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- PDB-4xzf: Crystal structure of HIRAN domain of human HLTF in complex with DNA -

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Basic information

Entry
Database: PDB / ID: 4xzf
TitleCrystal structure of HIRAN domain of human HLTF in complex with DNA
Components
  • (DA)(DC)(DC)(DG)(DC)(DC)(DG)(DG)(DG)(DT)(DG)(DC)(DC)
  • Helicase-like transcription factor
KeywordsDNA BINDING PROTEIN/DNA / DNA repair / DNA BINDING PROTEIN-DNA complex
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 / Zinc finger RING-type signature. ...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
DNA / DNA (> 10) / Helicase-like transcription factor
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.38 Å
AuthorsHishiki, A. / Hashimoto, H.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Structure of a Novel DNA-binding Domain of Helicase-like Transcription Factor (HLTF) and Its Functional Implication in DNA Damage Tolerance
Authors: Hishiki, A. / Hara, K. / Ikegaya, Y. / Yokoyama, H. / Shimizu, T. / Sato, M. / Hashimoto, H.
History
DepositionFeb 4, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 15, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2015Group: Database references
Revision 1.2Jun 3, 2015Group: Database references
Revision 1.3Feb 5, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy
Category: citation / diffrn_source ...citation / diffrn_source / entity_src_gen / pdbx_entity_src_syn / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_oper_list / pdbx_struct_special_symmetry
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site ..._citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: (DA)(DC)(DC)(DG)(DC)(DC)(DG)(DG)(DG)(DT)(DG)(DC)(DC)
A: Helicase-like transcription factor


Theoretical massNumber of molelcules
Total (without water)17,3042
Polymers17,3042
Non-polymers00
Water5,350297
1
B: (DA)(DC)(DC)(DG)(DC)(DC)(DG)(DG)(DG)(DT)(DG)(DC)(DC)
A: Helicase-like transcription factor

B: (DA)(DC)(DC)(DG)(DC)(DC)(DG)(DG)(DG)(DT)(DG)(DC)(DC)


Theoretical massNumber of molelcules
Total (without water)21,2573
Polymers21,2573
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
Unit cell
Length a, b, c (Å)147.399, 33.418, 36.797
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-7-

DG

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Components

#1: DNA chain (DA)(DC)(DC)(DG)(DC)(DC)(DG)(DG)(DG)(DT)(DG)(DC)(DC)


Mass: 3953.562 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: 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: 13350.282 Da / Num. of mol.: 1 / Fragment: UNP residues 58-174
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLTF, HIP116A, RNF80, SMARCA3, SNF2L3, ZBU1 / Plasmid: pGEX6P1 / 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)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 297 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.62 Å3/Da / Density % sol: 53.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: PEG 3350, Na acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 7, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.38→20 Å / Num. obs: 36316 / % possible obs: 94.1 % / Redundancy: 5.78 % / Net I/σ(I): 17.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.38→16.6 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.93 / SU B: 1.794 / SU ML: 0.033 / Cross valid method: THROUGHOUT / ESU R: 0.064 / ESU R Free: 0.062 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.20668 1807 5 %RANDOM
Rwork0.16458 ---
obs0.1667 34441 94.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.981 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å20 Å2
2---0.05 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.38→16.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms934 262 0 297 1493
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0171278
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0181.7311790
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8615122
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.95925.11145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.90415163
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.083154
X-RAY DIFFRACTIONr_chiral_restr0.1210.2181
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.021884
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.521.157485
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.8041.741605
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.582.164793
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined3.94917.8392316
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr8.87931278
X-RAY DIFFRACTIONr_sphericity_free27.099579
X-RAY DIFFRACTIONr_sphericity_bonded13.84551440
LS refinement shellResolution: 1.381→1.417 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.225 149 -
Rwork0.194 2492 -
obs--94.69 %

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