9IKZ | pdb_00009ikz

SARS-CoV-2 E-RTC bound to pRNA-nsp9 and GDP-BeF3-

PDB DOI: https://doi.org/10.2210/pdb9IKZ/pdb
NAKB: 9IKZ
EM Map EMD-60663: EMDB EMDataResource

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

Deposited: 2024-06-29 Released: 2025-06-18
Deposition Author(s): Yan, L.M., Huang, Y.C., Liu, Y.X., Rao, Z.H., Lou, Z.Y.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.14 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Substrate selection and transition reveal the mechanism for RNA capping catalyzed by SARS-CoV-2 NiRAN

Huang, Y.C., Tan, L.P., Zhao, H.S., Liu, Y.X., Wang, J.B., Ge, J., Ye, S.H., Liu, Z.Y., Lan, W.Q., Huang, B., Zhang, H.B., Gao, Y., Rao, Z.H., Yan, L.M., Lou, Z.Y.

To be published.

Macromolecule Content

Total Structure Weight: 319.06 kDa
Atom Count: 21,944
Modeled Residue Count: 2,719
Deposited Residue Count: 2,734
Unique protein chains: 5
Unique nucleic acid chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA-directed RNA polymerase nsp12	A	931	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0DTD1
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-structural protein 8	B, D	187	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0DTD1
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 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
UniProt
Find proteins for P0DTC1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC1 Go to UniProtKB: P0DTC1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0DTC1
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0DTD1
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0DTD1
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence | 3D Structure

Entity ID: 6
Molecule	Chains	Length	Organism	Image
RNA (25-MER)	H [auth I]	25	Severe acute respiratory syndrome coronavirus 2
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 7
Molecule	Chains	Length	Organism	Image
RNA (27-MER)	I [auth J]	27	Severe acute respiratory syndrome coronavirus 2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GDP (Subject of Investigation/LOI) Query on GDP Download Ideal Coordinates CCD File SDF format, chain L [auth A] MOL2 format, chain L [auth A] mmCIF format, chain L [auth A]	L [auth A]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain L [auth A] Interactions & Density Focus chain L [auth A]
BEF (Subject of Investigation/LOI) Query on BEF 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]	BERYLLIUM TRIFLUORIDE ION Be F₃ OGIAHMCCNXDTIE-UHFFFAOYSA-K		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 T [auth F] SDF format, chain S [auth F] SDF format, chain R [auth F] SDF format, chain Q [auth E] SDF format, chain P [auth E] SDF format, chain O [auth E] SDF format, chain K [auth A] SDF format, chain J [auth A] MOL2 format, chain T [auth F] MOL2 format, chain S [auth F] MOL2 format, chain R [auth F] MOL2 format, chain Q [auth E] MOL2 format, chain P [auth E] MOL2 format, chain O [auth E] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] mmCIF format, chain T [auth F] mmCIF format, chain S [auth F] mmCIF format, chain R [auth F] mmCIF format, chain Q [auth E] mmCIF format, chain P [auth E] mmCIF format, chain O [auth E] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A]	J [auth A] K [auth A] O [auth E] P [auth E] Q [auth E] J [auth A], K [auth A], O [auth E], P [auth E], Q [auth E], R [auth F], S [auth F], T [auth F]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain O [auth E] Focus chain P [auth E] Focus chain Q [auth E] Focus chain R [auth F] Focus chain S [auth F] Focus chain T [auth F] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain O [auth E] Focus chain P [auth E] Focus chain Q [auth E] Focus chain R [auth F] Focus chain S [auth F] Focus chain T [auth F]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain N [auth A] MOL2 format, chain N [auth A] mmCIF format, chain N [auth A]	N [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain N [auth A] Interactions & Density Focus chain N [auth A]