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9c9y

Human TOP3B-TDRD3 core complex in DNA pre-cleavage state

Method: ELECTRON MICROSCOPY
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1. Protein Identity and Related Structures Protein Identity & Related Structures

DNA topoisomerase 3-beta-1

Homo sapiens

UniProt O95985

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–DNA Heteromer Protein 2 DNA 1 Tudor domain-containing protein 3 × 1 （Q9H7E2） ;DNA (5'-D(P*AP*CP*TP*AP*AP*AP*AP*T)-3') ; × 1 MANGANESE (II) ION × 2 Consistent with all polymers

Other States of the Same Protein in the Database

Monomer
5gvc 5gvc

2 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
5gve 9c9w 9c9y 9ca0 9ca1 9ca4 9cag 9cah 9caj 9cak 9cal

11 assemblies

View Construct and Data Evidence
UniProt name TOP3B_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 2–612； UniProt 1–611

Tudor domain-containing protein 3

Homo sapiens

UniProt Q9H7E2

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–DNA Heteromer Protein 2 DNA 1 DNA topoisomerase 3-beta-1 × 1 （O95985） ;DNA (5'-D(P*AP*CP*TP*AP*AP*AP*AP*T)-3') ; × 1 MANGANESE (II) ION × 2 Consistent with all polymers

Other States of the Same Protein in the Database

Monomer
1wji 3pmt 3s6w 5gvd 5gvd 5yj8 6v9t 6v9t 8jtn

9 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
2lto 3pnw 3pnw 3pnw 3pnw 3pnw 3pnw 3pnw 3pnw 5gve 9c9w 9c9y

20 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name TDRD3_HUMAN
Isoform Q9H7E2-3
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–161； UniProt 1–161

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id9c9y
Deposition date deposition_date2024-06-16
Structure title titleHuman TOP3B-TDRD3 core complex in DNA pre-cleavage state
Keywords keywordsTopoisomerase, DNA, ISOMERASE-DNA complex; ISOMERASE/DNA
Experimental Method methodELECTRON MICROSCOPY
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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

9c9y__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

9c9y__assembly_1__model_1 | I(q)

10-2 10-1 106 107 108 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

9c9y__assembly_1__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）36.57 Å
Rg (electron density)36.58 Å
Total Rg37.00 Å
Atom count6225
Residues781
Excluded volume110510 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 9c9y__assembly_1__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (4)

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7. Citations (1)