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- PDB-4dqy: Structure of Human PARP-1 bound to a DNA double strand break -

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Basic information

Entry
Database: PDB / ID: 4dqy
TitleStructure of Human PARP-1 bound to a DNA double strand break
Components
  • (Poly [ADP-ribose] polymerase ...) x 3
  • DNA (26-MER)
KeywordsTRANSFERASE/DNA / PARP / poly(ADP-ribose) polymerase / DNA binding protein / adp-ribosyl transferase / PARP-like zinc finger / poly(adp-ribosyl)ation / DNA damage detection / TRANSFERASE-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 / NAD+-protein-tyrosine ADP-ribosyltransferase activity / NAD+-protein-histidine ADP-ribosyltransferase activity / negative regulation of ATP biosynthetic process / carbohydrate biosynthetic process / 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 / regulation of base-excision repair / positive regulation of myofibroblast differentiation / NAD+-protein-tyrosine ADP-ribosyltransferase activity / NAD+-protein-histidine ADP-ribosyltransferase activity / negative regulation of ATP biosynthetic process / carbohydrate biosynthetic process / regulation of circadian sleep/wake cycle, non-REM sleep / positive regulation of single strand break repair / vRNA Synthesis / NAD+-protein-serine ADP-ribosyltransferase activity / negative regulation of adipose tissue development / NAD DNA ADP-ribosyltransferase activity / mitochondrial DNA metabolic process / NAD+- protein-aspartate ADP-ribosyltransferase activity / NAD+-protein-glutamate ADP-ribosyltransferase activity / DNA ADP-ribosylation / regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / signal transduction involved in regulation of gene expression / replication fork reversal / positive regulation of necroptotic process / HDR through MMEJ (alt-NHEJ) / ATP generation from poly-ADP-D-ribose / regulation of catalytic activity / transcription regulator activator activity / : / NAD+ ADP-ribosyltransferase / positive regulation of DNA-templated transcription, elongation / cellular response to zinc ion / negative regulation of telomere maintenance via telomere lengthening / positive regulation of intracellular estrogen receptor signaling pathway / protein auto-ADP-ribosylation / response to aldosterone / mitochondrial DNA repair / negative regulation of cGAS/STING signaling pathway / positive regulation of double-strand break repair via homologous recombination / negative regulation of innate immune response / protein poly-ADP-ribosylation / positive regulation of cardiac muscle hypertrophy / nuclear replication fork / negative regulation of transcription elongation by RNA polymerase II / site of DNA damage / NAD+-protein ADP-ribosyltransferase activity / R-SMAD binding / positive regulation of SMAD protein signal transduction / positive regulation of mitochondrial depolarization / macrophage differentiation / protein autoprocessing / decidualization / NAD+ ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / nucleosome binding / POLB-Dependent Long Patch Base Excision Repair / protein localization to chromatin / SUMOylation of DNA damage response and repair proteins / mitochondrion organization / telomere maintenance / cellular response to nerve growth factor stimulus / transforming growth factor beta receptor signaling pathway / nucleotidyltransferase activity / nuclear estrogen receptor binding / protein-DNA complex / response to gamma radiation / 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 / positive regulation of protein localization to nucleus / histone deacetylase binding / cellular response to insulin stimulus / cellular response to amyloid-beta / cellular response to UV / NAD binding / regulation of protein localization / double-strand break repair / cellular response to oxidative stress / site of double-strand break / nuclear envelope / positive regulation of canonical NF-kappaB signal transduction / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / chromosome, telomeric region / damaged DNA binding / transcription by RNA polymerase II / nuclear body / DNA repair / innate immune response / negative regulation of DNA-templated transcription / apoptotic process / DNA damage response / chromatin binding / chromatin / ubiquitin protein ligase binding / nucleolus / protein kinase binding / enzyme binding / negative regulation of transcription by RNA polymerase II
Similarity search - Function
Histone, subunit A - #130 / N-terminal domain of TfIIb - #630 / Zinc finger, PARP-type / first zn-finger domain of poly(adp-ribose) polymerase-1 / Poly(ADP-ribose) polymerase, regulatory domain / Poly(ADP-ribose) Polymerase; domain 1 / : / PADR1, N-terminal helical domain / PADR1 domain profile. / Poly [ADP-ribose] polymerase ...Histone, subunit A - #130 / N-terminal domain of TfIIb - #630 / Zinc finger, PARP-type / first zn-finger domain of poly(adp-ribose) polymerase-1 / Poly(ADP-ribose) polymerase, regulatory domain / Poly(ADP-ribose) Polymerase; domain 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. / Phosphoenolpyruvate Carboxykinase; domain 3 - #10 / Histone, subunit A / Phosphoenolpyruvate Carboxykinase; domain 3 / N-terminal domain of TfIIb / 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 / Single Sheet / Alpha-Beta Complex / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Poly [ADP-ribose] polymerase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 Å
AuthorsLangelier, M.F. / Pascal, J.M.
CitationJournal: Science / Year: 2012
Title: Structural basis for DNA damage-dependent poly(ADP-ribosyl)ation by human PARP-1.
Authors: Langelier, M.F. / Planck, J.L. / Roy, S. / Pascal, J.M.
History
DepositionFeb 16, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 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_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_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_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_auth_seq_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: Poly [ADP-ribose] polymerase 1
D: Poly [ADP-ribose] polymerase 1
E: Poly [ADP-ribose] polymerase 1
F: Poly [ADP-ribose] polymerase 1
M: DNA (26-MER)
N: DNA (26-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,57113
Polymers193,2478
Non-polymers3245
Water0
1
A: Poly [ADP-ribose] polymerase 1
B: Poly [ADP-ribose] polymerase 1
C: Poly [ADP-ribose] polymerase 1
M: DNA (26-MER)
N: DNA (26-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,8068
Polymers104,6145
Non-polymers1933
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Poly [ADP-ribose] polymerase 1
E: Poly [ADP-ribose] polymerase 1
F: Poly [ADP-ribose] polymerase 1
M: DNA (26-MER)
N: DNA (26-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,7447
Polymers104,6145
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.095, 112.965, 294.724
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.999067, -0.041927, -0.010315), (-0.041497, 0.998383, -0.038861), (0.011927, -0.038396, -0.999191)33.92078, 10.23124, 82.94321

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Components

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Poly [ADP-ribose] polymerase ... , 3 types, 6 molecules ADBECF

#1: Protein Poly [ADP-ribose] polymerase 1


Mass: 13101.821 Da / Num. of mol.: 2 / Fragment: Zinc Finger 1 (Zn1)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P09874
#2: Protein Poly [ADP-ribose] polymerase 1


Mass: 18393.297 Da / Num. of mol.: 2 / Fragment: Zinc Finger 3 (Zn3)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P09874
#3: Protein Poly [ADP-ribose] polymerase 1 / PARP-1 / NAD(+) ADP-ribosyltransferase 1 / ADPRT 1 / Poly[ADP-ribose] synthase 1


Mass: 57138.160 Da / Num. of mol.: 2 / Fragment: WGR-CAT fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PARP1, ADPRT, PPOL / Production host: Escherichia coli (E. coli) / References: UniProt: P09874, NAD+ ADP-ribosyltransferase

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DNA chain , 1 types, 2 molecules MN

#4: DNA chain DNA (26-MER)


Mass: 7990.130 Da / Num. of mol.: 2 / Source method: obtained synthetically

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Non-polymers , 2 types, 5 molecules

#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2

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Details

Sequence detailsAUTHORS STATE THAT V762A IS A NATURAL VARIANT.

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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: 2.8 Å3/Da / Density % sol: 56.13 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 7% Peg 3350, 10% ethylene glycol, 100 mM Hepes, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 25, 2011
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 3.25→50 Å / Num. all: 33644 / Num. obs: 33644 / % possible obs: 94.7 %

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
REFMAC5.6.0119refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.25→20 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.904 / SU B: 79.761 / SU ML: 0.574 / Cross valid method: THROUGHOUT / ESU R Free: 0.625 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30414 1684 5.1 %RANDOM
Rwork0.2384 ---
obs0.24156 31628 94.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 152.939 Å2
Baniso -1Baniso -2Baniso -3
1-3.14 Å2-0 Å2-0 Å2
2--4.57 Å20 Å2
3----7.71 Å2
Refinement stepCycle: LAST / Resolution: 3.25→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10666 1060 8 0 11734
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01912113
X-RAY DIFFRACTIONr_bond_other_d0.0010.028139
X-RAY DIFFRACTIONr_angle_refined_deg0.951.90316556
X-RAY DIFFRACTIONr_angle_other_deg0.8363.00119909
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3751350
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.72924.828464
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.985152014
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.2261544
X-RAY DIFFRACTIONr_chiral_restr0.0550.21772
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02112560
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022368
LS refinement shellResolution: 3.25→3.332 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.407 97 -
Rwork0.365 2100 -
obs--97.04 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
17.825-5.819-7.07627.29340.939719.46680.47150.21780.6584-0.3190.51850.7158-2.2654-1.0905-0.99010.516-0.0631-0.23990.4509-0.02931.2287-19.288468.95487.6987
24.7867-2.9361-1.73187.05420.64095.5779-0.1433-0.76880.24270.85160.06231.07011.0548-0.940.0810.3455-0.3040.22480.5021-0.17750.6077-27.009751.453120.6618
39.3876-0.21291.01558.1234-0.55143.9538-0.0787-0.8287-0.32530.36220.3599-1.51190.98561.8445-0.28130.30660.5012-0.13831.2182-0.32390.55195.871945.0183-1.0856
41.8445-2.073-2.82045.29412.456512.33540.00450.12920.1879-0.5930.1821-0.70970.14431.0922-0.18660.53990.0363-0.09170.3071-0.09580.4384-5.918738.948-20.7049
54.87441.7157-1.54229.442-0.34548.02250.02470.9009-0.3008-1.0798-0.13890.19910.0658-0.07940.11410.84240.1586-0.13140.247-0.18730.325-11.14426.5845-40.1824
66.67152.7443-5.57115.9396-2.98178.62490.05390.84650.87440.16240.1141-0.886-1.36340.885-0.1680.5445-0.2232-0.27641.63990.1110.85450.219479.574372.3708
72.11812.2305-1.214.2219-0.25882.768-0.35720.203-0.1811-0.7760.0164-0.850.651.02260.34070.7110.33960.26452.2478-0.15711.113458.255961.548459.8131
88.11530.06720.30869.2467-1.4134.92460.02740.9611-0.7181-0.52570.57541.68041.1777-1.3972-0.60280.5305-0.1748-0.16541.1294-0.17710.926525.803855.210582.5844
91.17332.1624-1.7816.5195-3.3269.89210.14620.2331-0.52430.9010.05270.39780.3454-0.8152-0.19881.10810.1032-0.08260.6141-0.25481.179838.244249.4875101.6917
105.3199-0.11550.47883.5790.34116.97470.2183-0.1616-1.36191.12740.1557-0.00720.8371-0.1376-0.3742.18630.094-0.15880.1730.09521.297843.963937.229121.1006
113.80590.76822.57331.6192.04545.10570.4654-0.1066-0.03790.53350.1097-0.420.77441.1735-0.57520.19330.0237-0.15211.0172-0.36840.4936-1.549959.320312.6569
1219.3135-7.38337.49964.9863-4.559618.22-0.7079-0.5620.81320.53860.1383-0.0995-0.5234-0.40670.56960.5413-0.009-0.11960.1619-0.1450.51168.345360.143831.5408
1310.2354-3.14834.796216.7039-3.083628.709-0.2947-2.14670.34540.97530.45760.1816-0.03390.2611-0.16290.5832-0.0728-0.28281.2931-0.27270.726319.818963.792149.5277
148.31955.3316-1.03419.3551-1.78740.38270.04191.0307-0.5056-1.7185-0.11860.4690.3145-0.08370.07670.50910.1699-0.29541.7702-0.1030.652831.944168.132966.7321
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 200
2X-RAY DIFFRACTION2B224 - 400
3X-RAY DIFFRACTION3C531 - 644
4X-RAY DIFFRACTION4C662 - 781
5X-RAY DIFFRACTION5C782 - 1011
6X-RAY DIFFRACTION6D6 - 200
7X-RAY DIFFRACTION7E224 - 400
8X-RAY DIFFRACTION8F531 - 644
9X-RAY DIFFRACTION9F662 - 781
10X-RAY DIFFRACTION10F782 - 1011
11X-RAY DIFFRACTION11M1 - 6
12X-RAY DIFFRACTION11N21 - 26
13X-RAY DIFFRACTION12M7 - 13
14X-RAY DIFFRACTION12N14 - 20
15X-RAY DIFFRACTION13M14 - 19
16X-RAY DIFFRACTION13N8 - 13
17X-RAY DIFFRACTION14M20 - 26
18X-RAY DIFFRACTION14N1 - 7

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