzhou Laboratory, Guangzhou, China. Electronic address: louzy@mail.tsinghua.edu.cn.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RNA-directed RNA polymeraseA,
I [auth N]
932Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: rep1a-1b
EC: 2.7.7.48 (PDB Primary Data), 3.4.19.12 (UniProt), 3.4.22 (UniProt), 3.4.22.69 (UniProt), 3.6.4.12 (UniProt), 3.6.4.13 (UniProt), 3.1.13 (UniProt), 4.6.1 (UniProt), 2.1.1.57 (UniProt)
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Non-structural protein 8B,
D,
J [auth O],
L [auth Q]
198Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: rep1a-1b
EC: 3.4.19.12 (UniProt), 3.4.22 (UniProt), 3.4.22.69 (UniProt), 2.7.7.48 (UniProt), 3.6.4.12 (UniProt), 3.6.4.13 (UniProt), 3.1.13 (UniProt), 4.6.1 (UniProt), 2.1.1.57 (UniProt)
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Non-structural protein 7C,
K [auth P]
83Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: rep1a-1b
EC: 3.4.19.12 (UniProt), 3.4.22 (UniProt), 3.4.22.69 (UniProt), 2.7.7.48 (UniProt), 3.6.4.12 (UniProt), 3.6.4.13 (UniProt), 3.1.13 (UniProt), 4.6.1 (UniProt), 2.1.1.57 (UniProt)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
HelicaseE,
Q [auth F],
M [auth R],
R [auth S]
601Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: rep1a-1b
EC: 3.6.4.12 (PDB Primary Data), 3.6.4.13 (PDB Primary Data), 3.4.19.12 (UniProt), 3.4.22 (UniProt), 3.4.22.69 (UniProt), 2.7.7.48 (UniProt), 3.1.13 (UniProt), 4.6.1 (UniProt), 2.1.1.57 (UniProt)
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Non-structural protein 9F [auth G],
N [auth T]
117Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: rep1a-1b
EC: 3.4.19.12 (UniProt), 3.4.22 (UniProt), 3.4.22.69 (UniProt), 2.7.7.48 (UniProt), 3.6.4.12 (UniProt), 3.6.4.13 (UniProt), 3.1.13 (UniProt), 4.6.1 (UniProt), 2.1.1.57 (UniProt)
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Non-structural protein 10G [auth H],
O [auth U]
139Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: rep1a-1b
EC: 3.4.19.12 (UniProt), 3.4.22 (UniProt), 3.4.22.69 (UniProt), 2.7.7.48 (UniProt), 3.6.4.12 (UniProt), 3.6.4.13 (UniProt), 3.1.13 (UniProt), 4.6.1 (UniProt), 2.1.1.57 (UniProt)
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Proofreading exoribonucleaseH [auth K],
P [auth X]
527Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: rep1a-1b
EC: 3.1.13 (PDB Primary Data), 3.4.19.12 (UniProt), 3.4.22 (UniProt), 3.4.22.69 (UniProt), 2.7.7.48 (UniProt), 3.6.4.12 (UniProt), 3.6.4.13 (UniProt), 4.6.1 (UniProt), 2.1.1.57 (UniProt)
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Entity ID: 8
MoleculeChainsLengthOrganismImage
primer RNAS [auth I],
U [auth L]
25Severe acute respiratory syndrome coronavirus 2
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Entity ID: 9
MoleculeChainsLengthOrganismImage
Template RNAT [auth J],
V [auth M]
33Severe acute respiratory syndrome coronavirus 2
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Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
AA [auth E],
BA [auth H],
CA [auth H],
DA [auth K],
EA [auth K],
AA [auth E],
BA [auth H],
CA [auth H],
DA [auth K],
EA [auth K],
FA [auth K],
IA [auth N],
JA [auth N],
KA [auth R],
LA [auth R],
MA [auth R],
NA [auth U],
OA [auth U],
PA [auth X],
QA [auth X],
RA [auth X],
TA [auth F],
UA [auth F],
VA [auth F],
W [auth A],
WA [auth S],
X [auth A],
XA [auth S],
Y [auth E],
YA [auth S],
Z [auth E]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
GA [auth K],
HA [auth K],
SA [auth X]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.35 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, China)China2017YFC0840300
Ministry of Science and Technology (MoST, China)China2020YFA0707500

Revision History  (Full details and data files)

  • Version 1.0: 2021-07-21
    Type: Initial release