1ZXN

Human DNA topoisomerase IIa ATPase/ADP

PDB DOI: https://doi.org/10.2210/pdb1ZXN/pdb

Classification: ISOMERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2005-06-08 Released: 2005-08-23
Deposition Author(s): Wei, H., Ruthenburg, A.J., Bechis, S.K., Verdine, G.L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.51 Å
R-Value Free: 0.281
R-Value Work: 0.235
R-Value Observed: 0.235

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 4R1F

Literature

Nucleotide-dependent Domain Movement in the ATPase Domain of a Human Type IIA DNA Topoisomerase.

Wei, H., Ruthenburg, A.J., Bechis, S.K., Verdine, G.L.

(2005) J Biol Chem 280: 37041-37047

PubMed: 16100112 Search on PubMed
DOI: https://doi.org/10.1074/jbc.M506520200
Primary Citation of Related Structures:
1ZXM, 1ZXN

PubMed Abstract:
Type IIA DNA topoisomerases play multiple essential roles in the management of higher-order DNA structure, including modulation of topological state, chromosome segregation, and chromatin condensation. These diverse physiologic functions are all accomplished through a common molecular mechanism, wherein the protein catalyzes transient cleavage of a DNA duplex (the G-segment) to yield a double-stranded gap through which another duplex (the T-segment) is passed. The overall process is orchestrated by the opening and closing of molecular "gates" in the topoisomerase structure, which is regulated by ATP binding, hydrolysis, and release of ADP and inorganic phosphate. Here we present two crystal structures of the ATPase domain of human DNA topoisomerase IIalpha in different nucleotide-bound states. Comparison of these structures revealed rigid-body movement of the structural modules within the ATPase domain, suggestive of the motions of a molecular gate.

Organizational Affiliation

Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA.

Macromolecule Content

Total Structure Weight: 184.73 kDa
Atom Count: 11,646
Modelled Residue Count: 1,500
Deposited Residue Count: 1,600
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA topoisomerase II, alpha isozyme	A, B, C, D	400	Homo sapiens	Mutation(s): 0 Gene Names: TOP2A, TOP2 EC: 5.99.1.3
UniProt & NIH Common Fund Data Resources
Find proteins for P11388 (Homo sapiens) Explore P11388 Go to UniProtKB: P11388
PHAROS: P11388 GTEx: ENSG00000131747
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P11388
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP Query on ADP Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth B] SDF format, chain L [auth C] SDF format, chain O [auth D] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B] MOL2 format, chain L [auth C] MOL2 format, chain O [auth D]	F [auth A], J [auth B], L [auth C], O [auth D]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain F [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain O [auth D] Interactions & Density Focus chain F [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain O [auth D]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain N [auth D] MOL2 format, chain I [auth B] MOL2 format, chain N [auth D]	I [auth B], N [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain I [auth B] Focus chain N [auth D] Interactions & Density Focus chain I [auth B] Focus chain N [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A]	G [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain K [auth C] SDF format, chain H [auth B] SDF format, chain M [auth D] MOL2 format, chain E [auth A] MOL2 format, chain K [auth C] MOL2 format, chain H [auth B] MOL2 format, chain M [auth D]	E [auth A], H [auth B], K [auth C], M [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain M [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain M [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.51 Å
R-Value Free: 0.281
R-Value Work: 0.235
R-Value Observed: 0.235
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.015	α = 90
b = 90.492	β = 89.97
c = 148.293	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement
HKL-2000	data reduction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2005-08-23

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2005-08-23
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.3: 2024-02-14
Changes: Advisory, Data collection, Database references, Derived calculations