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- PDB-5bnh: Crystal structure of the HLTF HIRAN domain with a ssDNA fragment -

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Basic information

Entry
Database: PDB / ID: 5bnh
TitleCrystal structure of the HLTF HIRAN domain with a ssDNA fragment
Components
  • DNA (5'-D(*(GD)P*GP*TP*G)-3')
  • DNA (5'-D(*(TD)P*TP*G)-3')
  • Helicase-like transcription factor
KeywordsDNA BINDING PROTEIN/DNA / DNA damage / DNA recognition / DNA binding domain / DNA BINDING PROTEIN-DNA complex
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
ACETATE ION / PHOSPHATE ION / DNA / Helicase-like transcription factor
Similarity search - Component
Biological speciesHomo sapiens (human)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.7 Å
AuthorsNeculai, D. / Walker, J.R. / Weigelt, J. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / Dhe-Paganon, S.
CitationJournal: To Be Published
Title: Co-crystal structure of the HLTF HIRAN domain with a ssDNA fragment
Authors: Neculai, D. / Walker, J.R. / Weigelt, J. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / Dhe-Paganon, S.
History
DepositionMay 26, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 25, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2016Group: Source and taxonomy
Revision 1.2Mar 20, 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 / pdbx_struct_oper_list / struct_conn
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: DNA (5'-D(*(GD)P*GP*TP*G)-3')
C: DNA (5'-D(*(TD)P*TP*G)-3')
A: Helicase-like transcription factor
D: Helicase-like transcription factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,24512
Polymers28,7734
Non-polymers4728
Water2,666148
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.469, 50.117, 102.763
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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DNA chain , 2 types, 2 molecules BC

#1: DNA chain DNA (5'-D(*(GD)P*GP*TP*G)-3')


Mass: 917.647 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#2: DNA chain DNA (5'-D(*(TD)P*TP*G)-3')


Mass: 892.634 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)

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Protein , 1 types, 2 molecules AD

#3: 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: 13481.369 Da / Num. of mol.: 2 / Fragment: UNP residues 55-175
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLTF / Production host: Enterobacteria phage L1 (virus)
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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Non-polymers , 4 types, 156 molecules

#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#6: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / 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: 2.25 Å3/Da / Density % sol: 45.33 %
Crystal growTemperature: 291 K / Method: evaporation
Details: 0.1 M Sodium acetate trihydrate pH 5.0, 40% 2-Methyl-2,4-pentanediol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97921 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 11, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 1.7→51.38 Å / Num. obs: 28334 / % possible obs: 99.908 % / Redundancy: 9.4 % / Net I/σ(I): 3.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementResolution: 1.7→51.38 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.931 / SU B: 4.137 / SU ML: 0.067 / Cross valid method: THROUGHOUT / ESU R: 0.099 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21353 1414 5 %RANDOM
Rwork0.16482 ---
obs0.16719 26849 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.656 Å2
Baniso -1Baniso -2Baniso -3
1-1.35 Å20 Å20 Å2
2---1.48 Å20 Å2
3---0.13 Å2
Refinement stepCycle: LAST / Resolution: 1.7→51.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1898 96 28 148 2170
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0192063
X-RAY DIFFRACTIONr_bond_other_d0.0020.021947
X-RAY DIFFRACTIONr_angle_refined_deg1.9331.9122801
X-RAY DIFFRACTIONr_angle_other_deg0.90634464
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7145244
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.63725.21792
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.60115326
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.306158
X-RAY DIFFRACTIONr_chiral_restr0.1260.2294
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212322
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02478
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_it1.8431.533986
X-RAY DIFFRACTIONr_mcbond_other1.7161.524981
X-RAY DIFFRACTIONr_mcangle_it2.5832.2771224
X-RAY DIFFRACTIONr_mcangle_other2.5832.2771225
X-RAY DIFFRACTIONr_scbond_it3.6912.0721077
X-RAY DIFFRACTIONr_scbond_other3.6512.0531070
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.5852.8981566
X-RAY DIFFRACTIONr_long_range_B_refined7.73714.6042343
X-RAY DIFFRACTIONr_long_range_B_other7.61514.2472295
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 103 -
Rwork0.236 1945 -
obs--99.71 %
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)
10.2564-0.1963-0.13130.3657-0.05320.20140.00410.0117-0.03730.00740.00420.0348-0.0289-0.0018-0.00830.0178-0.00570.01310.0404-0.00520.04225.4193-13.7611-8.5797
26.58280.46332.37610.35321.67977.99250.6119-0.38330.1357-0.099-0.0212-0.1264-0.4492-0.1198-0.59070.1194-0.03730.07280.0224-0.00960.06050.9577-3.62973.2442
31.85693.53420.23428.0277-2.0874.9675-0.19780.0018-0.0494-0.43450.0239-0.18540.1004-0.02390.17390.0320.01630.02080.0450.00760.047732.1508-43.4316-16.0556
40.3973-0.0106-0.34540.32580.08520.5412-0.00240.01750.0137-0.02370.01810.03030.01330.0128-0.01570.01140.00230.01380.04030.00080.03919.0181-37.3846-11.4873
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A53 - 175
2X-RAY DIFFRACTION2B1 - 3
3X-RAY DIFFRACTION3C1 - 3
4X-RAY DIFFRACTION4D53 - 175

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