9O0G | pdb_00009o0g

CryoEM structure of M. mazei topoisomerase VI(A-E342Q)-minicircle DNA complex in cleavage state

PDB DOI: https://doi.org/10.2210/pdb9O0G/pdb
EM Map EMD-49972: EMDB EMDataResource

Classification: ISOMERASE/DNA
Organism(s): Methanosarcina mazei Go1, unidentified
Expression System: Escherichia coli BL21(DE3), Escherichia coli
Mutation(s): Yes

Deposited: 2025-04-02 Released: 2026-02-25
Deposition Author(s): Richman, D.E., Berger, J.M.
Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.50 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Models: other, experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Supercoiled DNA recognition and cleavage control in topoisomerase VI

Richman, D.E., Wendorff, T.J., Rashid, F., Beck, C., Yan, Q., Johnson, H.R., Eckerty, R.A., Fogg, J.M., Baker, M.L., Zechiedrich, L., Berger, J.M.

To be published.

Macromolecule Content

Total Structure Weight: 268.87 kDa
Atom Count: 18,322
Modeled Residue Count: 2,076
Deposited Residue Count: 2,128
Unique protein chains: 2
Unique nucleic acid chains: 4

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Type 2 DNA topoisomerase 6 subunit A	A, C	369	Methanosarcina mazei Go1	Mutation(s): 1 Gene Names: top6A, MM_2418 EC: 5.6.2.2
UniProt
Find proteins for Q8PUB7 (Methanosarcina mazei (strain ATCC BAA-159 / DSM 3647 / Goe1 / Go1 / JCM 11833 / OCM 88)) Explore Q8PUB7 Go to UniProtKB: Q8PUB7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8PUB7
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Type 2 DNA topoisomerase 6 subunit B	B, D	621	Methanosarcina mazei Go1	Mutation(s): 0 Gene Names: top6B, MM_2417 EC: 5.6.2.2
UniProt
Find proteins for Q8PUB8 (Methanosarcina mazei (strain ATCC BAA-159 / DSM 3647 / Goe1 / Go1 / JCM 11833 / OCM 88)) Explore Q8PUB8 Go to UniProtKB: Q8PUB8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8PUB8
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Length	Organism	Image
Minicircle DNA sequence	E [auth F]	35	unidentified
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Length	Organism	Image
Minicircle DNA sequence	F [auth G]	39	unidentified
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 5
Molecule	Chains	Length	Organism	Image
Minicircle DNA sequence	G [auth H]	37	unidentified
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 6
Molecule	Chains	Length	Organism	Image
Minicircle DNA sequence	H [auth I]	37	unidentified
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ANP Query on ANP Download Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain N [auth D] MOL2 format, chain J [auth B] MOL2 format, chain N [auth D] mmCIF format, chain J [auth B] mmCIF format, chain N [auth D]	J [auth B], N [auth D]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C₁₀ H₁₇ N₆ O₁₂ P₃ PVKSNHVPLWYQGJ-KQYNXXCUSA-N		Interactions Focus chain J [auth B] Focus chain N [auth D] Interactions & Density Focus chain J [auth B] Focus chain N [auth D]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain K [auth B] SDF format, chain M [auth C] SDF format, chain O [auth D] MOL2 format, chain I [auth A] MOL2 format, chain K [auth B] MOL2 format, chain M [auth C] MOL2 format, chain O [auth D] mmCIF format, chain I [auth A] mmCIF format, chain K [auth B] mmCIF format, chain M [auth C] mmCIF format, chain O [auth D]	I [auth A], K [auth B], M [auth C], O [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain K [auth B] Focus chain M [auth C] Focus chain O [auth D] Interactions & Density Focus chain I [auth A] Focus chain K [auth B] Focus chain M [auth C] Focus chain O [auth D]
K Query on K Download Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain P [auth D] MOL2 format, chain L [auth B] MOL2 format, chain P [auth D] mmCIF format, chain L [auth B] mmCIF format, chain P [auth D]	L [auth B], P [auth D]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain L [auth B] Focus chain P [auth D] Interactions & Density Focus chain L [auth B] Focus chain P [auth D]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.50 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.1_5286
RECONSTRUCTION	cryoSPARC	4.6.0
RECONSTRUCTION	EMReady	2.0

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2026-02-25

Deposition Author(s):

Richman, D.E.

Berger, J.M.

Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	5R35 CA263778
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	1F32 GM128269