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- PDB-3odc: Human PARP-1 zinc finger 2 (Zn2) bound to DNA -

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Basic information

Entry
Database: PDB / ID: 3odc
TitleHuman PARP-1 zinc finger 2 (Zn2) bound to DNA
Components
  • 5'-D(*CP*CP*CP*AP*GP*AP*CP*G)-3'
  • 5'-D(*CP*GP*TP*CP*TP*GP*GP*G)-3'
  • Poly [ADP-ribose] polymerase 1
KeywordsDNA BINDING PROTEIN/DNA / protein-DNA complex / PARP zinc finger / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


NAD+-histone H2BS6 serine ADP-ribosyltransferase activity / NAD+-histone H3S10 serine ADP-ribosyltransferase activity / NAD+-histone H2BE35 glutamate ADP-ribosyltransferase activity / positive regulation of myofibroblast differentiation / negative regulation of ATP biosynthetic process / NAD+-protein-tyrosine ADP-ribosyltransferase activity / NAD+-protein-histidine ADP-ribosyltransferase activity / non-sequence-specific DNA binding, bending / regulation of base-excision repair / mitochondrial DNA metabolic process ...NAD+-histone H2BS6 serine ADP-ribosyltransferase activity / NAD+-histone H3S10 serine ADP-ribosyltransferase activity / NAD+-histone H2BE35 glutamate ADP-ribosyltransferase activity / positive regulation of myofibroblast differentiation / negative regulation of ATP biosynthetic process / NAD+-protein-tyrosine ADP-ribosyltransferase activity / NAD+-protein-histidine ADP-ribosyltransferase activity / non-sequence-specific DNA binding, bending / regulation of base-excision repair / mitochondrial DNA metabolic process / regulation of circadian sleep/wake cycle, non-REM sleep / vRNA Synthesis / carbohydrate biosynthetic process / NAD+-protein-serine ADP-ribosyltransferase activity / NAD DNA ADP-ribosyltransferase activity / single-strand break-containing DNA binding / mitochondrial DNA repair / DNA ADP-ribosylation / regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / signal transduction involved in regulation of gene expression / ATP generation from poly-ADP-D-ribose / replication fork reversal / positive regulation of necroptotic process / establishment of protein localization to chromatin / positive regulation of intracellular estrogen receptor signaling pathway / transcription regulator activator activity / response to aldosterone / HDR through MMEJ (alt-NHEJ) / single strand break repair / positive regulation of DNA-templated transcription, elongation / NAD+ ADP-ribosyltransferase / protein auto-ADP-ribosylation / negative regulation of telomere maintenance via telomere lengthening / cellular response to zinc ion / NAD+-protein-aspartate ADP-ribosyltransferase activity / protein poly-ADP-ribosylation / NAD+-protein-glutamate ADP-ribosyltransferase activity / negative regulation of cGAS/STING signaling pathway / positive regulation of cardiac muscle hypertrophy / negative regulation of transcription elongation by RNA polymerase II / decidualization / NAD+-protein mono-ADP-ribosyltransferase activity / positive regulation of mitochondrial depolarization / protein autoprocessing / macrophage differentiation / R-SMAD binding / negative regulation of adipose tissue development / nuclear replication fork / Transferases; Glycosyltransferases; Pentosyltransferases / positive regulation of SMAD protein signal transduction / POLB-Dependent Long Patch Base Excision Repair / NAD+ poly-ADP-ribosyltransferase activity / transforming growth factor beta receptor signaling pathway / SUMOylation of DNA damage response and repair proteins / positive regulation of double-strand break repair via homologous recombination / nucleosome binding / protein localization to chromatin / nucleotidyltransferase activity / response to gamma radiation / negative regulation of innate immune response / telomere maintenance / nuclear estrogen receptor binding / protein modification process / site of DNA damage / mitochondrion organization / cellular response to nerve growth factor stimulus / Downregulation of SMAD2/3:SMAD4 transcriptional activity / positive regulation of protein localization to nucleus / protein-DNA complex / fibrillar center / transcription by RNA polymerase II / DNA Damage Recognition in GG-NER / NAD binding / cellular response to amyloid-beta / enzyme activator activity / histone deacetylase binding / Dual Incision in GG-NER / Formation of Incision Complex in GG-NER / cellular response to UV / double-strand break repair / cellular response to insulin stimulus / nuclear envelope / regulation of protein localization / site of double-strand break / transcription regulator complex / cellular response to oxidative stress / damaged DNA binding / response to ethanol / RNA polymerase II-specific DNA-binding transcription factor binding / nuclear body / positive regulation of canonical NF-kappaB signal transduction / chromosome, telomeric region / innate immune response / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / DNA repair / apoptotic process / chromatin binding / DNA damage response / nucleolus
Similarity search - Function
Zinc finger, PARP-type / first zn-finger domain of poly(adp-ribose) polymerase-1 / Poly [ADP-ribose] polymerase / PADR1 domain / PADR1 domain superfamily / : / PADR1 domain, zinc ribbon fold / PADR1, N-terminal helical domain / PADR1 domain profile. / PADR1 ...Zinc finger, PARP-type / first zn-finger domain of poly(adp-ribose) polymerase-1 / Poly [ADP-ribose] polymerase / PADR1 domain / PADR1 domain superfamily / : / PADR1 domain, zinc ribbon fold / PADR1, N-terminal helical domain / PADR1 domain profile. / PADR1 / Zinc finger poly(ADP-ribose) polymerase (PARP)-type signature. / Zinc finger, PARP-type superfamily / Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region / Zinc finger poly(ADP-ribose) polymerase (PARP)-type profile. / Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region / Zinc finger, PARP-type / : / Poly(ADP-ribose) polymerase, regulatory domain / WGR domain / WGR domain superfamily / WGR domain / WGR domain profile. / Proposed nucleic acid binding domain / Poly(ADP-ribose) polymerase, regulatory domain superfamily / Poly(ADP-ribose) polymerase, regulatory domain / PARP alpha-helical domain profile. / BRCA1 C Terminus (BRCT) domain / Poly(ADP-ribose) polymerase catalytic domain / Poly(ADP-ribose) polymerase, catalytic domain / PARP catalytic domain profile. / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / Poly [ADP-ribose] polymerase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsPascal, J.M. / Langelier, M.-F.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Crystal Structures of Poly(ADP-ribose) Polymerase-1 (PARP-1) Zinc Fingers Bound to DNA: STRUCTURAL AND FUNCTIONAL INSIGHTS INTO DNA-DEPENDENT PARP-1 ACTIVITY.
Authors: Langelier, M.F. / Planck, J.L. / Roy, S. / Pascal, J.M.
History
DepositionAug 11, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Feb 21, 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_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_atom_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_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_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Poly [ADP-ribose] polymerase 1
B: Poly [ADP-ribose] polymerase 1
C: 5'-D(*CP*CP*CP*AP*GP*AP*CP*G)-3'
D: 5'-D(*CP*GP*TP*CP*TP*GP*GP*G)-3'
E: 5'-D(*CP*CP*CP*AP*GP*AP*CP*G)-3'
F: 5'-D(*CP*GP*TP*CP*TP*GP*GP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2858
Polymers35,1546
Non-polymers1312
Water70339
1
A: Poly [ADP-ribose] polymerase 1
C: 5'-D(*CP*CP*CP*AP*GP*AP*CP*G)-3'
D: 5'-D(*CP*GP*TP*CP*TP*GP*GP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6424
Polymers17,5773
Non-polymers651
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Poly [ADP-ribose] polymerase 1
E: 5'-D(*CP*CP*CP*AP*GP*AP*CP*G)-3'
F: 5'-D(*CP*GP*TP*CP*TP*GP*GP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6424
Polymers17,5773
Non-polymers651
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.731, 63.731, 192.405
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Poly [ADP-ribose] polymerase 1 / PARP-1 / NAD(+) ADP-ribosyltransferase 1 / ADPRT 1 / Poly[ADP-ribose] synthase 1


Mass: 12721.641 Da / Num. of mol.: 2 / Fragment: PARP-1 zinc finger 2, Zn2, UNP residues 105-206
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ADPRT, PARP1, PPOL / Plasmid: pET24 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Rosetta2 / References: UniProt: P09874, NAD+ ADP-ribosyltransferase
#2: DNA chain 5'-D(*CP*CP*CP*AP*GP*AP*CP*G)-3'


Mass: 2396.595 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Chemically synthesized DNA
#3: DNA chain 5'-D(*CP*GP*TP*CP*TP*GP*GP*G)-3'


Mass: 2458.615 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Chemically synthesized DNA
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 3.21 Å3/Da / Density % sol: 61.67 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6.5
Details: 1.36-1.42 M sodium citrate pH 6.5, vapor diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.99 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Sep 18, 2009
RadiationMonochromator: silicon(111) crystal / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 11845 / % possible obs: 99.9 % / Redundancy: 8.1 % / Rmerge(I) obs: 0.092 / Χ2: 1 / Net I/σ(I): 8.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.8-2.858.20.7175710.982100
2.85-2.97.90.6256020.992100
2.9-2.968.30.6395520.986100
2.96-3.028.20.4595850.95100
3.02-3.088.20.3855821.02100
3.08-3.158.20.3085800.973100
3.15-3.238.20.2125720.979100
3.23-3.328.30.1635801.021100
3.32-3.428.20.1295711.034100
3.42-3.538.10.1135970.974100
3.53-3.658.30.15791.012100
3.65-3.88.20.0975900.991100
3.8-3.978.10.0875950.986100
3.97-4.188.30.0675731.025100
4.18-4.448.20.0635940.996100
4.44-4.798.10.066041.008100
4.79-5.278.10.0566041.03100
5.27-6.038.10.0546060.996100
6.03-7.597.90.0526221.027100
7.59-507.10.0366861.00898.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.6.2_432refinement
PDB_EXTRACT3.1data extraction
CBASSdata collection
HKL-2000data reduction
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.8→36.262 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8113 / SU ML: 0.35 / σ(F): 1.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2398 556 4.71 %
Rwork0.1927 --
obs0.195 11798 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.698 Å2 / ksol: 0.337 e/Å3
Displacement parametersBiso max: 96.76 Å2 / Biso mean: 48.3666 Å2 / Biso min: 26.78 Å2
Baniso -1Baniso -2Baniso -3
1--0.5071 Å2-0 Å2-0 Å2
2---0.5071 Å20 Å2
3---1.0142 Å2
Refinement stepCycle: LAST / Resolution: 2.8→36.262 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1514 644 2 39 2199
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012277
X-RAY DIFFRACTIONf_angle_d1.3053173
X-RAY DIFFRACTIONf_chiral_restr0.071337
X-RAY DIFFRACTIONf_plane_restr0.005300
X-RAY DIFFRACTIONf_dihedral_angle_d24.867917
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.8001-3.08180.34681280.286427602888
3.0818-3.52740.26361450.2127462891
3.5274-4.44290.22381410.170927842925
4.4429-36.26550.21221420.176529523094

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