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- PDB-4cgy: Crystal structure of the human topoisomerase III alpha-RMI1 complex -

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Basic information

Entry
Database: PDB / ID: 4cgy
TitleCrystal structure of the human topoisomerase III alpha-RMI1 complex
Components
  • DNA TOPOISOMERASE 3-ALPHA
  • RECQ-MEDIATED GENOME INSTABILITY PROTEIN 1
KeywordsDNA REPLICATION/ISOMERASE / DNA REPLICATION-ISOMERASE COMPLEX / DOUBLE HOLLIDAY JUNCTION DISSOLUTION / DECATENATION / MINIMAL DISSOLVASOME
Function / homology
Function and homology information


RecQ family helicase-topoisomerase III complex / reduction of food intake in response to dietary excess / resolution of DNA recombination intermediates / chromosome separation / DNA topoisomerase / DNA topoisomerase type I (single strand cut, ATP-independent) activity / resolution of meiotic recombination intermediates / Strand-asynchronous mitochondrial DNA replication / mitochondrial DNA metabolic process / Impaired BRCA2 binding to PALB2 ...RecQ family helicase-topoisomerase III complex / reduction of food intake in response to dietary excess / resolution of DNA recombination intermediates / chromosome separation / DNA topoisomerase / DNA topoisomerase type I (single strand cut, ATP-independent) activity / resolution of meiotic recombination intermediates / Strand-asynchronous mitochondrial DNA replication / mitochondrial DNA metabolic process / Impaired BRCA2 binding to PALB2 / Homologous DNA Pairing and Strand Exchange / Defective homologous recombination repair (HRR) due to BRCA1 loss of function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA1 binding function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA2/RAD51/RAD51C binding function / Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) / Resolution of D-loop Structures through Holliday Junction Intermediates / HDR through Single Strand Annealing (SSA) / Impaired BRCA2 binding to RAD51 / DNA topological change / Presynaptic phase of homologous DNA pairing and strand exchange / response to glucose / meiotic cell cycle / double-strand break repair via homologous recombination / PML body / G2/M DNA damage checkpoint / HDR through Homologous Recombination (HRR) / Meiotic recombination / multicellular organism growth / glucose homeostasis / single-stranded DNA binding / Processing of DNA double-strand break ends / DNA recombination / Regulation of TP53 Activity through Phosphorylation / DNA replication / nuclear body / mitochondrial matrix / DNA repair / nucleotide binding / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
RecQ-mediated genome instability protein 1, N-terminal domain / RecQ-mediated genome instability protein Rmi1, C-terminal domain / RecQ-mediated genome instability protein 1, C-terminal OB-fold domain / RecQ-mediated genome instability protein 1, N-terminal helical domain superfamily / : / Recq-mediated genome instability protein 1, C-terminal OB-fold / RMI1, N-terminal helical domain / DUF1767 / Zinc finger, GRF-type / GRF zinc finger ...RecQ-mediated genome instability protein 1, N-terminal domain / RecQ-mediated genome instability protein Rmi1, C-terminal domain / RecQ-mediated genome instability protein 1, C-terminal OB-fold domain / RecQ-mediated genome instability protein 1, N-terminal helical domain superfamily / : / Recq-mediated genome instability protein 1, C-terminal OB-fold / RMI1, N-terminal helical domain / DUF1767 / Zinc finger, GRF-type / GRF zinc finger / Zinc finger GRF-type profile. / DNA topoisomerase, type IA, zn finger / Topoisomerase DNA binding C4 zinc finger / Topoisomerase I, domain 3 / DNA topoisomerase 3-like, TOPRIM domain / Topoisomerase I; domain 2 / Topoisomerase I, domain 2 / RecQ mediated genome instability protein 1, N-terminal / RecQ mediated genome instability protein, N-terminal OB-fold superfamily / RMI1, N-terminal OB-fold domain / Rossmann fold - #140 / Topoisomerase I; domain 4 / Topoisomerase I, domain 4 / Topoisomerase I; domain 3 / DNA topoisomerase, type IA / DNA topoisomerase, type IA, central region, subdomain 2 / DNA topoisomerase, type IA, active site / Topoisomerase (Topo) IA-type active site signature. / Topoisomerase (Topo) IA-type catalytic domain profile. / DNA topoisomerase, type IA, domain 2 / DNA topoisomerase, type IA, DNA-binding domain / DNA topoisomerase, type IA, central / DNA topoisomerase, type IA, central region, subdomain 1 / DNA topoisomerase, type IA, central region, subdomain 3 / DNA topoisomerase, type IA, core domain / DNA topoisomerase / Bacterial DNA topoisomeraes I ATP-binding domain / Bacterial DNA topoisomerase I DNA-binding domain / TOPRIM / Toprim domain / Toprim domain profile. / TOPRIM domain / Helicase, Ruva Protein; domain 3 / Distorted Sandwich / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA topoisomerase 3-alpha / RecQ-mediated genome instability protein 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsBocquet, N. / Bunker, R.D. / Thoma, N.H.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2014
Title: Structural and Mechanistic Insight Into Holliday-Junction Dissolution by Topoisomerase Iiialpha and Rmi1
Authors: Bocquet, N. / Bizard, A.H. / Abdulrahman, W. / Larsen, N.B. / Faty, M. / Cavadini, S. / Bunker, R.D. / Kowalczykowski, S.C. / Cejka, P. / Hickson, I.D. / Thoma, N.H.
History
DepositionNov 27, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 12, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2014Group: Database references
Revision 1.2Mar 19, 2014Group: Database references
Revision 1.3Apr 3, 2019Group: Data collection / Other / Source and taxonomy
Category: entity_src_gen / pdbx_database_proc / pdbx_database_status
Item: _entity_src_gen.pdbx_host_org_cell_line / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA TOPOISOMERASE 3-ALPHA
B: RECQ-MEDIATED GENOME INSTABILITY PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,2533
Polymers111,2292
Non-polymers241
Water79344
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2770 Å2
ΔGint-16.1 kcal/mol
Surface area37990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.010, 94.010, 381.690
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein DNA TOPOISOMERASE 3-ALPHA / DNA TOPOISOMERASE III ALPHA


Mass: 86584.641 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-753
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): High Five / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: Q13472, EC: 5.99.1.2
#2: Protein RECQ-MEDIATED GENOME INSTABILITY PROTEIN 1 / BLM-ASSOCIATED PROTEIN OF 75 KDA / BLAP75 / FAAP75


Mass: 24644.457 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-219
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): High Five / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: Q9H9A7
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 5.4 Å3/Da / Density % sol: 77 % / Description: NONE
Crystal growpH: 7
Details: 8-12% (W/V) PEG 2000, 100 MM TRIS-HCL PH 7.0, 200 MM MGCL2

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Data collection

DiffractionMean temperature: 10 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 19, 2010 / Details: DYNAMICALLY BENDABLE MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.85→62.78 Å / Num. obs: 41328 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 100 % / Biso Wilson estimate: 93.75 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 16.7
Reflection shellResolution: 2.85→2.97 Å / Redundancy: 14.7 % / Mean I/σ(I) obs: 2.2 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.11.4refinement
XDSdata reduction
XDSAIMLESSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1ECL AND 3NBI

1ecl

3nbi


Resolution: 2.85→65.49 Å / Cor.coef. Fo:Fc: 0.9298 / Cor.coef. Fo:Fc free: 0.9116 / SU R Cruickshank DPI: 0.374 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.376 / SU Rfree Blow DPI: 0.26 / SU Rfree Cruickshank DPI: 0.263
RfactorNum. reflection% reflectionSelection details
Rfree0.231 2075 5.03 %RANDOM
Rwork0.1973 ---
obs0.1989 41229 99.96 %-
Displacement parametersBiso mean: 80.28 Å2
Baniso -1Baniso -2Baniso -3
1--8.6474 Å20 Å20 Å2
2---8.6474 Å20 Å2
3---17.2947 Å2
Refine analyzeLuzzati coordinate error obs: 0.439 Å
Refinement stepCycle: LAST / Resolution: 2.85→65.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6557 0 1 44 6602
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0096700HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.049086HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3142SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes184HARMONIC2
X-RAY DIFFRACTIONt_gen_planes956HARMONIC5
X-RAY DIFFRACTIONt_it6700HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.69
X-RAY DIFFRACTIONt_other_torsion3.05
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion869SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact7326SEMIHARMONIC4
LS refinement shellResolution: 2.85→2.92 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2759 136 4.59 %
Rwork0.2403 2829 -
all0.2419 2965 -
obs--99.96 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.4358-0.1675-0.01751.33130.25731.67440.00630.0628-0.0481-0.154-0.0120.1392-0.12490.19850.0057-0.0998-0.10540.0099-0.2789-0.0034-0.197-20.85647.529831.4428
22.00832.4241.93322.7452.44682.8026-0.2244-0.2050.1526-0.1383-0.01560.0414-0.4143-0.28040.24-0.07890.0128-0.1457-0.0087-0.0348-0.1631-50.2695-14.2355-10.602
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B

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