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- PDB-3od8: Human PARP-1 zinc finger 1 (Zn1) bound to DNA -

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Basic information

Entry
Database: PDB / ID: 3od8
TitleHuman PARP-1 zinc finger 1 (Zn1) bound to DNA
Components
  • 5'-D(*CP*CP*CP*AP*AP*GP*CP*GP*GP*C)-3'
  • 5'-D(*GP*CP*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 / regulation of base-excision repair / positive regulation of myofibroblast differentiation / negative regulation of ATP biosynthetic process / NAD+-protein-tyrosine ADP-ribosyltransferase activity / NAD+-protein-histidine ADP-ribosyltransferase activity / carbohydrate biosynthetic process / positive regulation of single strand break repair ...NAD+-histone H2BS6 serine ADP-ribosyltransferase activity / NAD+-histone H3S10 serine ADP-ribosyltransferase activity / NAD+-histone H2BE35 glutamate ADP-ribosyltransferase activity / regulation of base-excision repair / positive regulation of myofibroblast differentiation / negative regulation of ATP biosynthetic process / NAD+-protein-tyrosine ADP-ribosyltransferase activity / NAD+-protein-histidine ADP-ribosyltransferase activity / carbohydrate biosynthetic process / positive regulation of single strand break repair / regulation of circadian sleep/wake cycle, non-REM sleep / vRNA Synthesis / negative regulation of adipose tissue development / NAD+-protein-serine ADP-ribosyltransferase activity / NAD DNA ADP-ribosyltransferase activity / NAD+-protein-aspartate ADP-ribosyltransferase activity / NAD+-protein-glutamate ADP-ribosyltransferase activity / mitochondrial DNA metabolic process / DNA ADP-ribosylation / regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / signal transduction involved in regulation of gene expression / positive regulation of necroptotic process / regulation of catalytic activity / ATP generation from poly-ADP-D-ribose / replication fork reversal / transcription regulator activator activity / HDR through MMEJ (alt-NHEJ) / positive regulation of DNA-templated transcription, elongation / positive regulation of intracellular estrogen receptor signaling pathway / NAD+ ADP-ribosyltransferase / cellular response to zinc ion / negative regulation of telomere maintenance via telomere lengthening / protein auto-ADP-ribosylation / positive regulation of mitochondrial depolarization / response to aldosterone / mitochondrial DNA repair / negative regulation of cGAS/STING signaling pathway / protein poly-ADP-ribosylation / positive regulation of cardiac muscle hypertrophy / negative regulation of transcription elongation by RNA polymerase II / nuclear replication fork / NAD+-protein ADP-ribosyltransferase activity / site of DNA damage / R-SMAD binding / positive regulation of SMAD protein signal transduction / macrophage differentiation / protein autoprocessing / decidualization / Transferases; Glycosyltransferases; Pentosyltransferases / positive regulation of double-strand break repair via homologous recombination / NAD+-protein poly-ADP-ribosyltransferase activity / POLB-Dependent Long Patch Base Excision Repair / SUMOylation of DNA damage response and repair proteins / nucleosome binding / protein localization to chromatin / negative regulation of innate immune response / telomere maintenance / nucleotidyltransferase activity / mitochondrion organization / transforming growth factor beta receptor signaling pathway / cellular response to nerve growth factor stimulus / nuclear estrogen receptor binding / response to gamma radiation / protein-DNA complex / Downregulation of SMAD2/3:SMAD4 transcriptional activity / DNA Damage Recognition in GG-NER / protein modification process / Dual Incision in GG-NER / Formation of Incision Complex in GG-NER / histone deacetylase binding / positive regulation of protein localization to nucleus / cellular response to amyloid-beta / cellular response to insulin stimulus / regulation of protein localization / cellular response to UV / NAD binding / double-strand break repair / nuclear envelope / site of double-strand break / cellular response to oxidative stress / positive regulation of canonical NF-kappaB signal transduction / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / transcription by RNA polymerase II / chromosome, telomeric region / damaged DNA binding / nuclear body / DNA repair / innate immune response / negative regulation of DNA-templated transcription / apoptotic process / ubiquitin protein ligase binding / DNA damage response / chromatin binding / chromatin / nucleolus / protein kinase binding / 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 / : / PADR1, N-terminal helical domain / PADR1 domain profile. / Poly [ADP-ribose] polymerase / PADR1 domain / PADR1 domain superfamily / PADR1 domain, zinc ribbon fold / PADR1 ...Zinc finger, PARP-type / first zn-finger domain of poly(adp-ribose) polymerase-1 / : / PADR1, N-terminal helical domain / PADR1 domain profile. / Poly [ADP-ribose] polymerase / PADR1 domain / PADR1 domain superfamily / PADR1 domain, zinc ribbon fold / 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 / WGR domain profile. / Poly(ADP-ribose) polymerase, regulatory domain / WGR domain / WGR domain superfamily / WGR domain / 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: 2.4 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Poly [ADP-ribose] polymerase 1
B: Poly [ADP-ribose] polymerase 1
C: Poly [ADP-ribose] polymerase 1
D: Poly [ADP-ribose] polymerase 1
E: Poly [ADP-ribose] polymerase 1
F: Poly [ADP-ribose] polymerase 1
G: Poly [ADP-ribose] polymerase 1
H: Poly [ADP-ribose] polymerase 1
I: 5'-D(*GP*CP*CP*GP*CP*TP*TP*GP*GP*G)-3'
J: 5'-D(*CP*CP*CP*AP*AP*GP*CP*GP*GP*C)-3'
K: 5'-D(*GP*CP*CP*GP*CP*TP*TP*GP*GP*G)-3'
L: 5'-D(*CP*CP*CP*AP*AP*GP*CP*GP*GP*C)-3'
M: 5'-D(*GP*CP*CP*GP*CP*TP*TP*GP*GP*G)-3'
N: 5'-D(*CP*CP*CP*AP*AP*GP*CP*GP*GP*C)-3'
O: 5'-D(*GP*CP*CP*GP*CP*TP*TP*GP*GP*G)-3'
P: 5'-D(*CP*CP*CP*AP*AP*GP*CP*GP*GP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,58224
Polymers131,05816
Non-polymers5238
Water6,161342
1
A: Poly [ADP-ribose] polymerase 1
B: Poly [ADP-ribose] polymerase 1
I: 5'-D(*GP*CP*CP*GP*CP*TP*TP*GP*GP*G)-3'
J: 5'-D(*CP*CP*CP*AP*AP*GP*CP*GP*GP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8956
Polymers32,7654
Non-polymers1312
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Poly [ADP-ribose] polymerase 1
D: Poly [ADP-ribose] polymerase 1
K: 5'-D(*GP*CP*CP*GP*CP*TP*TP*GP*GP*G)-3'
L: 5'-D(*CP*CP*CP*AP*AP*GP*CP*GP*GP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8956
Polymers32,7654
Non-polymers1312
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Poly [ADP-ribose] polymerase 1
F: Poly [ADP-ribose] polymerase 1
M: 5'-D(*GP*CP*CP*GP*CP*TP*TP*GP*GP*G)-3'
N: 5'-D(*CP*CP*CP*AP*AP*GP*CP*GP*GP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8956
Polymers32,7654
Non-polymers1312
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Poly [ADP-ribose] polymerase 1
H: Poly [ADP-ribose] polymerase 1
O: 5'-D(*GP*CP*CP*GP*CP*TP*TP*GP*GP*G)-3'
P: 5'-D(*CP*CP*CP*AP*AP*GP*CP*GP*GP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8956
Polymers32,7654
Non-polymers1312
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.219, 107.696, 86.138
Angle α, β, γ (deg.)90.000, 100.200, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
31E
41G
12A
22C
13B
23D
33F
43H

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain 'A' and (resseq 6:38 or resseq 49:59 or resseq...A0
211chain 'C' and (resseq 6:38 or resseq 49:59 or resseq...C0
311chain 'E' and (resseq 6:38 or resseq 49:59 or resseq...E0
411chain 'G' and (resseq 6:38 or resseq 49:59 or resseq...G0
112chain 'A' and (resseq 39:48) and (not element H) and (not element D) and backboneA0
212chain 'C' and (resseq 39:48) and (not element H) and (not element D) and backboneC0
113chain 'B' and (resseq 6:38 or resseq 49:59 or resseq...B0
213chain 'D' and (resseq 6:38 or resseq 49:59 or resseq...D0
313chain 'F' and (resseq 6:38 or resseq 49:59 or resseq...F0
413chain 'H' and (resseq 6:38 or resseq 49:59 or resseq...H0

NCS ensembles :
ID
1
2
3

NCS oper:
IDCodeMatrixVector
1given(0.993714, 0.052799, 0.098714), (0.061859, -0.993919, -0.091097), (0.093304, 0.09663, -0.990937)22.039801, 93.182999, 76.869202
2given(0.995436, 0.009796, 0.094922), (0.020521, -0.993419, -0.112679), (0.093194, 0.114113, -0.989087)-1.18618, 88.195, 116.216003
3given(0.997879, -0.021369, -0.061491), (0.022031, 0.999706, 0.010118), (0.061257, -0.011452, 0.998056)46.491402, -10.989, -40.575199
4given(0.966156, 0.075125, 0.246778), (0.097072, -0.992217, -0.07799), (0.238998, 0.099306, -0.965929)14.3365, 92.879997, 76.815804
5given(0.993591, -0.017003, 0.111751), (-0.0305, -0.992281, 0.120202), (0.108845, -0.12284, -0.98644)28.0334, 84.084099, 89.116699
6given(0.99159, 0.023333, 0.127295), (0.005705, -0.990537, 0.137125), (0.12929, -0.135246, -0.98234)-3.66194, 67.862999, 126.463997
7given(0.998734, -0.015259, -0.047935), (0.015029, 0.999874, -0.005145), (0.048007, 0.004418, 0.998837)42.397099, -9.52867, -42.454102

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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: 13336.297 Da / Num. of mol.: 8 / Fragment: PARP-1 zinc finger 1, Zn1, UNP residues 2-96
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ADPRT, PARP1, PPOL / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Rosetta2 / References: UniProt: P09874, NAD+ ADP-ribosyltransferase
#2: DNA chain
5'-D(*GP*CP*CP*GP*CP*TP*TP*GP*GP*G)-3'


Mass: 3077.002 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: Chemically synthesized DNA
#3: DNA chain
5'-D(*CP*CP*CP*AP*AP*GP*CP*GP*GP*C)-3'


Mass: 3014.982 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: Chemically synthesized DNA
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 342 / 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: 2.2 Å3/Da / Density % sol: 44.14 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8.5
Details: 30% PEG 3350, 100 mM NaAcetate, 100 mM Tris pH 8.5, 0.1 mM TCEP, 20% ethylene glycol, vapor diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 17, 2009
RadiationMonochromator: Double silicon(111) crystal / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 44580 / % possible obs: 100 % / Redundancy: 8.3 % / Rmerge(I) obs: 0.138 / Χ2: 1.029 / Net I/σ(I): 8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.4-2.448.40.70622361.0341100
2.44-2.498.40.65821521.0391100
2.49-2.538.40.63122661.0391100
2.53-2.598.40.51422101.0491100
2.59-2.648.40.46422491.0491100
2.64-2.78.40.44421981.0171100
2.7-2.778.40.422501.0491100
2.77-2.858.40.32721871.0411100
2.85-2.938.40.30522261.0331100
2.93-3.028.40.26422201.0341100
3.02-3.138.40.20122401.0461100
3.13-3.268.40.13121961.0421100
3.26-3.418.40.10522321.0251100
3.41-3.588.40.10922431.0331100
3.58-3.818.30.08622231.0231100
3.81-4.18.30.08222270.9861100
4.1-4.528.30.07522601.0161100
4.52-5.178.20.07722240.9931100
5.17-6.517.80.08122421.013199.6
6.51-508.30.07322991.011199.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.6.1_357refinement
PDB_EXTRACT3.1data extraction
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
SHELXSphasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→42.609 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8173 / SU ML: 0.38 / σ(F): 1.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.241 2242 5.04 %
Rwork0.1915 --
obs0.1941 44511 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.826 Å2 / ksol: 0.339 e/Å3
Displacement parametersBiso max: 127.57 Å2 / Biso mean: 32.691 Å2 / Biso min: 10.25 Å2
Baniso -1Baniso -2Baniso -3
1-8.1853 Å2-0 Å22.4908 Å2
2---10.5909 Å2-0 Å2
3---2.4056 Å2
Refinement stepCycle: LAST / Resolution: 2.4→42.609 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5697 1616 8 342 7663
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097731
X-RAY DIFFRACTIONf_angle_d1.26910682
X-RAY DIFFRACTIONf_chiral_restr0.0721092
X-RAY DIFFRACTIONf_plane_restr0.0051085
X-RAY DIFFRACTIONf_dihedral_angle_d21.432990
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A268X-RAY DIFFRACTIONPOSITIONAL0.113
12C268X-RAY DIFFRACTIONPOSITIONAL0.113
13E268X-RAY DIFFRACTIONPOSITIONAL0.122
14G268X-RAY DIFFRACTIONPOSITIONAL0.126
21A40X-RAY DIFFRACTIONPOSITIONAL0.149
22C40X-RAY DIFFRACTIONPOSITIONAL0.149
31B271X-RAY DIFFRACTIONPOSITIONAL0.139
32D271X-RAY DIFFRACTIONPOSITIONAL0.139
33F272X-RAY DIFFRACTIONPOSITIONAL0.168
34H272X-RAY DIFFRACTIONPOSITIONAL0.132
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4-2.48240.31412180.23284122434099
2.4824-2.58180.25742290.220142344463100
2.5818-2.69920.2822100.220442544464100
2.6992-2.84150.32062010.226442324433100
2.8415-3.01950.29552360.225242064442100
3.0195-3.25260.26132320.198542064438100
3.2526-3.57970.23452230.171842534476100
3.5797-4.09740.20532160.162542174433100
4.0974-5.16080.1862340.142242604494100
5.1608-42.61620.19262430.162442854528100

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