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- PDB-2kv2: Solution Structure of the human BLM HRDC domain -

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Basic information

Entry
Database: PDB / ID: 2kv2
TitleSolution Structure of the human BLM HRDC domain
ComponentsBloom syndrome protein
KeywordsGENE REGULATION / Bloom syndrome / HRDC domain / Disease mutation / DNA replication / DNA-binding / Nucleotide-binding / Nucleus
Function / homology
Function and homology information


regulation of DNA-templated DNA replication / RecQ family helicase-topoisomerase III complex / telomeric G-quadruplex DNA binding / resolution of DNA recombination intermediates / forked DNA-dependent helicase activity / 8-hydroxy-2'-deoxyguanosine DNA binding / DNA/DNA annealing activity / telomeric D-loop binding / telomere maintenance via semi-conservative replication / cellular response to camptothecin ...regulation of DNA-templated DNA replication / RecQ family helicase-topoisomerase III complex / telomeric G-quadruplex DNA binding / resolution of DNA recombination intermediates / forked DNA-dependent helicase activity / 8-hydroxy-2'-deoxyguanosine DNA binding / DNA/DNA annealing activity / telomeric D-loop binding / telomere maintenance via semi-conservative replication / cellular response to camptothecin / G-quadruplex DNA unwinding / t-circle formation / telomeric D-loop disassembly / DNA double-strand break processing / Y-form DNA binding / negative regulation of cell division / DNA 3'-5' helicase / four-way junction helicase activity / G-quadruplex DNA binding / cellular response to hydroxyurea / lateral element / negative regulation of DNA recombination / bubble DNA binding / Processive synthesis on the C-strand of the telomere / Impaired BRCA2 binding to PALB2 / 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 / Homologous DNA Pairing and Strand Exchange / 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 duplex unwinding / HDR through Single Strand Annealing (SSA) / Impaired BRCA2 binding to RAD51 / nuclear chromosome / DNA unwinding involved in DNA replication / replication fork processing / regulation of cyclin-dependent protein serine/threonine kinase activity / mitotic G2 DNA damage checkpoint signaling / 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 / DNA helicase activity / telomere maintenance / replication fork / molecular function activator activity / helicase activity / cellular response to ionizing radiation / double-strand break repair via homologous recombination / protein homooligomerization / HDR through Homologous Recombination (HRR) / G2/M DNA damage checkpoint / PML body / Meiotic recombination / nuclear matrix / p53 binding / single-stranded DNA binding / protein complex oligomerization / chromosome / Processing of DNA double-strand break ends / DNA recombination / Regulation of TP53 Activity through Phosphorylation / DNA replication / DNA repair / DNA damage response / nucleolus / positive regulation of DNA-templated transcription / ATP hydrolysis activity / protein homodimerization activity / protein-containing complex / 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 / 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 / ATP-dependent DNA helicase RecQ, zinc-binding domain / RecQ zinc-binding / DNA helicase, ATP-dependent, RecQ type / Helicase and RNase D C-terminal / HRDC domain / HRDC domain / 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 / DEAD/DEAH box helicase domain / Helicase conserved C-terminal domain / DNA polymerase; domain 1 / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
RecQ-like DNA helicase BLM
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model 1
AuthorsKim, Y.M. / Choi, B.-S.
CitationJournal: Nucleic Acids Res. / Year: 2010
Title: Structure and function of the regulatory HRDC domain from human Bloom syndrome protein
Authors: Kim, Y.M. / Choi, B.-S.
History
DepositionMar 4, 2010Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Dec 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bloom syndrome protein


Theoretical massNumber of molelcules
Total (without water)9,5951
Polymers9,5951
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 9594.915 Da / Num. of mol.: 1 / Fragment: HRDC domain, UNP residues 1210-1294
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BLM / Production host: Escherichia coli (E. coli) / References: UniProt: P54132

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D 1H-15N NOESY
1323D 1H-13C NOESY
1423D (H)CCH-TOCSY
1513D HN(CA)CB
1613D CBCA(CO)NH
1713D HNCO
1813D C(CO)NH
1913D H(CCCO)NH

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM [U-99% 13C; U-99% 15N] BLM HRDC domain; 1mM DTT; 20mM HEPES; 100mM sodium chloride; 0.02% sodium azide; 90% H2O/10% D2O90% H2O/10% D2O
21mM [U-99% 13C; U-99% 15N] BLM HRDC domain; 1mM DTT; 20mM HEPES; 100mM sodium chloride; 0.02% sodium azide; 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMBLM HRDC domain-1[U-99% 13C; U-99% 15N]1
90 %H2O-21
10 %D2O-31
1 mMDTT-41
20 mMHEPES-51
100 mMsodium chloride-61
0.02 %sodium azide-71
1 mMBLM HRDC domain-8[U-99% 13C; U-99% 15N]2
100 %D2O-92
1 mMDTT-102
20 mMHEPES-112
100 mMsodium chloride-122
0.02 %sodium azide-132
Sample conditionsIonic strength: 100 / pH: 7.0 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR softwareName: CYANA / Version: 2.1 / Developer: Guntert, Mumenthaler and Wuthrich / Classification: refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1

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