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- PDB-4xzg: Crystal structure of HIRAN domain of human HLTF -

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Basic information

Entry
Database: PDB / ID: 4xzg
TitleCrystal structure of HIRAN domain of human HLTF
ComponentsHelicase-like transcription factor
KeywordsDNA BINDING PROTEIN / DNA repair
Function / homology
Function and homology information


hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / regulation of neurogenesis / ATP-dependent activity, acting on DNA / helicase activity / mRNA transcription by RNA polymerase II / RING-type E3 ubiquitin transferase / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / RNA polymerase II transcription regulator complex / nuclear matrix / ubiquitin protein ligase activity ...hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / regulation of neurogenesis / ATP-dependent activity, acting on DNA / helicase activity / mRNA transcription by RNA polymerase II / RING-type E3 ubiquitin transferase / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / RNA polymerase II transcription regulator complex / nuclear matrix / ubiquitin protein ligase activity / E3 ubiquitin ligases ubiquitinate target proteins / chromatin organization / 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 / nucleus / membrane / 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å
AuthorsIkegaya, Y. / Hara, K. / 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_struct_assembly / pdbx_struct_oper_list
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_struct_assembly.oligomeric_details / _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
A: Helicase-like transcription factor
B: Helicase-like transcription factor
C: Helicase-like transcription factor
D: Helicase-like transcription factor
E: Helicase-like transcription factor
F: Helicase-like transcription factor
G: Helicase-like transcription factor
H: Helicase-like transcription factor
I: Helicase-like transcription factor


Theoretical massNumber of molelcules
Total (without water)138,0649
Polymers138,0649
Non-polymers00
Water6,557364
1
A: Helicase-like transcription factor


Theoretical massNumber of molelcules
Total (without water)15,3401
Polymers15,3401
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Helicase-like transcription factor


Theoretical massNumber of molelcules
Total (without water)15,3401
Polymers15,3401
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Helicase-like transcription factor


Theoretical massNumber of molelcules
Total (without water)15,3401
Polymers15,3401
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Helicase-like transcription factor


Theoretical massNumber of molelcules
Total (without water)15,3401
Polymers15,3401
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Helicase-like transcription factor


Theoretical massNumber of molelcules
Total (without water)15,3401
Polymers15,3401
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Helicase-like transcription factor


Theoretical massNumber of molelcules
Total (without water)15,3401
Polymers15,3401
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Helicase-like transcription factor


Theoretical massNumber of molelcules
Total (without water)15,3401
Polymers15,3401
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Helicase-like transcription factor


Theoretical massNumber of molelcules
Total (without water)15,3401
Polymers15,3401
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
I: Helicase-like transcription factor


Theoretical massNumber of molelcules
Total (without water)15,3401
Polymers15,3401
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)129.441, 129.441, 143.972
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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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: 15340.396 Da / Num. of mol.: 9 / Fragment: UNP residues 57-174
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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 364 / 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: 2.18 Å3/Da / Density % sol: 43.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jan 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.29→20 Å / Num. obs: 55080 / % possible obs: 99.6 % / Redundancy: 14.2 % / Net I/σ(I): 17.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementResolution: 2.4→20 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.943 / SU B: 15.336 / SU ML: 0.182 / Cross valid method: THROUGHOUT / ESU R: 0.484 / ESU R Free: 0.249 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.23123 2430 5 %RANDOM
Rwork0.2137 ---
obs0.2146 45744 99.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.986 Å2
Baniso -1Baniso -2Baniso -3
1--0.97 Å20 Å20 Å2
2---0.97 Å20 Å2
3---1.94 Å2
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8489 0 0 364 8853
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0198671
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6281.9411693
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3351084
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.77425.082425
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.412151471
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2561536
X-RAY DIFFRACTIONr_chiral_restr0.1070.21229
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216693
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_it3.4353.2824363
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.264.8985438
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.1953.9264304
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined10.61628.99112926
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: 2.4→2.461 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 184 -
Rwork0.246 3262 -
obs--99.97 %
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)
13.2708-0.77380.8270.8855-0.61930.46630.03850.0297-0.125-0.0020.0320.06290.011-0.0201-0.07050.0739-0.0375-0.05880.04990.00380.1527-42.48426.8429.592
23.2016-0.31041.21091.0778-0.39510.53420.0477-0.038-0.15290.00640.0154-0.01460.018-0.03-0.06320.0779-0.0201-0.06740.07620.03160.1263-1.84326.84910.744
30.69450.2047-0.11282.9194-0.2540.7325-0.0931-0.1581-0.076-0.20590.07010.1052-0.11410.14590.0230.06850.0135-0.02160.12330.01530.0705-38.08618.784-26.057
43.11130.1373-0.10321.66450.62810.24510.0207-0.1519-0.0325-0.00580.0456-0.1618-0.00020.0218-0.06620.0252-0.0191-0.0790.02190.0540.2678-22.9745.22724.004
53.70070.4980.08620.21360.39311.17250.1996-0.18070.26430.07570.0701-0.02640.20440.1725-0.26970.06660.0303-0.09220.1198-0.0930.2324-23.10147.49425.034
62.4394-0.11090.37981.8642-0.15040.0984-0.0399-0.06730.0955-0.0042-0.0021-0.27590.029-0.05780.0420.0664-0.0591-0.04830.0795-0.00270.1677-63.4615.00522.961
71.3945-0.02650.93142.12210.06680.71380.18120.14110.05550.1196-0.05230.00050.1590.0257-0.12890.04080.0005-0.03120.06590.12020.2596-60.69547.387-11.391
80.94140.56140.55362.18540.15361.33190.25830.05840.0610.16440.02890.00380.16050.1232-0.28720.1241-0.0374-0.02650.0670.01550.1421-1847.086-10.671
91.1372-0.49031.10743.47350.00371.18950.1764-0.0942-0.14280.19540.0153-0.11440.1653-0.1221-0.19170.1271-0.0262-0.05440.08230.07120.1305-17.327-1.109-11.87
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A53 - 173
2X-RAY DIFFRACTION2B53 - 173
3X-RAY DIFFRACTION3C54 - 173
4X-RAY DIFFRACTION4D53 - 173
5X-RAY DIFFRACTION5E53 - 173
6X-RAY DIFFRACTION6F52 - 173
7X-RAY DIFFRACTION7G51 - 173
8X-RAY DIFFRACTION8H53 - 174
9X-RAY DIFFRACTION9I52 - 173

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