7OYG | pdb_00007oyg

Dimeric form of SARS-CoV-2 RNA-dependent RNA polymerase

PDB DOI: https://doi.org/10.2210/pdb7OYG/pdb
NAKB: 7OYG
EM Map EMD-13116: EMDB EMDataResource

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

Deposited: 2021-06-24 Released: 2021-08-25
Deposition Author(s): Jochheim, F.A., Tegunov, D., Hillen, H.S., Schmitzova, J., Kokic, G., Dienemann, C., Cramer, P.
Funding Organization(s): European Research Council (ERC), German Research Foundation (DFG)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 5.50 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

The structure of a dimeric form of SARS-CoV-2 polymerase

Jochheim, F.A., Tegunov, D., Hillen, H.S., Schmitzova, J., Kokic, G., Dienemann, C., Cramer, P.

(2021) Communications Biology 4: 999

DOI: https://doi.org/10.1038/s42003-021-02529-9

Macromolecule Content

Total Structure Weight: 323.65 kDa
Atom Count: 16,274
Modeled Residue Count: 1,958
Deposited Residue Count: 2,588
Unique protein chains: 3
Unique nucleic acid chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SARS-CoV-2 RNA-dependent RNA polymerase (nsp12)	A, F [auth D]	935	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0 Gene Names: rep, 1a-1b EC: 3.4.19.12 (PDB Primary Data), 3.4.22 (PDB Primary Data), 3.4.22.69 (PDB Primary Data), 2.7.7.48 (PDB Primary Data), 3.6.4.12 (PDB Primary Data), 3.6.4.13 (PDB Primary Data), 3.1.13 (PDB Primary Data), 3.1 (PDB Primary Data), 2.1.1 (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
SARS-CoV-2 nsp8	B, G [auth E]	201	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0 Gene Names: rep, 1a-1b EC: 3.4.19.12 (PDB Primary Data), 3.4.22 (PDB Primary Data), 3.4.22.69 (PDB Primary Data), 2.7.7.48 (PDB Primary Data), 3.6.4.12 (PDB Primary Data), 3.6.4.13 (PDB Primary Data), 3.1.13 (PDB Primary Data), 3.1 (PDB Primary Data), 2.1.1 (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: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
SARS-CoV-2 nsp7	C, H [auth F]	86	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0 Gene Names: rep, 1a-1b EC: 3.4.19.12 (PDB Primary Data), 3.4.22 (PDB Primary Data), 3.4.22.69 (PDB Primary Data), 2.7.7.48 (PDB Primary Data), 3.6.4.12 (PDB Primary Data), 3.6.4.13 (PDB Primary Data), 3.1.13 (PDB Primary Data), 3.1 (PDB Primary Data), 2.1.1 (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

Find similar nucleic acids by: Sequence

Molecule	Chains	Length	Organism
Entity ID: 4
RNA (5'-R(PCPUPAPCPGPCPAPGPUPG)-3')	D [auth P], I [auth G]	15	Severe acute respiratory syndrome coronavirus 2
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 5
RNA (5'-R(PUPGPCPAPCPUPGPCPGPUPAPG)-3')	E [auth T], J [auth H]	57	Severe acute respiratory syndrome coronavirus 2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain N [auth D] SDF format, chain M [auth D] SDF format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain N [auth D] MOL2 format, chain M [auth D] MOL2 format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain N [auth D] mmCIF format, chain M [auth D] mmCIF format, chain L [auth A]	K [auth A], L [auth A], M [auth D], N [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth D] Focus chain N [auth D] Interactions & Density Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth D] Focus chain N [auth D]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 5.50 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2021-08-25

Deposition Author(s):

Funding Organization	Location	Grant Number
European Research Council (ERC)	Germany	882357
German Research Foundation (DFG)	Germany	EXC 2067/1 39072994
German Research Foundation (DFG)	Germany	SFB860
German Research Foundation (DFG)	Germany	SPP2191
German Research Foundation (DFG)	Germany	EXC 2067/1 39072994
German Research Foundation (DFG)	Germany	SFB1190
German Research Foundation (DFG)	Germany	FOR2848