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- PDB-2kmu: RecQL4 Amino-terminal Domain -

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Basic information

Entry
Database: PDB / ID: 2kmu
TitleRecQL4 Amino-terminal Domain
ComponentsATP-dependent DNA helicase Q4
KeywordsHYDROLASE / RECQL4 / HELICASE / DNA-REPLICATION / HOMEODOMAIN-LIKE / ATP-binding / Cataract / Craniosynostosis / Disease mutation / Dwarfism / Nucleotide-binding
Function / homology
Function and homology information


DNA/DNA annealing activity / telomeric D-loop binding / telomeric D-loop disassembly / DNA 3'-5' helicase / four-way junction helicase activity / bubble DNA binding / oxidized purine DNA binding / DNA duplex unwinding / DNA unwinding involved in DNA replication / isomerase activity ...DNA/DNA annealing activity / telomeric D-loop binding / telomeric D-loop disassembly / DNA 3'-5' helicase / four-way junction helicase activity / bubble DNA binding / oxidized purine DNA binding / DNA duplex unwinding / DNA unwinding involved in DNA replication / isomerase activity / telomere maintenance / helicase activity / double-strand break repair via homologous recombination / chromosome / DNA replication / chromosome, telomeric region / DNA repair / ATP hydrolysis activity / nucleoplasm / ATP binding / membrane / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Arc Repressor Mutant, subunit A - #1460 / DNA replication/checkpoint protein / DNA replication and checkpoint protein / DNA helicase, ATP-dependent, RecQ type / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / 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. ...Arc Repressor Mutant, subunit A - #1460 / DNA replication/checkpoint protein / DNA replication and checkpoint protein / DNA helicase, ATP-dependent, RecQ type / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / 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 / Arc Repressor Mutant, subunit A / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ATP-dependent DNA helicase Q4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
Model detailsclosest to the average, model 1
AuthorsOhlenschlager, O. / Gorlach, M. / Pospiech, H.
CitationJournal: Nucleic Acids Res. / Year: 2012
Title: The N-terminus of the human RecQL4 helicase is a homeodomain-like DNA interaction motif
Authors: Ohlenschlager, O. / Kuhnert, A. / Schneider, A. / Haumann, S. / Bellstedt, P. / Keller, H. / Saluz, H.P. / Hortschansky, P. / Hanel, F. / Grosse, F. / Gorlach, M. / Pospiech, H.
History
DepositionAug 5, 2009Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jul 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 4, 2013Group: Database references
Revision 1.3Feb 26, 2020Group: Data collection / Database references / Other
Category: pdbx_database_status / pdbx_nmr_software ...pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name ..._pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.5May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATP-dependent DNA helicase Q4


Theoretical massNumber of molelcules
Total (without water)6,8511
Polymers6,8511
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 / 100target function
RepresentativeModel #1closest to the average

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Components

#1: Protein ATP-dependent DNA helicase Q4 / RecQL4 / RecQ protein-like 4 / RecQ4 / RTS


Mass: 6850.646 Da / Num. of mol.: 1 / Fragment: N-terminal domain, UNP residues 1-54
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RECQL4, RECQ4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3
References: UniProt: O94761, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-13C HSQC
1323D HN(CA)CB
1423D H(CCO)NH
1513D HNHA
1623D (H)CCH-TOCSY
1723D (H)CCH-COSY
1813D 1H-15N NOESY
1923D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.2mM [U-99% 15N] RECQL4NT-1, 20mM [U-2H] TRIS-2, 100mM sodium chloride-3, 90% H2O/10% D2O90% H2O/10% D2O
21.0mM [U-99% 13C; U-99% 15N] RECQL4NT-4, 20mM [U-2H] TRIS-5, 100mM sodium chloride-6, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.2 mMRECQL4NT-1[U-99% 15N]1
20 mMTRIS-2[U-2H]1
100 mMsodium chloride-31
1.0 mMRECQL4NT-4[U-99% 13C; U-99% 15N]2
20 mMTRIS-5[U-2H]2
100 mMsodium chloride-62
Sample conditionsIonic strength: 0.100M NaCl / pH: 7.4 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE7502

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
CARAKeller and Wuthrichchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1

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