9UHT | pdb_00009uht

SARS-CoV-2 E-RTC in complex with RNA-nsp9 and GMPPNP

PDB DOI: https://doi.org/10.2210/pdb9UHT/pdb
EM Map EMD-64175: EMDB EMDataResource
NAKB: 9UHT

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

Deposited: 2025-04-14 Released: 2025-06-11
Deposition Author(s): Huang, Y.C., Liu, Y.X., Lou, Z.Y., Rao, Z.H., Yan, L.M.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.89 Å
Resolution: 2.89 Å
Resolution: 2.89 Å
Resolution: 2.89 Å
Resolution: 2.89 Å
Resolution: 2.66 Å
Resolution: 2.89 Å
Resolution: 2.66 Å
Resolution: 2.66 Å
Resolution: 2.89 Å
Resolution: 2.66 Å
Resolution: 2.66 Å
Resolution: 2.89 Å
Resolution: 2.89 Å
Resolution: 2.89 Å
Resolution: 2.89 Å
Resolution: 2.89 Å
Resolution: 2.66 Å
Resolution: 2.89 Å
Resolution: 2.66 Å
Resolution: 2.66 Å
Resolution: 2.89 Å
Resolution: 2.66 Å
Resolution: 2.66 Å
Resolution: 2.89 Å
Resolution: 2.89 Å
Resolution: 2.89 Å
Resolution: 2.89 Å
Resolution: 2.89 Å
Resolution: 2.66 Å
Resolution: 2.89 Å
Resolution: 2.66 Å
Resolution: 2.66 Å
Resolution: 2.89 Å
Resolution: 2.66 Å
Resolution: 2.66 Å
Resolution: 2.89 Å
Resolution: 2.89 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Response to Matter Arising: Substrate selection and transition state support the mechanism for GTP-mediate RNA capping catalyzed by SARS-CoV-2 NiRAN

Huang, Y., Tan, L., Liu, Y., Yan, L., Rao, Z., Lou, Z.

To be published.

Macromolecule Content

Total Structure Weight: 322.6 kDa
Atom Count: 22,068
Modeled Residue Count: 2,727
Deposited Residue Count: 2,761
Unique protein chains: 5
Unique nucleic acid chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA-directed RNA polymerase nsp12	A	932	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0 Gene Names: rep, 1a-1b EC: 2.7.7.48 (PDB Primary Data), 2.7.7.50 (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: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-structural protein 8	B, D	198	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: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-structural protein 7	C	78	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 nsp13	E, F	593	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0 Gene Names: rep, 1a-1b 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
Viral protein genome-linked nsp9	G	113	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

Find similar nucleic acids by: Sequence

Molecule	Chains	Length	Organism
Entity ID: 6
RNA (5'-R(PAPUPUPA)-3')	H	4	Severe acute respiratory syndrome coronavirus 2
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 7
PRIMER	I	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: 8
TEMPLATE	J	27	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
GNP (Subject of Investigation/LOI) Query on GNP Download:Ideal Coordinates CCD File SDF format, chain M [auth A] MOL2 format, chain M [auth A] mmCIF format, chain M [auth A]	M [auth A]	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER C₁₀ H₁₇ N₆ O₁₃ P₃ UQABYHGXWYXDTK-UUOKFMHZSA-N		Interactions Focus chain M [auth A] Interactions & Density Focus chain M [auth A]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain O [auth E] SDF format, chain P [auth E] SDF format, chain R [auth F] SDF format, chain S [auth F] SDF format, chain Q [auth F] SDF format, chain N [auth E] SDF format, chain L [auth A] SDF format, chain K [auth A] MOL2 format, chain O [auth E] MOL2 format, chain P [auth E] MOL2 format, chain R [auth F] MOL2 format, chain S [auth F] MOL2 format, chain Q [auth F] MOL2 format, chain N [auth E] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] mmCIF format, chain O [auth E] mmCIF format, chain P [auth E] mmCIF format, chain R [auth F] mmCIF format, chain S [auth F] mmCIF format, chain Q [auth F] mmCIF format, chain N [auth E] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A]	K [auth A] L [auth A] N [auth E] O [auth E] P [auth E] K [auth A], L [auth A], N [auth E], O [auth E], P [auth E], Q [auth F], R [auth F], S [auth F]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain L [auth A] Focus chain N [auth E] Focus chain O [auth E] Focus chain P [auth E] Focus chain Q [auth F] Focus chain R [auth F] Focus chain S [auth F] Interactions & Density Focus chain K [auth A] Focus chain L [auth A] Focus chain N [auth E] Focus chain O [auth E] Focus chain P [auth E] Focus chain Q [auth F] Focus chain R [auth F] Focus chain S [auth F]