[English] 日本語
Yorodumi
- PDB-4o3m: Ternary complex of Bloom's syndrome helicase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4o3m
TitleTernary complex of Bloom's syndrome helicase
Components
  • 5'-D(*AP*GP*CP*GP*TP*CP*GP*AP*GP*AP*TP*CP*CP*AP*AP*G)-3'
  • 5'-D(*CP*TP*TP*GP*GP*AP*TP*CP*TP*CP*GP*AP*CP*GP*CP*TP*CP*TP*CP*CP*CP*TP*TP*A)-3'
  • Bloom syndrome protein
KeywordsHydrolase/DNA / Winged Helix / Helicase / Hydrolase-DNA complex
Function / homology
Function and homology information


RecQ family helicase-topoisomerase III complex / resolution of DNA recombination intermediates / DNA/DNA annealing activity / forked DNA-dependent helicase activity / telomeric G-quadruplex DNA binding / 8-hydroxy-2'-deoxyguanosine DNA binding / telomeric D-loop binding / negative regulation of cell division / DNA geometric change / telomere maintenance via semi-conservative replication ...RecQ family helicase-topoisomerase III complex / resolution of DNA recombination intermediates / DNA/DNA annealing activity / forked DNA-dependent helicase activity / telomeric G-quadruplex DNA binding / 8-hydroxy-2'-deoxyguanosine DNA binding / telomeric D-loop binding / negative regulation of cell division / DNA geometric change / telomere maintenance via semi-conservative replication / Y-form DNA binding / telomeric D-loop disassembly / DNA double-strand break processing / four-way junction helicase activity / t-circle formation / G-quadruplex DNA binding / negative regulation of DNA recombination / cellular response to hydroxyurea / bubble DNA binding / cellular response to camptothecin / lateral element / regulation of cyclin-dependent protein serine/threonine kinase activity / Impaired BRCA2 binding to PALB2 / Processive synthesis on the C-strand of the telomere / HDR through Single Strand Annealing (SSA) / 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 / nuclear chromosome / Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) / Resolution of D-loop Structures through Holliday Junction Intermediates / mitotic G2 DNA damage checkpoint signaling / protein complex oligomerization / Impaired BRCA2 binding to RAD51 / 3'-5' DNA helicase activity / DNA 3'-5' helicase / replication fork processing / Presynaptic phase of homologous DNA pairing and strand exchange / response to X-ray / ATP-dependent activity, acting on DNA / SUMOylation of DNA damage response and repair proteins / four-way junction DNA binding / telomere maintenance / replication fork / DNA helicase activity / helicase activity / cellular response to ionizing radiation / protein homooligomerization / PML body / G2/M DNA damage checkpoint / double-strand break repair via homologous recombination / Meiotic recombination / HDR through Homologous Recombination (HRR) / nuclear matrix / p53 binding / single-stranded DNA binding / chromosome / Processing of DNA double-strand break ends / DNA recombination / Regulation of TP53 Activity through Phosphorylation / DNA replication / DNA repair / DNA damage response / positive regulation of DNA-templated transcription / nucleolus / protein homodimerization activity / ATP hydrolysis activity / protein-containing complex / DNA binding / zinc ion binding / nucleoplasm / ATP binding / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
RecQ-like DNA helicase BLM, N-terminal domain / RecQ-like DNA helicase BLM, BDHCT-box associated domain / N-terminal region of Bloom syndrome protein / BDHCT-box associated domain on Bloom syndrome protein / BDHCT / BDHCT (NUC031) domain / HRDC domain / RQC domain / RQC / RQC domain ...RecQ-like DNA helicase BLM, N-terminal domain / RecQ-like DNA helicase BLM, BDHCT-box associated domain / N-terminal region of Bloom syndrome protein / BDHCT-box associated domain on Bloom syndrome protein / BDHCT / BDHCT (NUC031) domain / HRDC domain / RQC domain / RQC / RQC domain / Helicase and RNase D C-terminal / ATP-dependent DNA helicase RecQ, zinc-binding domain / RecQ zinc-binding / HRDC domain / HRDC domain / DNA helicase, ATP-dependent, RecQ type / HRDC domain profile. / HRDC domain superfamily / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / DEAH-box subfamily ATP-dependent helicases signature. / HRDC-like superfamily / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Helicase conserved C-terminal domain / DNA polymerase; domain 1 / Arc Repressor Mutant, subunit A / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleotide triphosphate hydrolases / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / DNA / DNA (> 10) / RecQ-like DNA helicase BLM
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsSwan, M.K. / Bertrand, J.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Structure of human Bloom's syndrome helicase in complex with ADP and duplex DNA.
Authors: Swan, M.K. / Legris, V. / Tanner, A. / Reaper, P.M. / Vial, S. / Bordas, R. / Pollard, J.R. / Charlton, P.A. / Golec, J.M. / Bertrand, J.A.
History
DepositionDec 18, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 12, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 2, 2014Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Bloom syndrome protein
P: 5'-D(*AP*GP*CP*GP*TP*CP*GP*AP*GP*AP*TP*CP*CP*AP*AP*G)-3'
T: 5'-D(*CP*TP*TP*GP*GP*AP*TP*CP*TP*CP*GP*AP*CP*GP*CP*TP*CP*TP*CP*CP*CP*TP*TP*A)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,21114
Polymers87,1823
Non-polymers1,02911
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5900 Å2
ΔGint-25 kcal/mol
Surface area30560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.930, 164.680, 50.980
Angle α, β, γ (deg.)90.00, 90.14, 90.00
Int Tables number5
Space group name H-MC121

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Bloom syndrome protein / DNA helicase / RecQ-like type 2 / RecQ2 / RecQ protein-like 3


Mass: 75002.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BLM, RECQ2, RECQL3 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-2 BL21(DE3) / References: UniProt: P54132, DNA helicase

-
DNA chain , 2 types, 2 molecules PT

#2: DNA chain 5'-D(*AP*GP*CP*GP*TP*CP*GP*AP*GP*AP*TP*CP*CP*AP*AP*G)-3'


Mass: 4932.219 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Chemically synthesised oligonucleotide.
#3: DNA chain 5'-D(*CP*TP*TP*GP*GP*AP*TP*CP*TP*CP*GP*AP*CP*GP*CP*TP*CP*TP*CP*CP*CP*TP*TP*A)-3'


Mass: 7247.664 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Chemically synthesised oligonucleotide.

-
Non-polymers , 5 types, 71 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#7: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 6-10% Isopropanol, 50mM MES, 10mM magnesium chloride., pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 5, 2013 / Details: slits
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.3→35.91 Å / Num. all: 36392 / Num. obs: 36392 / % possible obs: 98.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.4 % / Biso Wilson estimate: 59.56 Å2 / Rmerge(I) obs: 0.03 / Rsym value: 0.025 / Net I/σ(I): 18.4
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.695 / Mean I/σ(I) obs: 2.1 / Num. unique all: 2666 / Rsym value: 0.498 / % possible all: 99

-
Processing

Software
NameVersionClassification
SHARPphasing
BUSTER2.11.5refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MAD
Starting model: PDB ENTRY 2V1X

2v1x


Resolution: 2.3→35.91 Å / Cor.coef. Fo:Fc: 0.9351 / Cor.coef. Fo:Fc free: 0.9204 / SU R Cruickshank DPI: 0.274 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2153 1735 5.01 %RANDOM
Rwork0.1811 ---
all0.1829 34639 --
obs0.1829 34639 94.05 %-
Displacement parametersBiso mean: 85.6 Å2
Baniso -1Baniso -2Baniso -3
1--33.2893 Å20 Å21.9695 Å2
2--18.9673 Å20 Å2
3---14.322 Å2
Refine analyzeLuzzati coordinate error obs: 0.355 Å
Refinement stepCycle: LAST / Resolution: 2.3→35.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4721 570 61 60 5412
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.015518HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.077580HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1816SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes108HARMONIC2
X-RAY DIFFRACTIONt_gen_planes754HARMONIC5
X-RAY DIFFRACTIONt_it5518HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.99
X-RAY DIFFRACTIONt_other_torsion20.71
X-RAY DIFFRACTIONt_chiral_improper_torsion739SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact6064SEMIHARMONIC4
LS refinement shellResolution: 2.3→2.37 Å / Total num. of bins used: 17
RfactorNum. reflection% reflection
Rfree0.2336 125 5.03 %
Rwork0.2141 2359 -
all0.2152 2484 -
obs--94.05 %
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)
12.0331-0.74320.15182.8195-0.4142.3938-0.09170.10440.1319-0.02210.00650.108-0.0150.07860.0852-0.2556-0.005-0.016-0.42590.0365-0.4082119.341923.505658.2881
21.80850.3909-1.01984.06470.13133.30210.1337-0.1556-0.17160.4443-0.14150.15630.14830.00020.0077-0.1410.05660.0384-0.39880.0117-0.4355120.9827-6.458668.6107
32.1456-0.4618-0.29318.6766-0.14474.0707-0.14050.6618-0.1671-0.40550.25110.72540.0237-0.678-0.1106-0.03720.06270.0037-0.1939-0.0425-0.2463117.4028-14.932449.7463
44.957-0.1307-1.26421.09120.53845.8626-0.2123-0.12010.4048-0.27870.136-1.5439-0.53011.17310.07630.13470.03010.0541-0.1498-0.06610.2303137.7842-4.437454.9265
54.2479-1.23590.085512.48541.58422.3610.14970.1896-0.1248-0.95590.0424-0.4354-0.301-0.2027-0.1921-0.06570.04030.0437-0.4033-0.0079-0.3637125.022-30.155143.9357
64.2526-0.1353-0.01411.9166-0.44925.7201-0.1158-0.3230.14660.2955-0.1074-0.2241-0.0960.88810.2233-0.11110.0675-0.0548-0.17310.019-0.443132.155913.213284.1131
77.06794.4478-3.62320-7.08463.9954-0.1325-0.2099-0.91140.4028-0.18510.84910.5223-0.8370.31760.078-0.22810.3664-0.59130.0155-0.1288112.1717-36.45257.5364
84.66212.69751.75162.0649-4.20250.0085-0.0966-0.26510.15940.42010.2496-0.04380.15030.2706-0.1530.42760.2701-0.0921-0.54490.1281-0.4982124.2676-34.24167.4404
93.3217-1.6252-3.53990.6015-5.487-0.0173-0.08020.187-0.47260.18560.0894-0.32780.31190.2796-0.00920.41520.547-0.2411-0.02440.32880.467136.0595-42.79367.4843
101.10921.75582.26193.8532-1.48133.06510.01-0.30560.29330.0030.0824-0.0005-0.34780.1342-0.09240.38790.0273-0.61370.03030.2580.1677138.7558-33.839265.3098
111.901-0.9888-1.88925.0542-2.397214.3362-0.0251-0.3886-0.51261.3072-0.06361.02250.317-0.54620.08870.06080.11210.0996-0.47440.1031-0.2864123.2701-40.44963.9568
123.260.2942-5.262110.033511.2206-0.0257-0.1426-0.385-0.084-0.1205-0.33610.59210.5631-0.48470.4786-0.2931-0.022-0.0288-0.4906-0.0324-0.4623108.7164-20.713461.7505
130.0788-1.25730.40630.21720.23360.4764-0.03340.05630.026-0.01380.0390.03510.0045-0.0208-0.00560.58830.2647-0.07120.0923-0.09430.1359104.1594-1.436958.0734
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|636 - 856 }A636 - 856
2X-RAY DIFFRACTION2{ A|857 - 993 }A857 - 993
3X-RAY DIFFRACTION3{ A|994 - 1032 }A994 - 1032
4X-RAY DIFFRACTION4{ A|1033 - 1068 }A1033 - 1068
5X-RAY DIFFRACTION5{ A|1069 - 1195 }A1069 - 1195
6X-RAY DIFFRACTION6{ A|1205 - 1298 }A1205 - 1298
7X-RAY DIFFRACTION7{ P|1 - 5 }P1 - 5
8X-RAY DIFFRACTION8{ P|6 - 9 }P6 - 9
9X-RAY DIFFRACTION9{ P|10 - 16 }P10 - 16
10X-RAY DIFFRACTION10{ T|1 - 6 }T1 - 6
11X-RAY DIFFRACTION11{ T|7 - 12 }T7 - 12
12X-RAY DIFFRACTION12{ T|13 - 18 }T13 - 18
13X-RAY DIFFRACTION13{ T|19 - 24 }T19 - 24

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more