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- PDB-6kcs: Crystal structure of HIRAN domain of HLTF in complex with duplex DNA -

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Basic information

Entry
Database: PDB / ID: 6kcs
TitleCrystal structure of HIRAN domain of HLTF in complex with duplex DNA
Components
  • DNA (5'-D(*AP*CP*TP*GP*TP*AP*CP*GP*TP*AP*CP*AP*GP*T)-3')
  • Helicase-like transcription factor
KeywordsDNA BINDING PROTEIN/DNA / DNA complex / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


G-quadruplex unwinding activity / histone H3K23 ubiquitin ligase activity / chromosomal DNA methylation maintenance following DNA replication / DNA translocase activity / replication fork reversal / hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / histone H3K9me2/3 reader activity / ATP-dependent chromatin remodeler activity / nuclear replication fork / regulation of neurogenesis ...G-quadruplex unwinding activity / histone H3K23 ubiquitin ligase activity / chromosomal DNA methylation maintenance following DNA replication / DNA translocase activity / replication fork reversal / hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / histone H3K9me2/3 reader activity / ATP-dependent chromatin remodeler activity / nuclear replication fork / regulation of neurogenesis / protein K63-linked ubiquitination / ATP-dependent activity, acting on DNA / protein localization to chromatin / helicase activity / RING-type E3 ubiquitin transferase / mRNA transcription by RNA polymerase II / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / RNA polymerase II transcription regulator complex / nuclear matrix / protein polyubiquitination / ubiquitin protein ligase activity / single-stranded DNA binding / E3 ubiquitin ligases ubiquitinate target proteins / protein ubiquitination / DNA repair / DNA damage response / ubiquitin protein ligase binding / chromatin / nucleolus / positive regulation of transcription by RNA polymerase II / 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 / Zinc finger RING-type profile. / Helicase conserved C-terminal domain / 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) / DNA-dependent ATPase/E3 ubiquitin-protein ligase HLTF
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsHishiki, A. / Hashimoto, A.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science25291017 Japan
Japan Society for the Promotion of Science16H04755 Japan
Japan Society for the Promotion of Science23770125 Japan
CitationJournal: J.Biochem. / Year: 2020
Title: Structure of HIRAN domain of human HLTF bound to duplex DNA provides structural basis for DNA unwinding to initiate replication fork regression.
Authors: Hishiki, A. / Sato, M. / Hashimoto, H.
History
DepositionJun 28, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 10, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 23, 2020Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details ..._pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
A: Helicase-like transcription factor
B: DNA (5'-D(*AP*CP*TP*GP*TP*AP*CP*GP*TP*AP*CP*AP*GP*T)-3')


Theoretical massNumber of molelcules
Total (without water)17,6302
Polymers17,6302
Non-polymers00
Water86548
1
A: Helicase-like transcription factor
B: DNA (5'-D(*AP*CP*TP*GP*TP*AP*CP*GP*TP*AP*CP*AP*GP*T)-3')

A: Helicase-like transcription factor
B: DNA (5'-D(*AP*CP*TP*GP*TP*AP*CP*GP*TP*AP*CP*AP*GP*T)-3')


Theoretical massNumber of molelcules
Total (without water)35,2604
Polymers35,2604
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area4260 Å2
ΔGint-28 kcal/mol
Surface area15700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.363, 45.363, 125.827
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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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: 13350.282 Da / Num. of mol.: 1
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, RING-type E3 ubiquitin transferase, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#2: DNA chain DNA (5'-D(*AP*CP*TP*GP*TP*AP*CP*GP*TP*AP*CP*AP*GP*T)-3')


Mass: 4279.804 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 2.12 Å3/Da / Density % sol: 41.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: PEG

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jul 27, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 9284 / % possible obs: 99.7 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 11.9
Reflection shellResolution: 2.1→2.21 Å / Rmerge(I) obs: 0.605 / Num. unique obs: 1336

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4xzf

4xzf


Resolution: 2.1→19.95 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.93 / SU B: 14.156 / SU ML: 0.192 / Cross valid method: THROUGHOUT / ESU R: 0.269 / ESU R Free: 0.209
RfactorNum. reflection% reflectionSelection details
Rfree0.26406 470 5.1 %RANDOM
Rwork0.22869 ---
obs0.23038 8806 99.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 58.363 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å2-0.1 Å20 Å2
2---0.2 Å20 Å2
3---0.65 Å2
Refinement stepCycle: 1 / Resolution: 2.1→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms908 247 0 48 1203
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0111202
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9931.5121672
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9665116
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.16923.87849
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.1515160
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.826154
X-RAY DIFFRACTIONr_chiral_restr0.0750.2146
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02840
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_it0.9373.225467
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.6874.823582
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.9713.271734
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined5.6641.4791864
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 57 -
Rwork0.289 619 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.82291.44850.79271.53220.6240.3249-0.2393-0.3355-0.2170.10530.2118-0.08880.0111-0.05650.02760.05880.1070.01850.54840.06630.1795-1.02716.2786-12.9667
20.41240.61030.95631.04431.85.7055-0.04020.18590.04430.08830.19910.0205-0.0896-0.0017-0.15890.2230.1291-0.02720.39850.0510.198114.486126.9525-3.1957
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A56 - 172
2X-RAY DIFFRACTION2B3 - 14

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