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- PDB-5k5f: NMR structure of the HLTF HIRAN domain -

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Basic information

Entry
Database: PDB / ID: 5k5f
TitleNMR structure of the HLTF HIRAN domain
ComponentsHelicase-like transcription factor
KeywordsDNA BINDING PROTEIN / DNA-binding / DNA replication / Structural Genomics / PSI-Biology / Protein Structure Initiative / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / ATP-dependent chromatin remodeler activity / regulation of neurogenesis / ATP-dependent activity, acting on DNA / helicase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / mRNA transcription by RNA polymerase II / RING-type E3 ubiquitin transferase / nuclear matrix / RNA polymerase II transcription regulator complex ...hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / ATP-dependent chromatin remodeler activity / regulation of neurogenesis / ATP-dependent activity, acting on DNA / helicase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / mRNA transcription by RNA polymerase II / RING-type E3 ubiquitin transferase / nuclear matrix / RNA polymerase II transcription regulator complex / ubiquitin protein ligase activity / E3 ubiquitin ligases ubiquitinate target proteins / protein ubiquitination / DNA repair / ubiquitin protein ligase binding / nucleolus / positive regulation of transcription by RNA polymerase II / DNA binding / RNA binding / zinc ion binding / nucleoplasm / ATP binding / membrane / nucleus / plasma membrane / cytoplasm
Similarity search - Function
HIRAN domain / HIRAN domain / HIRAN / : / Zinc finger, C3HC4 type (RING finger) / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / Zinc finger, RING-type, conserved site ...HIRAN domain / HIRAN domain / HIRAN / : / Zinc finger, C3HC4 type (RING finger) / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Helicase conserved C-terminal domain / Zinc finger RING-type profile. / Zinc finger, RING-type / 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 / Zinc finger, RING/FYVE/PHD-type / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Helicase-like transcription factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsBezsonova, I. / Neculai, D. / Korzhnev, D. / Weigelt, J. / Bountra, C. / Edwards, A. / Arrowsmith, C. / Dhe-Paganon, S. / Structural Genomics Consortium (SGC)
Funding support United States, 2items
OrganizationGrant numberCountry
Connecticut Innovations13-SCA-UCHC-03 United States
Connecticut Department of Public Health2013-0203 United States
CitationJournal: To Be Published
Title: NMR structure of the HLTF HIRAN domain
Authors: Bezsonova, I. / Neculai, D. / Korzhnev, D. / Arrowsmith, C. / Dhe-Paganon, S.
History
DepositionMay 23, 2016Deposition site: RCSB / Processing site: RCSB
SupersessionJun 8, 2016ID: 2L1I
Revision 1.0Jun 8, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Structure summary
Category: database_2 / entity ...database_2 / entity / pdbx_database_status / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_number_of_molecules / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name
Revision 1.2May 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:
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Assembly

Deposited unit
A: Helicase-like transcription factor


Theoretical massNumber of molelcules
Total (without water)13,5321
Polymers13,5321
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Helicase-like transcription factor / DNA-binding protein/plasminogen activator inhibitor 1 regulator / HIP116 / RING finger protein 80 / ...DNA-binding protein/plasminogen activator inhibitor 1 regulator / HIP116 / RING finger protein 80 / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 3 / Sucrose nonfermenting protein 2-like 3


Mass: 13532.326 Da / Num. of mol.: 1 / Fragment: residues 51-171
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLTF, HIP116A, RNF80, SMARCA3, SNF2L3, ZBU1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q14527, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ...References: UniProt: Q14527, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic12D 1H-13C HSQC aliphatic
131isotropic13D HNCO
141isotropic13D HNCA
151isotropic13D HN(CO)CA
191isotropic13D (H)CCH-TOCSY
181isotropic13D CCH-TOCSY
171isotropic13D 1H-15N NOESY
161isotropic13D 1H-13C NOESY
1111isotropic13D 1H-13C NOESY aromatic
1101isotropic13D CBCA(CO)NH
1121isotropic13D HBHA(CO)NH

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Sample preparation

DetailsType: solution
Contents: 1 mM [U-99% 13C; U-99% 15N] HLTF HIRAN domain, 20 mM sodium phosphate, 100 mM sodium chloride, 90% H2O/10% D2O
Label: 15N_13C_sample / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMHLTF HIRAN domain[U-99% 13C; U-99% 15N]1
20 mMsodium phosphatenatural abundance1
100 mMsodium chloridenatural abundance1
Sample conditionsIonic strength: 0.1 M / Label: condition 1 / pH: 6.8 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Agilent VNMRS / Manufacturer: Agilent / Model: VNMRS / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
VNMRVariancollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardpeak picking
SparkyGoddardchemical shift assignment
TALOSCornilescu, Delaglio and Baxdata analysis
ABACUSLemak and Arrowsmithdata analysis
CYANAGuntert, Mumenthaler and Wuthrichrefinement
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure calculation
RefinementMethod: simulated annealing / Software ordinal: 2 / Details: water refinement
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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