[English] 日本語
Yorodumi
- PDB-7auc: Crystal structure of an engineered helicase domain construct for ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7auc
TitleCrystal structure of an engineered helicase domain construct for human Bloom syndrome protein (BLM)
ComponentsBloom syndrome protein,Bloom syndrome protein
KeywordsNUCLEAR PROTEIN / Helicase / RecQ / BLM / DNA Repair
Function / homology
Function and homology information


RecQ family helicase-topoisomerase III complex / telomeric G-quadruplex DNA binding / resolution of DNA recombination intermediates / 8-hydroxy-2'-deoxyguanosine DNA binding / telomeric D-loop binding / DNA/DNA annealing activity / telomere maintenance via semi-conservative replication / t-circle formation / telomeric D-loop disassembly / cellular response to camptothecin ...RecQ family helicase-topoisomerase III complex / telomeric G-quadruplex DNA binding / resolution of DNA recombination intermediates / 8-hydroxy-2'-deoxyguanosine DNA binding / telomeric D-loop binding / DNA/DNA annealing activity / telomere maintenance via semi-conservative replication / t-circle formation / telomeric D-loop disassembly / cellular response to camptothecin / DNA geometric change / Y-form DNA binding / negative regulation of cell division / cellular response to hydroxyurea / G-quadruplex DNA binding / lateral element / negative regulation of DNA recombination / bubble DNA binding / DNA double-strand break processing / Impaired BRCA2 binding to PALB2 / Processive synthesis on the C-strand of the telomere / regulation of cyclin-dependent protein serine/threonine kinase activity / 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) / 3'-5' DNA helicase activity / Resolution of D-loop Structures through Holliday Junction Intermediates / DNA 3'-5' helicase / HDR through Single Strand Annealing (SSA) / nuclear chromosome / Impaired BRCA2 binding to RAD51 / mitotic G2 DNA damage checkpoint signaling / protein complex oligomerization / replication fork processing / Presynaptic phase of homologous DNA pairing and strand exchange / ATP-dependent activity, acting on DNA / response to X-ray / SUMOylation of DNA damage response and repair proteins / DNA helicase activity / four-way junction DNA binding / telomere maintenance / replication fork / cellular response to ionizing radiation / isomerase activity / helicase activity / double-strand break repair via homologous recombination / G2/M DNA damage checkpoint / PML body / protein homooligomerization / 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 / forked DNA-dependent helicase activity / single-stranded 3'-5' DNA helicase activity / four-way junction helicase activity / double-stranded DNA helicase activity / DNA replication / DNA repair / DNA damage response / positive regulation of DNA-templated transcription / nucleolus / protein homodimerization activity / protein-containing complex / ATP hydrolysis activity / DNA binding / zinc ion binding / nucleoplasm / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
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 / RQC domain / RQC / RQC domain / Helicase and RNase D C-terminal ...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 / RQC domain / RQC / RQC domain / Helicase and RNase D C-terminal / HRDC domain / HRDC domain / HRDC domain profile. / ATP-dependent DNA helicase RecQ, zinc-binding domain / RecQ zinc-binding / DNA helicase, ATP-dependent, RecQ type / 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 / Helicase conserved C-terminal domain / 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 / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ACETATE ION / ADENOSINE-5'-DIPHOSPHATE / RecQ-like DNA helicase BLM
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å
AuthorsChen, X. / Oliver, A.W.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Cancer Research UKC302/A24386 United Kingdom
Wellcome Trust110578/Z/15/Z United Kingdom
Citation
Journal: Elife / Year: 2021
Title: Uncovering an allosteric mode of action for a selective inhibitor of human Bloom syndrome protein.
Authors: Chen, X. / Ali, Y.I. / Fisher, C.E. / Arribas-Bosacoma, R. / Rajasekaran, M.B. / Williams, G. / Walker, S. / Booth, J.R. / Hudson, J.J. / Roe, S.M. / Pearl, L.H. / Ward, S.E. / Pearl, F.M. / Oliver, A.W.
#1: Journal: Biorxiv / Year: 2020
Title: Uncovering an allosteric mode of action for a selective inhibitor of human Bloom syndrome protein
Authors: Chen, X. / Ali, Y. / Fisher, C.E.L. / Arribas-Bosacoma, R. / Rajasekaran, M.B. / Williams, G. / Walker, S. / Roe, S.M. / Pearl, L.H. / Ward, S.E. / Pearl, F.M.G. / Oliver, A.W.
History
DepositionNov 2, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 16, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 17, 2021Group: Database references / Category: citation / citation_author
Revision 1.2Jan 31, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Bloom syndrome protein,Bloom syndrome protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,59520
Polymers63,8841
Non-polymers1,71119
Water7,764431
1


  • Idetical with deposited unit
  • defined by author&software
  • monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4250 Å2
ΔGint-26 kcal/mol
Surface area21830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.28, 107.69, 55.2
Angle α, β, γ (deg.)90, 109.31, 90
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 1 molecules A

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


Mass: 63884.465 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BLM, RECQ2, RECQL3 / Plasmid: pET-17b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P54132, DNA helicase

-
Non-polymers , 9 types, 450 molecules

#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#8: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#9: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 431 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.39 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Morpheus-HT, condition A8, Molecular Dimensions 0.06 M divalents, 37.5% Buffer System 2 and 37.5% Precipitant Mix 4 Divalents = 0.3M magnesium chloride, 0.3M calcium chloride Buffer system 2 ...Details: Morpheus-HT, condition A8, Molecular Dimensions 0.06 M divalents, 37.5% Buffer System 2 and 37.5% Precipitant Mix 4 Divalents = 0.3M magnesium chloride, 0.3M calcium chloride Buffer system 2 = 1M sodium HEPES, MOPS (acid) pH 7.5 75% Precipitant Mix 4 = 25% w/v MPD, 25% v/v PEG1000, 25% w/v PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97794 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97794 Å / Relative weight: 1
ReflectionResolution: 1.53→51.23 Å / Num. obs: 88499 / % possible obs: 98.3 % / Redundancy: 1.9 % / Biso Wilson estimate: 32.58 Å2 / CC1/2: 1 / Net I/σ(I): 12.7
Reflection shellResolution: 1.53→1.56 Å / Mean I/σ(I) obs: 1.2 / Num. unique obs: 8096 / CC1/2: 0.61 / % possible all: 90.3

-
Processing

Software
NameVersionClassification
BUSTER2.10.3 (6-FEB-2020)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4O3M

4o3m


Resolution: 1.53→51.23 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.94 / SU R Cruickshank DPI: 0.072 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.074 / SU Rfree Blow DPI: 0.072 / SU Rfree Cruickshank DPI: 0.071
RfactorNum. reflection% reflectionSelection details
Rfree0.2084 4388 -RANDOM
Rwork0.1891 ---
obs0.1901 88464 98.3 %-
Displacement parametersBiso mean: 32.6 Å2
Baniso -1Baniso -2Baniso -3
1-2.2284 Å20 Å25.847 Å2
2--6.3269 Å20 Å2
3----8.5553 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: LAST / Resolution: 1.53→51.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3817 0 95 431 4343
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0084026HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.95444HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1871SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes688HARMONIC5
X-RAY DIFFRACTIONt_it4026HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion534SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies7HARMONIC1
X-RAY DIFFRACTIONt_ideal_dist_contact3933SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.72
X-RAY DIFFRACTIONt_other_torsion2.37
LS refinement shellResolution: 1.53→1.54 Å
RfactorNum. reflection% reflection
Rfree0.2186 91 -
Rwork0.2325 --
obs0.2318 1770 83.88 %

+
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