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

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Basic information

Entry
Database: PDB / ID: 3ode
TitleHuman PARP-1 zinc finger 2 (Zn2) bound to DNA
Components
  • 5'-D(*CP*CP*CP*AP*AP*GP*CP*G)-3'
  • 5'-D(*CP*GP*CP*TP*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 / regulation of base-excision repair / positive regulation of single strand break repair / regulation of circadian sleep/wake cycle, non-REM sleep ...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 / regulation of base-excision repair / positive regulation of single strand break repair / regulation of circadian sleep/wake cycle, non-REM sleep / vRNA Synthesis / carbohydrate biosynthetic process / NAD+-protein-serine ADP-ribosyltransferase activity / negative regulation of adipose tissue development / NAD DNA ADP-ribosyltransferase activity / DNA ADP-ribosylation / mitochondrial DNA metabolic process / regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / replication fork reversal / ATP generation from poly-ADP-D-ribose / positive regulation of necroptotic process / transcription regulator activator activity / response to aldosterone / HDR through MMEJ (alt-NHEJ) / positive regulation of DNA-templated transcription, elongation / NAD+ ADP-ribosyltransferase / signal transduction involved in regulation of gene expression / negative regulation of telomere maintenance via telomere lengthening / protein auto-ADP-ribosylation / mitochondrial DNA repair / NAD+-protein-aspartate ADP-ribosyltransferase activity / protein poly-ADP-ribosylation / positive regulation of intracellular estrogen receptor signaling pathway / negative regulation of cGAS/STING signaling pathway / positive regulation of cardiac muscle hypertrophy / NAD+-protein-glutamate ADP-ribosyltransferase activity / positive regulation of mitochondrial depolarization / cellular response to zinc ion / NAD+-protein mono-ADP-ribosyltransferase activity / nuclear replication fork / decidualization / protein autoprocessing / R-SMAD binding / site of DNA damage / macrophage differentiation / negative regulation of transcription elongation by RNA polymerase II / Transferases; Glycosyltransferases; Pentosyltransferases / NAD+ poly-ADP-ribosyltransferase activity / positive regulation of SMAD protein signal transduction / POLB-Dependent Long Patch Base Excision Repair / 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 / telomere maintenance / transforming growth factor beta receptor signaling pathway / negative regulation of innate immune response / nuclear estrogen receptor binding / response to gamma radiation / mitochondrion organization / Downregulation of SMAD2/3:SMAD4 transcriptional activity / enzyme activator activity / protein-DNA complex / cellular response to nerve growth factor stimulus / DNA Damage Recognition in GG-NER / protein modification process / Dual Incision in GG-NER / positive regulation of protein localization to nucleus / Formation of Incision Complex in GG-NER / histone deacetylase binding / cellular response to insulin stimulus / NAD binding / cellular response to amyloid-beta / cellular response to UV / nuclear envelope / double-strand break repair / regulation of protein localization / site of double-strand break / cellular response to oxidative stress / transcription regulator complex / damaged DNA binding / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II / chromosome, telomeric region / positive regulation of canonical NF-kappaB signal transduction / nuclear body / innate immune response / DNA repair / negative regulation of DNA-templated transcription / apoptotic process / DNA damage response / ubiquitin protein ligase binding / chromatin binding / protein kinase binding / chromatin / nucleolus / enzyme binding / negative regulation of transcription by RNA polymerase II / protein homodimerization activity
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: 2.95 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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*AP*GP*CP*G)-3'
D: 5'-D(*CP*GP*CP*TP*TP*GP*GP*G)-3'
E: 5'-D(*CP*CP*CP*AP*AP*GP*CP*G)-3'
F: 5'-D(*CP*GP*CP*TP*TP*GP*GP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2858
Polymers35,1546
Non-polymers1312
Water34219
1
A: Poly [ADP-ribose] polymerase 1
C: 5'-D(*CP*CP*CP*AP*AP*GP*CP*G)-3'
D: 5'-D(*CP*GP*CP*TP*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*AP*GP*CP*G)-3'
F: 5'-D(*CP*GP*CP*TP*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)62.804, 62.804, 196.049
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13A
23B

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and resseq 114:141 and backboneA0
211chain B and resseq 114:141 and backboneB0
112chain A and resseq 157:171 and backboneA0
212chain B and resseq 157:171 and backboneB0
113chain A and resseq 186:197 and backboneA0
213chain B and resseq 186:197 and backboneB0

NCS ensembles :
ID
1
2
3

NCS oper:
IDCodeMatrixVector
1given(0.53519, -0.373507, 0.757671), (-0.844228, -0.205542, 0.495006), (-0.029155, -0.904569, -0.425329)-37.443001, 23.840599, 85.497498
2given(0.502748, -0.401694, 0.765432), (-0.863341, -0.188837, 0.467956), (-0.043434, -0.896093, -0.441736)-37.0037, 24.9177, 86.063301
3given(0.486634, -0.342168, 0.803809), (-0.872937, -0.22647, 0.43208), (0.034195, -0.911939, -0.408899)-40.256302, 27.816299, 84.757301

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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*AP*GP*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*CP*TP*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.: 19 / 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: 3.18 Å3/Da / Density % sol: 61.26 %
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: ALS / Beamline: 12.3.1 / Wavelength: 0.99 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 31, 2009
RadiationMonochromator: silicon(111) crystal and multilayer / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 2.95→50 Å / Num. obs: 9957 / % possible obs: 98.6 % / Redundancy: 7.7 % / Rmerge(I) obs: 0.103 / Χ2: 0.997 / Net I/σ(I): 11.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.95-37.50.8694750.99996
3-3.067.90.6544540.95397.8
3.06-3.117.50.4994970.98699
3.11-3.187.70.4684701.04696.9
3.18-3.257.50.34930.99198.4
3.25-3.327.50.2434961.0196.7
3.32-3.417.50.2044701.04197.9
3.41-3.57.20.2284781.04598
3.5-3.67.60.1694770.95998.8
3.6-3.727.20.1734951.00198
3.72-3.857.50.144860.97999.2
3.85-47.20.1335021.02998.6
4-4.197.10.0935210.96398.7
4.19-4.417.60.1064741.034100
4.41-4.687.50.0845061.00399
4.68-5.047.40.0735090.981100
5.04-5.557.80.0635130.982100
5.55-6.358.40.0645230.99899.8
6.35-89.70.0565390.969100
8-509.10.0435790.99898.3

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.6.2_432refinement
PDB_EXTRACT3.1data extraction
Blu-IceIcedata collection
HKL-2000data reduction
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.95→41.805 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8192 / SU ML: 0.39 / σ(F): 1.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2444 474 4.78 %
Rwork0.1987 --
obs0.2009 9907 98.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.595 Å2 / ksol: 0.334 e/Å3
Displacement parametersBiso max: 119.67 Å2 / Biso mean: 58.178 Å2 / Biso min: 26.64 Å2
Baniso -1Baniso -2Baniso -3
1--6.6361 Å20 Å20 Å2
2---6.6361 Å2-0 Å2
3---13.2722 Å2
Refinement stepCycle: LAST / Resolution: 2.95→41.805 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1464 644 2 19 2129
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112227
X-RAY DIFFRACTIONf_angle_d1.4733105
X-RAY DIFFRACTIONf_chiral_restr0.078328
X-RAY DIFFRACTIONf_plane_restr0.007291
X-RAY DIFFRACTIONf_dihedral_angle_d25.359903
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A111X-RAY DIFFRACTIONPOSITIONAL0.04
12B111X-RAY DIFFRACTIONPOSITIONAL0.04
21A60X-RAY DIFFRACTIONPOSITIONAL0.048
22B60X-RAY DIFFRACTIONPOSITIONAL0.048
31A48X-RAY DIFFRACTIONPOSITIONAL0.034
32B48X-RAY DIFFRACTIONPOSITIONAL0.034
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.95-3.37560.31411490.24573037318698
3.3756-4.25230.24541700.19343084325498
4.2523-41.80910.221550.185533123467100

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