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- PDB-4s0n: Crystal Structure of HLTF HIRAN Domain bound to DNA -

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Basic information

Entry
Database: PDB / ID: 4s0n
TitleCrystal Structure of HLTF HIRAN Domain bound to DNA
Components
  • 5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3'
  • Helicase-like transcription factor
KeywordsDNA binding Protein/DNA / alpha+beta / DNA 3'-end binding / 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
THYMIDINE-5'-PHOSPHATE / DNA / DNA-dependent ATPase/E3 ubiquitin-protein ligase HLTF
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.501 Å
AuthorsChavez, D.A. / Eichman, B.F.
CitationJournal: Mol.Cell / Year: 2015
Title: HLTF's Ancient HIRAN Domain Binds 3' DNA Ends to Drive Replication Fork Reversal.
Authors: Kile, A.C. / Chavez, D.A. / Bacal, J. / Eldirany, S. / Korzhnev, D.M. / Bezsonova, I. / Eichman, B.F. / Cimprich, K.A.
History
DepositionJan 2, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2015Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Feb 12, 2025Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / chem_comp_atom / chem_comp_bond / entity / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.auth_comp_id ..._atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.auth_comp_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_comp_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_comp_id / _struct_site.details / _struct_site.pdbx_auth_comp_id / _struct_site_gen.auth_comp_id / _struct_site_gen.label_comp_id

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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: 5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3'
F: 5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3'
G: 5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3'
H: 5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,64116
Polymers68,7218
Non-polymers9218
Water10,611589
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11010 Å2
ΔGint-109 kcal/mol
Surface area25110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.026, 74.211, 66.180
Angle α, β, γ (deg.)90.00, 113.68, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / DNA chain , 2 types, 8 molecules ABCDEFGH

#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: 14183.203 Da / Num. of mol.: 4 / Fragment: HIRAN Domain, UNP residues 55-180
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)
#2: DNA chain
5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3'


Mass: 2996.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 597 molecules

#3: Chemical ChemComp-TMP / THYMIDINE-5'-PHOSPHATE


Mass: 322.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N2O8P
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 589 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationN

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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: 1.91 Å3/Da / Density % sol: 35.72 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 25% PEG 4000, 250 mM sodium acetate trihydrate, 100 mM Tris-HCl pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289.15K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 4, 2013
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.5→100 Å / Num. obs: 86121 / % possible obs: 99.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 7.6 % / Rsym value: 0.068 / Net I/σ(I): 27.2
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 7.5 % / Mean I/σ(I) obs: 3.9 / Rsym value: 0.455 / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
SHARPphasing
PHENIX(phenix.refine: dev_1839)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SIRAS / Resolution: 1.501→34.721 Å / SU ML: 0.13 / σ(F): 1.36 / Phase error: 16.9 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.1849 4317 5.01 %RANDOM
Rwork0.1528 ---
obs0.1544 86121 99.8 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.501→34.721 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3838 344 41 589 4812
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064475
X-RAY DIFFRACTIONf_angle_d0.9736149
X-RAY DIFFRACTIONf_dihedral_angle_d16.0361717
X-RAY DIFFRACTIONf_chiral_restr0.039671
X-RAY DIFFRACTIONf_plane_restr0.005753
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.501-1.52680.2532210.18314046X-RAY DIFFRACTION99
1.5268-1.55460.21722090.15954072X-RAY DIFFRACTION100
1.5546-1.58450.19862210.14264084X-RAY DIFFRACTION100
1.5845-1.61680.19612320.1454074X-RAY DIFFRACTION100
1.6168-1.6520.19782250.1394078X-RAY DIFFRACTION100
1.652-1.69040.19272260.13914085X-RAY DIFFRACTION100
1.6904-1.73270.18641930.13884063X-RAY DIFFRACTION100
1.7327-1.77950.18162500.14264074X-RAY DIFFRACTION100
1.7795-1.83190.18922110.14234062X-RAY DIFFRACTION100
1.8319-1.8910.18972140.14214097X-RAY DIFFRACTION100
1.891-1.95860.17942250.14154103X-RAY DIFFRACTION100
1.9586-2.0370.18742000.13544082X-RAY DIFFRACTION100
2.037-2.12970.17622010.13754133X-RAY DIFFRACTION100
2.1297-2.24190.17872090.14734079X-RAY DIFFRACTION100
2.2419-2.38240.17172110.14774106X-RAY DIFFRACTION100
2.3824-2.56630.19922140.15674106X-RAY DIFFRACTION100
2.5663-2.82440.18872070.16594132X-RAY DIFFRACTION100
2.8244-3.23280.17022130.16324128X-RAY DIFFRACTION100
3.2328-4.0720.19732020.14814151X-RAY DIFFRACTION100
4.072-34.73040.17542330.16614049X-RAY DIFFRACTION97

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