7EGQ | pdb_00007egq

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

PDB DOI: https://doi.org/10.2210/pdb7EGQ/pdb
EM Map EMD-31138: EMDB EMDataResource
NAKB: 7EGQ

Classification: VIRAL PROTEIN/RNA
Organism(s): Severe acute respiratory syndrome coronavirus 2
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2021-03-25 Released: 2021-07-21
Deposition Author(s): Yan, L.M., Yang, Y.X., Li, M.Y., Zhang, Y., Zheng, L.T., Ge, J., Huang, Y.C., Liu, Z.Y., Wang, T., Gao, S., Zhang, R., Huang, Y.Y., Guddat, L.W., Gao, Y., Rao, Z.H., Lou, Z.Y.
Funding Organization(s): Ministry of Science and Technology (MoST, China)

Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

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

PubMed: 34143953 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1016/j.cell.2021.05.033
Primary Citation 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. Nsp9 and nsp12 NiRAN recruit nsp10/nsp14 into the Cap(0)-RTC, forming the N7-CCC to yield cap(0) ( ^7MeGpppA) 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; Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China.

Macromolecule Content

Total Structure Weight: 801.37 kDa
Atom Count: 54,547
Modeled Residue Count: 6,760
Deposited Residue Count: 6,908
Unique protein chains: 7
Unique nucleic acid chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA-directed RNA polymerase	A, I [auth N]	932	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0 EC: 2.7.7.48
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1 Go to UniProtKB: P0DTD1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0DTD1
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-structural protein 8	B, D, J [auth O], L [auth Q]	198	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1 Go to UniProtKB: P0DTD1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0DTD1
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-structural protein 7	C, K [auth P]	83	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0 Gene Names: rep, 1a-1b
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1 Go to UniProtKB: P0DTD1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0DTD1
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Helicase	E, M [auth R], Q [auth F], R [auth S]	601	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0 EC: 3.6.4.12 (PDB Primary Data), 3.6.4.13 (PDB Primary Data)
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1 Go to UniProtKB: P0DTD1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0DTD1
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-structural protein 9	F [auth G], N [auth T]	117	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1 Go to UniProtKB: P0DTD1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0DTD1
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-structural protein 10	G [auth H], O [auth U]	139	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1 Go to UniProtKB: P0DTD1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0DTD1
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Proofreading exoribonuclease	H [auth K], P [auth X]	527	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0 EC: 3.1.13
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1 Go to UniProtKB: P0DTD1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0DTD1
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 8
primer RNA	S [auth I], U [auth L]	25	Severe acute respiratory syndrome coronavirus 2
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 9
Template RNA	T [auth J], V [auth M]	33	Severe acute respiratory syndrome coronavirus 2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain Z [auth E] SDF format, chain YA [auth S] SDF format, chain Y [auth E] SDF format, chain XA [auth S] SDF format, chain X [auth A] SDF format, chain WA [auth S] SDF format, chain W [auth A] SDF format, chain VA [auth F] SDF format, chain UA [auth F] SDF format, chain TA [auth F] SDF format, chain RA [auth X] SDF format, chain QA [auth X] SDF format, chain PA [auth X] SDF format, chain OA [auth U] SDF format, chain NA [auth U] SDF format, chain MA [auth R] SDF format, chain LA [auth R] SDF format, chain KA [auth R] SDF format, chain JA [auth N] SDF format, chain IA [auth N] SDF format, chain FA [auth K] SDF format, chain EA [auth K] SDF format, chain DA [auth K] SDF format, chain CA [auth H] SDF format, chain BA [auth H] SDF format, chain AA [auth E] MOL2 format, chain Z [auth E] MOL2 format, chain YA [auth S] MOL2 format, chain Y [auth E] MOL2 format, chain XA [auth S] MOL2 format, chain X [auth A] MOL2 format, chain WA [auth S] MOL2 format, chain W [auth A] MOL2 format, chain VA [auth F] MOL2 format, chain UA [auth F] MOL2 format, chain TA [auth F] MOL2 format, chain RA [auth X] MOL2 format, chain QA [auth X] MOL2 format, chain PA [auth X] MOL2 format, chain OA [auth U] MOL2 format, chain NA [auth U] MOL2 format, chain MA [auth R] MOL2 format, chain LA [auth R] MOL2 format, chain KA [auth R] MOL2 format, chain JA [auth N] MOL2 format, chain IA [auth N] MOL2 format, chain FA [auth K] MOL2 format, chain EA [auth K] MOL2 format, chain DA [auth K] MOL2 format, chain CA [auth H] MOL2 format, chain BA [auth H] MOL2 format, chain AA [auth E] mmCIF format, chain Z [auth E] mmCIF format, chain YA [auth S] mmCIF format, chain Y [auth E] mmCIF format, chain XA [auth S] mmCIF format, chain X [auth A] mmCIF format, chain WA [auth S] mmCIF format, chain W [auth A] mmCIF format, chain VA [auth F] mmCIF format, chain UA [auth F] mmCIF format, chain TA [auth F] mmCIF format, chain RA [auth X] mmCIF format, chain QA [auth X] mmCIF format, chain PA [auth X] mmCIF format, chain OA [auth U] mmCIF format, chain NA [auth U] mmCIF format, chain MA [auth R] mmCIF format, chain LA [auth R] mmCIF format, chain KA [auth R] mmCIF format, chain JA [auth N] mmCIF format, chain IA [auth N] mmCIF format, chain FA [auth K] mmCIF format, chain EA [auth K] mmCIF format, chain DA [auth K] mmCIF format, chain CA [auth H] mmCIF format, chain BA [auth H] mmCIF format, chain AA [auth E]	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		Interactions Focus chain AA [auth E] Focus chain BA [auth H] Focus chain CA [auth H] Focus chain DA [auth K] Focus chain EA [auth K] Focus chain FA [auth K] Focus chain IA [auth N] Focus chain JA [auth N] Focus chain KA [auth R] Focus chain LA [auth R] Focus chain MA [auth R] Focus chain NA [auth U] Focus chain OA [auth U] Focus chain PA [auth X] Focus chain QA [auth X] Focus chain RA [auth X] Focus chain TA [auth F] Focus chain UA [auth F] Focus chain VA [auth F] Focus chain W [auth A] Focus chain WA [auth S] Focus chain X [auth A] Focus chain XA [auth S] Focus chain Y [auth E] Focus chain YA [auth S] Focus chain Z [auth E] Interactions & Density Focus chain AA [auth E] Focus chain BA [auth H] Focus chain CA [auth H] Focus chain DA [auth K] Focus chain EA [auth K] Focus chain FA [auth K] Focus chain IA [auth N] Focus chain JA [auth N] Focus chain KA [auth R] Focus chain LA [auth R] Focus chain MA [auth R] Focus chain NA [auth U] Focus chain OA [auth U] Focus chain PA [auth X] Focus chain QA [auth X] Focus chain RA [auth X] Focus chain TA [auth F] Focus chain UA [auth F] Focus chain VA [auth F] Focus chain W [auth A] Focus chain WA [auth S] Focus chain X [auth A] Focus chain XA [auth S] Focus chain Y [auth E] Focus chain YA [auth S] Focus chain Z [auth E]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain SA [auth X] SDF format, chain HA [auth K] SDF format, chain GA [auth K] MOL2 format, chain SA [auth X] MOL2 format, chain HA [auth K] MOL2 format, chain GA [auth K] mmCIF format, chain SA [auth X] mmCIF format, chain HA [auth K] mmCIF format, chain GA [auth K]	GA [auth K], HA [auth K], SA [auth X]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain GA [auth K] Focus chain HA [auth K] Focus chain SA [auth X] Interactions & Density Focus chain GA [auth K] Focus chain HA [auth K] Focus chain SA [auth X]