9c9w

Dimerized human TOP3B-TDRD3 core complex with a DNA mismatch bubble

Method: ELECTRON MICROSCOPY

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

DNA topoisomerase 3-beta-1

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 4 DNA 3	Tudor domain-containing protein 3 × 2 （Q9H7E2） ;DNA (5'-D(PCPAPGPAPTPCPAPGPAPAPTPGPAPAPTPAPTPAPCPTPAPAPA)-3') ; × 1 ;DNA (5'-D(APTPTPGPGPAPGPTPTPCPAPTPGPTPGPAPTPGPC)-3') ; × 1 DNA (38-MER) × 1 MANGANESE (II) ION × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TOP3B_HUMAN
Isoform	—
PDB entities	1, 3
Chains and sequence ranges	Author chain A； PDBConstruct 2–612； UniProt 1–611 Author chain C； 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 4 DNA 3	DNA topoisomerase 3-beta-1 × 1 （O95985） DNA topoisomerase 3-beta-1 × 1 （O95985） ;DNA (5'-D(PCPAPGPAPTPCPAPGPAPAPTPGPAPAPTPAPTPAPCPTPAPAPA)-3') ; × 1 ;DNA (5'-D(APTPTPGPGPAPGPTPTPCPAPTPGPTPGPAPTPGPC)-3') ; × 1 DNA (38-MER) × 1 MANGANESE (II) ION × 1	Consistent with all polymers

Other States of the Same Protein in the Database

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 Author chain D； 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_id	9c9w
Deposition date deposition_date	2024-06-16
Last revision last_revision	2025-02-05
Structure title title	Dimerized human TOP3B-TDRD3 core complex with a DNA mismatch bubble
Keywords keywords	Topoisomerase, DNA, Supercoiling, ISOMERASE-DNA complex; ISOMERASE/DNA
Experimental Method method	ELECTRON 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.

9c9w__assembly_1__model_1

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

Download this curve (.dat)

9c9w__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9c9w__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	46.04 Å
Rg (electron density)	46.63 Å
Total Rg	46.77 Å
Atom count	13761
Residues	1625
Excluded volume	240150 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9c9w__assembly_1__model_1`	heptameric （7）	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 (7)

Entity 1 Entity 1 polymer

Description description	DNA topoisomerase 3-beta-1
Molecular weight formula_weight	69037.9 kDa
EC 编号 ec_number	5.6.2.1
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	13761

VMKTVLMVAEKPSLAQSIAKILSRGSLSSHKGLNGACSVHEYTGTFAGQPVRFKMTSVCGHVMTLDFLGKYNKWDKVDPAELFSQAPTEKKEANPKLNMVKFLQVEGRGCDYIVLWLDCDKEGENICFEVLDAVLPVMNKAHGGEKTVFRARFSSITDTDICNAMACLGEPDHNEALSVDARQELDLRIGCAFTRFQTKYFQGKYGDLDSSLISFGPCQTPTLGFCVERHDKIQSFKPETYWVLQAKVNTDKDRSLLLDWDRVRVFDREIAQMFLNMTKLEKEAQVEATSRKEKAKQRPLALNTVEMLRVASSSLGMGPQHAMQTAERLYTQGYISYPRTETTHYPENFDLKGSLRQQANHPYWADTVKRLLAEGINRPRKGHDAGDHPPITPMKSATEAELGGDAWRLYEYITRHFIATVSHDCKYLQSTISFRIGPELFTCSGKTVLSPGFTEVMPWQSVPLEESLPTCQRGDAFPVGEVKMLEKQTNPPDYLTEAELITLMEKHGIGTDASIPVHINNICQRNYVTVESGRRLKPTNLGIVLVHGYYKIDAELVLPTIRSAVEKQLNLIAQGKADYRQVLGHTLDVFKRKFHYFVDSIAGMDELMEVSF

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Homo sapiens

Entity 2 Entity 2 polymer

Description description	Tudor domain-containing protein 3
Molecular weight formula_weight	17429.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D

MAQVAGAALSQAGWYLSDEGIEACTSSPDKVNVNDIILIALNTDLRTIGKKFLPSDINSGKVEKLEGPCVLQIQKIRNVAAPKDNEESQAAPRMLRLQMTDGHISCTAVEFSYMSKISLNTPPGTKVKLSGIVDIKNGFLLLNDSNTTVLGGEVEHLIEKW

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Homo sapiens

Entity 3 Entity 3 polymer

Description description	DNA topoisomerase 3-beta-1
Molecular weight formula_weight	69117.9 kDa
EC 编号 ec_number	5.6.2.1
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Homo sapiens

Entity 4 Entity 4 polymer

Description description	;DNA (5'-D(PCPAPGPAPTPCPAPGPAPAPTPGPAPAPTPAPTPAPCPTPAPAP*A)-3') ;
Molecular weight formula_weight	7089.7 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	E

CAGATCAGAATGAATATACTAAA

Entity 5 Entity 5 polymer

Description description	;DNA (5'-D(APTPTPGPGPAPGPTPTPCPAPTPGPTPGPAPTPGP*C)-3') ;
Molecular weight formula_weight	5890.8 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	F

ATTGGAGTTCATGTGATGC

Entity 6 Entity 6 polymer

Description description	DNA (38-MER)
Molecular weight formula_weight	12379.8 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	L

GCATCACATGAACTCCNNNNGTGTTCAATTCATTCTGATCTG

Entity 7 Entity 7 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	1

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	4.25 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	63358

Dimerized human TOP3B-TDRD3 core complex with a DNA mismatch bubble

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

DNA topoisomerase 3-beta-1

State in the Current Structure

Other States of the Same Protein in the Database

Tudor domain-containing protein 3

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9c9w__assembly_1__model_1

9c9w__assembly_1__model_1 | I(q)

9c9w__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 polymer

Polymer Polymer

Entity 6 Entity 6 polymer

Polymer Polymer

Entity 7 Entity 7 non-polymer

7. Citations (1)

Dimerized human TOP3B-TDRD3 core complex with a DNA mismatch bubble

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

DNA topoisomerase 3-beta-1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Tudor domain-containing protein 3

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9c9w__assembly_1__model_1

9c9w__assembly_1__model_1 | I(q)

9c9w__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 polymer

Polymer Polymer

Entity 6 Entity 6 polymer

Polymer Polymer

Entity 7 Entity 7 non-polymer

7. Citations (1)