1ej9

CRYSTAL STRUCTURE OF HUMAN TOPOISOMERASE I DNA COMPLEX

Method: X-RAY DIFFRACTION Dmax: 80.1 Å Quality: EXCELLENT

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

DNA TOPOISOMERASE I

Homo sapiens

UniProt P11387

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 Monomer Protein × 1 DNA 2 PDB declaration: trimeric(3) Consistent with all polymer counts Chain A; UniProt 203–765 Fragment:C-TERMINAL DOMAIN, RESIDUES 203-765 Mutation:Y723F ;DNA (5'-D(*C*AP*AP*AP*AP*AP*GP*AP*CP*TP*CP*AP*GP*AP*AP*AP*AP*AP*TP*TP*TP*TP*T)-3') ; × 1 ;DNA (5'-D(*C*AP*AP*AP*AP*AP*TP*TP*TP*TP*TP*CP*TP*GP*AP*GP*TP*CP*TP*TP*TP*TP*T)-3') ; × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6.8;295 K;27% PEG 400, 145 mM MgCl2, 20 mM MES pH 6.8, 5 mM Tris pH 8.0, 30 mM DTT, VAPOR DIFFUSION, SITTING DROP, temperature 295K Resolution 2.60 Å R-free 0.281

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.

13 other PDB entries and 13 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TOP1_HUMAN
Isoform
PDB entities 3
Chains and sequence ranges Author chain A; PDBConstruct 1–563; UniProt 203–765

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 1ej9

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1ej9
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1ej9
Deposition date deposition_date2000-03-01
Structure title titleCRYSTAL STRUCTURE OF HUMAN TOPOISOMERASE I DNA COMPLEX
Keywords keywordsprotein-dna complex, type I topoisomerase, human, 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_guinier26.48
Radius of gyration Rg (electron density) rg_electron26.09
Forward intensity I(0) i096354900.00
Molecular weight molecular_weight69773.0 kDa
Excluded volume excluded_volume84138 ų
Envelope volume envelope_volume107130 ų
Hydration-shell volume shell_volume33891 ų
Envelope diameter envelope_diameter84.8
Shell Rg shell_rg33.72
Envelope Rg envelope_rg26.01
Shape Rg shape_rg26.09
Total Rg total_rg26.78
Total atoms total_atoms4862
Residues n_residues527
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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 dmax80.1
Rg (real space) rg_real26.35
Rg uncertainty (real space) rg_real_error0.51
I(0) (real space) i0_real9.6350e+07
I(0) uncertainty (real space) i0_real_error1.3330e+06
Rg (reciprocal space) rg_reciprocal26.39
I(0) (reciprocal space) i0_reciprocal96360000.0000
Solution quality estimate total_estimate0.9097
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary77.4
Skewness Skewness skewness0.189
Kurtosis Kurtosis kurtosis-0.464
Angular range angular_range— – 0.3000 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha10680000.0000
Real-space data points n_real_points61
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.951; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.983

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1ej9a1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.163 — DNA breaking-rejoining enzymes
Superfamily Superfamily superfamilyd.163.1 — DNA breaking-rejoining enzymes
Family Family familyd.163.1.2 — Eukaryotic DNA topoisomerase I, catalytic core
Domain ID domain_idd1ej9a2
Class classe — Multi-domain proteins (alpha and beta)
Fold Fold folde.15 — Eukaryotic DNA topoisomerase I, N-terminal DNA-binding fragment
Superfamily Superfamily superfamilye.15.1 — Eukaryotic DNA topoisomerase I, N-terminal DNA-binding fragment
Family Family familye.15.1.1 — Eukaryotic DNA topoisomerase I, N-terminal DNA-binding fragment

CATH v4.4 (4 domains)

Domain ID domain_id1ej9A01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily41 — Yeast DNA topoisomerase - domain 1
Domain ID domain_id1ej9A02
Class class2 — Mainly Beta
Architecture architecture170 — Beta Complex
Topology topology11 — DNA Topoisomerase I; domain 2
Homologous superfamily homologous superfamily10 — DNA Topoisomerase I, domain 2
Domain ID domain_id1ej9A03
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology15 — Topoisomerase I; Chain A, domain 3
Homologous superfamily homologous superfamily10 — Topoisomerase I; Chain A, domain 3
Domain ID domain_id1ej9A04
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology132 — Topoisomerase I; Chain A, domain 4
Homologous superfamily homologous superfamily10

8. Citations (1)

9. Files and Curves (10)