SAXSdb — 4cgy

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

DNA TOPOISOMERASE 3-ALPHA

HOMO SAPIENS

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 2–753	Fragment：RESIDUES 2-753	RECQ-MEDIATED GENOME INSTABILITY PROTEIN 1 × 1 （Q9H9A7） MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7；8-12% (W/V) PEG 2000, 100 MM TRIS-HCL PH 7.0, 200 MM MGCL2	Resolution 2.85 Å R-free 0.231

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 4CGY	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4CHT Crystal structure of the human topoisomerase III alpha-RMI1 complex with bound calcium ion Deposited 2013-12-04	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 2–753（752 aa）	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；8% (W/V) PEG 5000 MME, 200 MM CALCIUM CITRATE, 100 MM TRIS/HCL PH 7.0	Resolution 3.25 Å R-free 0.225

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	TOP3A_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–754； UniProt 2–753

RECQ-MEDIATED GENOME INSTABILITY PROTEIN 1

HOMO SAPIENS

UniProt Q9H9A7

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 1–219	Fragment：RESIDUES 1-219	DNA TOPOISOMERASE 3-ALPHA × 1 （Q13472） MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7；8-12% (W/V) PEG 2000, 100 MM TRIS-HCL PH 7.0, 200 MM MGCL2	Resolution 2.85 Å R-free 0.231

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 4CGY	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3MXN Crystal structure of the RMI core complex Deposited 2010-05-07	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 473–625（153 aa） Fragment：C-terminal OB domain (unp residues 473-625)	Not recorded	BEN BENZAMIDINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.1；298 K；10 mM Hepes pH 7.1, 0.05 M NaSCN, 20% ethylene glycol, 2 mM DTT, 13% polyethylene glycol 3350, with benzamidine (1%) added to the drop, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.55 Å R-free 0.231
3NBH Crystal structure of human RMI1C-RMI2 complex Deposited 2010-06-03	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 475–625（151 aa） Fragment：RMI1C, residues 475-625	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；The precipitant/well solution contained 18% PEG 3350, 300 mM NaSCN, and 10 mM DTT. , pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K	Resolution 2.00 Å R-free 0.258
3NBI Crystal structure of human RMI1 N-terminus Deposited 2010-06-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–213（212 aa） Fragment：RMI1N, residues 2-213	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277.15 K；The precipitant/well solution contained 100 mM Tris-HCl pH 8.5, 18% PEG 3350, 300 mM NaSCN, 10 mM NiCl2 and 10 mM DTT., VAPOR DIFFUSION, HANGING DROP, temperature 277.15K	Resolution 2.00 Å R-free 0.255
4CHT Crystal structure of the human topoisomerase III alpha-RMI1 complex with bound calcium ion Deposited 2013-12-04	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–219（219 aa） Fragment：RESIDUES 1-219	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；8% (W/V) PEG 5000 MME, 200 MM CALCIUM CITRATE, 100 MM TRIS/HCL PH 7.0	Resolution 3.25 Å R-free 0.225
4DAY Crystal structure of the RMI core complex with MM2 peptide from FANCM Deposited 2012-01-13	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 473–625（153 aa） Fragment：C-terminal OB domain (residues 473-625)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.8；298 K；200 mM Na2SO4, 5% polyethylene glycol 3350, pH 8.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.30 Å R-free 0.325
7XUV Crystal structure of RPA70N-RMI1 fusion Deposited 2022-05-20	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 243–262（20 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；278 K；30% PEG 2000 MME	Resolution 1.60 Å R-free 0.220
9DHK RMI1-RMI2 bound to cyclic peptide L3 Deposited 2024-09-03	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 475–625（151 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；1.8 M sodium phosphate monobasic monohydrate / potassium phosphate dibasic pH 5.0	Resolution 2.35 Å R-free 0.247
9DHK RMI1-RMI2 bound to cyclic peptide L3 Deposited 2024-09-03	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 475–625（151 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；1.8 M sodium phosphate monobasic monohydrate / potassium phosphate dibasic pH 5.0	Resolution 2.35 Å R-free 0.247
9DHK RMI1-RMI2 bound to cyclic peptide L3 Deposited 2024-09-03	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain G 482–625（144 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；1.8 M sodium phosphate monobasic monohydrate / potassium phosphate dibasic pH 5.0	Resolution 2.35 Å R-free 0.247
9DHK RMI1-RMI2 bound to cyclic peptide L3 Deposited 2024-09-03	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain J 475–625（151 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；1.8 M sodium phosphate monobasic monohydrate / potassium phosphate dibasic pH 5.0	Resolution 2.35 Å R-free 0.247
9DI4 RMI1-RMI2 bound to cyclic peptide L4 Deposited 2024-09-05	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 475–625（151 aa）	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5；293 K；0.01M zinc chloride, 0.1M sodium acetate pH 5.0, 20% w/v PEG 6000	Resolution 2.70 Å R-free 0.248
9PFD RMI1-RMI2 bound to synthetic peptide P4Ser Deposited 2025-07-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 475–625（151 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；1.8 M sodium phosphate monobasic monohydrate, potassium phosphate dibasic, pH 5.0	Resolution 2.01 Å R-free 0.224

9 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RMI1_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–219； UniProt 1–219

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	4cgy
Deposition date deposition_date	2013-11-27
Structure title title	Crystal structure of the human topoisomerase III alpha-RMI1 complex
Keywords keywords	DNA REPLICATION-ISOMERASE COMPLEX, DOUBLE HOLLIDAY JUNCTION DISSOLUTION, DECATENATION, MINIMAL DISSOLVASOME; DNA REPLICATION/ISOMERASE
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	37.28 Å
Radius of gyration Rg (electron density) rg_electron	37.27 Å
Forward intensity I(0) i0	132380000.00
Molecular weight molecular_weight	93177.0 kDa
Excluded volume excluded_volume	117020 Å³
Envelope volume envelope_volume	161350 Å³
Hydration-shell volume shell_volume	37926 Å³
Envelope diameter envelope_diameter	130.3 Å
Shell Rg shell_rg	41.02 Å
Envelope Rg envelope_rg	36.86 Å
Shape Rg shape_rg	37.25 Å
Total Rg total_rg	37.63 Å
Total atoms total_atoms	6558
Residues n_residues	824
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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

Maximum dimension Dmax dmax	131.8 Å
Rg (real space) rg_real	37.55 Å
Rg uncertainty (real space) rg_real_error	1.60 Å
I(0) (real space) i0_real	1.3240e+08
I(0) uncertainty (real space) i0_real_error	2.6920e+06
Rg (reciprocal space) rg_reciprocal	37.39 Å
I(0) (reciprocal space) i0_reciprocal	132400000.0000
Solution quality estimate total_estimate	0.6298
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	37.7 Å
Skewness Skewness skewness	0.446
Kurtosis Kurtosis kurtosis	-0.393
Angular range angular_range	— – 0.2100 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	12250000.0000
Real-space data points n_real_points	43
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.796; Stabil: 1.000; Sysdev: 0.020; Positv: 1.000; Valcen: 0.850; Smooth: 0.886

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	DNA TOPOISOMERASE 3-ALPHA
Molecular weight formula_weight	86584.6 kDa
EC 编号 ec_number	5.99.1.2
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	6602

GRIFPVARYALRWLRRPEDRAFSRAAMEMALRGVRKVLCVAEKNDAAKGIADLLSNGRMRRREGLSKFNKIYEFDYHLYGQNVTMVMTSVSGHLLAHDFQMQFRKWQSCNPLVLFEAEIEKYCPENFVDIKKTLERETRQCQALVIWTDCDREGENIGFEIIHVCKAVKPNLQVLRARFSEITPHAVRTACENLTEPDQRVSDAVDVRQELDLRIGAAFTRFQTLRLQRIFPEVLAEQLISYGSCQFPTLGFVVERFKAIQAFVPEIFHRIKVTHDHKDGIVEFNWKRHRLFNHTACLVLYQLCVEDPMATVVEVRSKPKSKWRPQALDTVELEKLASRKLRINAKETMRIAEKLYTQGYISYPRTETNIFPRDLNLTVLVEQQTPDPRWGAFAQSILERGGPTPRNGNKSDQAHPPIHPTKYTNNLQGDEQRLYEFIVRHFLACCSQDAQGQETTVEIDIAQERFVAHGLMILARNYLDVYPYDHWSDKILPVYEQGSHFQPSTVEMVDGETSPPKLLTEADLIALMEKHGIGTDATHAEHIETIKARMYVGLTPDKRFLPGHLGMGLVEGYDSMGYEMSKPDLRAELEADLKLICDGKKDKFVVLRQQVQKYKQVFIEAVAKAKKLDEALAQYFGNGTELAQQEDIYPAMPEPIRKCPQCNKDMVLKTKKNGGFYLSCMGFPECRSAVWLPDSVLEASRDSSVCPVCQPHPVYRLKLKFKRGSLPPTMPLEFVCCIGGCDDTLREILDLRFS

来源 Source

来源生物 organism	HOMO SAPIENS
通用名 common_name	HUMAN
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	TRICHOPLUSIA NI

Entity 2 Entity 2 polymer

Description description	RECQ-MEDIATED GENOME INSTABILITY PROTEIN 1
Molecular weight formula_weight	24644.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MNVTSIALRAETWLLAAWHVKVPPMWLEACINWIQEENNNVNLSQAQMNKQVFEQWLLTDLRDLEHPLLPDGILEIPKGELNGFYALQINSLVDVSQPAYSQIQKLRGKNTTNDLVTAEAQVTPKPWEAKPSRMLMLQLTDGIVQIQGMEYQPIPILHSDLPPGTKILIYGNISFRLGVLLLKPENVKVLGGEVDALLEEYAQEKVLARLIGEPDLVVS

来源 Source

来源生物 organism	HOMO SAPIENS
通用名 common_name	HUMAN
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	TRICHOPLUSIA NI

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	44

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7. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	4cgyA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	140 —

Domain ID domain_id	4cgyA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	460 — Topoisomerase I; domain 2
Homologous superfamily homologous superfamily	10 — Topoisomerase I, domain 2

Domain ID domain_id	4cgyA03
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	20 — Topoisomerase I; domain 3
Homologous superfamily homologous superfamily	10 — Topoisomerase I, domain 3

Domain ID domain_id	4cgyA04
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	290 — Topoisomerase I; domain 4
Homologous superfamily homologous superfamily	10 — Topoisomerase I, domain 4

Domain ID domain_id	4cgyB01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	1020 — RecQ-mediated genome instability protein 1, N-terminal domain

Domain ID domain_id	4cgyB02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	770 — RecQ-mediated genome instability protein Rmi1, C-terminal domain

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8. Citations (1)

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Unit-cell length a length_a	94.010 Å
Unit-cell length b length_b	94.010 Å
Unit-cell length c length_c	381.690 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	8

Space group space_group	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	2.850 Å
Low-resolution limit resolution_low	65.490 Å
R factor r_factor	0.1989
R_work r_work	0.1973
R_free r_free	0.2310

fit	/app/data/saxs_computation/cg/4cgy/4cgy.fit
pddf	/app/data/pr_computation/cg/4cgy/4cgy.pr.out
profile	/app/data/saxs_computation/cg/4cgy/4cgy.dat

Crystal structure of the human topoisomerase III alpha-RMI1 complex

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

DNA TOPOISOMERASE 3-ALPHA

State in the Current Structure

Other States of the Same Protein in the Database

RECQ-MEDIATED GENOME INSTABILITY PROTEIN 1

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)