8P28

Cryo-EM structure of the anaerobic ribonucleotide reductase from Prevotella copri in its tetrameric, dATP-bound state

PDB DOI: https://doi.org/10.2210/pdb8P28/pdb
EM Map EMD-17359: EMDB EMDataResource

Classification: OXIDOREDUCTASE
Organism(s): Segatella copri
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-05-15 Released: 2023-08-30
Deposition Author(s): Banerjee, I., Bimai, O., Sjoberg, B.M., Logan, D.T.
Funding Organization(s): Swedish Research Council, Cancerfonden, Wenner-Gren Foundation

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.77 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

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.

To be published.

Macromolecule Content

Total Structure Weight: 344.54 kDa
Atom Count: 21,141
Modelled Residue Count: 2,584
Deposited Residue Count: 2,972
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Anaerobic ribonucleoside-triphosphate reductase	A, B, C, D	743	Segatella copri	Mutation(s): 0 Gene Names: BN510_01369
UniProt
Find proteins for A0A3E4SF67 (Segatella copri) Explore A0A3E4SF67 Go to UniProtKB: A0A3E4SF67
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A3E4SF67
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DTP (Subject of Investigation/LOI) Query on DTP Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain M [auth C] SDF format, chain N [auth C] SDF format, chain O [auth C] SDF format, chain R [auth D] SDF format, chain S [auth D] SDF format, chain T [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain M [auth C] MOL2 format, chain N [auth C] MOL2 format, chain O [auth C] MOL2 format, chain R [auth D] MOL2 format, chain S [auth D] MOL2 format, chain T [auth D]	E [auth A] F [auth A] G [auth A] I [auth B] J [auth B] E [auth A], F [auth A], G [auth A], I [auth B], J [auth B], K [auth B], M [auth C], N [auth C], O [auth C], R [auth D], S [auth D], T [auth D]	2'-DEOXYADENOSINE 5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₂ P₃ SUYVUBYJARFZHO-RRKCRQDMSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C] Focus chain R [auth D] Focus chain S [auth D] Focus chain T [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C] Focus chain R [auth D] Focus chain S [auth D] Focus chain T [auth D]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain L [auth B] SDF format, chain P [auth C] SDF format, chain Q [auth C] MOL2 format, chain H [auth A] MOL2 format, chain L [auth B] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C]	H [auth A], L [auth B], P [auth C], Q [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain Q [auth C] Interactions & Density Focus chain H [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain Q [auth C]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.77 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	3.3.2
MODEL REFINEMENT	PHENIX	1.19.2-4158

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2023-08-30

Deposition Author(s):

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 (Full details and data files)

Version 1.0: 2023-08-30
Type: Initial release

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Help and Resources

8P28

Cryo-EM structure of the anaerobic ribonucleotide reductase from Prevotella copri in its tetrameric, dATP-bound state

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

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)