8P2S

Cryo-EM structure of the anaerobic ribonucleotide reductase from Prevotella copri in its dimeric, ATP/dTTP/GTP-bound state

• PDB DOI: https://doi.org/10.2210/pdb8P2S/pdb
• EM Map EMD-17373: EMDB EMDataResource

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Segatella copri
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-05-16 Released: 2023-09-13 
• Deposition Author(s): Bimai, O., Banerjee, I., Sjoberg, B.M., Logan, D.T.
• Funding Organization(s): Swedish Research Council, Cancerfonden, Wenner-Gren Foundation

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.40 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Activity modulation in anaerobic ribonucleotide reductase: nucleotide binding to the ATP-cone mediates long-range order-disorder transitions in the active site

Bimai, O., Banerjee, I., Rozman Grinberg, I., Huang, P., Lundin, D., Sjoberg, B.M., Logan, D.T.

(2023) Elife 

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 170.87 kDa 
• Atom Count: 9,694 
• Modelled Residue Count: 1,201 
• Deposited Residue Count: 1,486 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Anaerobic ribonucleoside-triphosphate reductase	A, B	743	Segatella copri	Mutation(s): 0  Gene Names: BN510_01369
UniProt
Find proteins for A0A3E4SF67 (Segatella copri) Explore A0A3E4SF67  Go to UniProtKB:  A0A3E4SF67

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GTP (Subject of Investigation/LOI)	G [auth B]	GUANOSINE-5'-TRIPHOSPHATE C10 H16 N5 O14 P3 XKMLYUALXHKNFT-UUOKFMHZSA-N
TTP (Subject of Investigation/LOI)	C [auth A], F [auth B]	THYMIDINE-5'-TRIPHOSPHATE C10 H17 N2 O14 P3 NHVNXKFIZYSCEB-XLPZGREQSA-N
ZN	H [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)	D [auth A], E [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.40 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.19.2-4158
RECONSTRUCTION	cryoSPARC	4.1.2

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-09-13 
Deposition Author(s): Bimai, O., Banerjee, I., Sjoberg, B.M., Logan, D.T.

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Funding Organization	Location	Grant Number
Swedish Research Council	Sweden	2016-04855
Swedish Research Council	Sweden	2019-01400
Cancerfonden	Sweden	CAN 20 1210 PjF
Wenner-Gren Foundation	United States	--

Revision History  

• Version 1.0: 2023-09-13
  Type: Initial release