← Back to search
4gfh

Topoisomerase II-DNA-AMPPNP complex

Method: X-RAY DIFFRACTION Dmax: 164.7 Å Quality: GOOD
▼

1. Protein Identity and Related Structures Protein Identity & Related Structures

DNA topoisomerase 2

Saccharomyces cerevisiae

UniProt P06786

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Homooligomer Protein × 2 DNA 8 PDB declaration: decameric（10） Consistent with all polymer counts Chain A； UniProt 1–1177 Chain F； UniProt 1–1177 Fragment：UNP RESIDUES 1-1177 Non-standard monomer：Yes (specific site not provided by mmCIF) ;DNA (5'-D(P*CP*CP*TP*AP*CP*TP*GP*CP*TP*AP*C)-3') ; × 2 ;DNA (5'-D(*CP*GP*CP*GP*GP*TP*AP*GP*CP*AP*GP*TP*AP*GP*G)-3') ; × 2 ;DNA (5'-D(P*GP*GP*AP*TP*GP*AP*CP*GP*AP*TP*(TSP))-3') ; × 2 ;DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*CP*GP*TP*CP*AP*TP*CP*C)-3') ; × 2 MG MAGNESIUM ION × 2 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；23% PEG 300, 100 mM Tris (8.0), VAPOR DIFFUSION, HANGING DROP, temperature 291K Resolution 4.41 Å R-free 0.275

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 4GFH Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1BGW TOPOISOMERASE RESIDUES 410-1202, Deposited 1996-02-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 409–1201（793 aa） Fragment：RESIDUES 410 - 1202
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.70 Å R-free 0.277
1BJT TOPOISOMERASE II RESIDUES 409-1201 Deposited 1998-06-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 409–1201（793 aa） Fragment：DNA-BINDING AND CLEAVAGE CORE, RESIDUES 409-1201
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；pH 8.0
Resolution 2.50 Å R-free 0.269
1PVG Crystal Structure of the ATPase region of Saccharomyces Cerevisiae topoisomerase II Deposited 2003-06-27 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–413（413 aa） Fragment：N-terminal ATPase region
Chain B 1–413（413 aa） Fragment：N-terminal ATPase region
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) MG MAGNESIUM ION × 2 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 X-RAY DIFFRACTION
X-ray crystallization conditions microbatch under oil；pH 6.5；293 K；PEG 1500, Potassium Chloride, Glycerol, Sodium Cacodylate, pH 6.5, microbatch under oil, temperature 293K
Resolution 1.80 Å R-free 0.241
1QZR CRYSTAL STRUCTURE OF THE ATPASE REGION OF SACCHAROMYCES CEREVISIAE TOPOISOMERASE II BOUND TO ICRF-187 (DEXRAZOXANE) Deposited 2003-09-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–413（413 aa） Fragment：N-terminal ATPase Region
Chain B 1–413（413 aa） Fragment：N-terminal ATPase Region
Not recorded MG MAGNESIUM ION × 2 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 CDX (S)-4,4'-(1-METHYL-1,2-ETHANEDIYL)BIS-2,6-PIPERAZINEDIONE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions microbatch under oil；pH 6.5；293 K；PEG 1500, POTASSIUM CHLORIDE, GLYCEROL, SODIUM CACODYLATE, pH 6.5, microbatch under oil, temperature 293K
Resolution 1.90 Å R-free 0.237
2RGR Topoisomerase IIA bound to G-segment DNA Deposited 2007-10-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: hexameric
Chain A 419–1177（759 aa） Fragment：DNA binding and cleavage domain (residues 419-1177)
Not recorded MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；12-20% PEG 1000, 100-250 mM MgCl2, 100 mM sodium cacodylate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 3.00 Å R-free 0.278
3L4J Topoisomerase II-DNA cleavage complex, apo Deposited 2009-12-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: pentameric
Chain A 421–1177（757 aa） Fragment：RESIDUES 421-1177
Non-standard monomer：Yes (specific site not provided by mmCIF) TSP 3'-THIO-THYMIDINE-5'-PHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；291 K；20% 1,4-BUTANEDIOL, 0.1M SODIUM ACETATE, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.48 Å R-free 0.259
3L4K Topoisomerase II-DNA cleavage complex, metal-bound Deposited 2009-12-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: pentameric
Chain A 421–1177（757 aa） Fragment：RESIDUES 421-1177
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 8 TSP 3'-THIO-THYMIDINE-5'-PHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；20% 1,4-BUTANEDIOL, 0.1M SODIUM ACETATE, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.98 Å R-free 0.273

7 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TOP2_YEAST
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–1177； UniProt 1–1177 Author chain F； PDBConstruct 1–1177； UniProt 1–1177

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 4gfh

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4gfh
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id4gfh
Deposition date deposition_date2012-08-03
Structure title titleTopoisomerase II-DNA-AMPPNP complex
Keywords keywords;TOPOISOMERASE, PROTEIN-DNA COMPLEX, DNA SUPERCOILING, DNA REPLICATION, ATP-BINDING, DNA-BINDING, ISOMERASE, NUCLEOTIDE-BINDING, NUCLEUS, PHOSPHOPROTEIN, ISOMERASE-DNA COMPLEX ;; Isomerase/DNA
Experimental Method methodX-RAY DIFFRACTION
▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier47.38 Å
Radius of gyration Rg (electron density) rg_electron48.15 Å
Forward intensity I(0) i01117220000.00
Molecular weight molecular_weight272740.0 kDa
Excluded volume excluded_volume339700 ų
Envelope volume envelope_volume478170 ų
Hydration-shell volume shell_volume84619 ų
Envelope diameter envelope_diameter173.1 Å
Shell Rg shell_rg50.63 Å
Envelope Rg envelope_rg47.61 Å
Shape Rg shape_rg48.18 Å
Total Rg total_rg48.17 Å
Total atoms total_atoms19152
Residues n_residues2250
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax164.7 Å
Rg (real space) rg_real47.65 Å
Rg uncertainty (real space) rg_real_error1.81 Å
I(0) (real space) i0_real1.1170e+09
I(0) uncertainty (real space) i0_real_error2.2030e+07
Rg (reciprocal space) rg_reciprocal47.38 Å
I(0) (reciprocal space) i0_reciprocal1117000000.0000
Solution quality estimate total_estimate0.8367
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary54.9 Å
Skewness Skewness skewness0.562
Kurtosis Kurtosis kurtosis0.086
Angular range angular_range— – 0.1650 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha153600000.0000
Real-space data points n_real_points34
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.766; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.580
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (7)

▶

8. Citations (1)

▶

9. Files and Curves (10)