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- PDB-4oqa: Structure of Human PARP-1 bound to a DNA double strand break in c... -

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Basic information

Entry
Database: PDB / ID: 4oqa
TitleStructure of Human PARP-1 bound to a DNA double strand break in complex with (2Z)-2-(2,4-dihydroxybenzylidene)-3-oxo-2,3-dihydro-1-benzofuran-7-carboxamide
Components
  • (Poly [ADP-ribose] polymerase 1) x 2
  • DNA (26-MER)
KeywordsTRANSFERASE/DNA/TRANSFERASE INHIBITOR / zinc finger / DNA binding / PARP / polymerase / DNA repair / poly(ADP-ribosyl)ation / TRANSFERASE-DNA-TRANSFERASE INHIBITOR 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 / NAD+- protein-aspartate ADP-ribosyltransferase activity / NAD+-protein-glutamate ADP-ribosyltransferase activity / DNA ADP-ribosylation / mitochondrial DNA metabolic process / 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 / ATP generation from poly-ADP-D-ribose / regulation of catalytic activity / HDR through MMEJ (alt-NHEJ) / transcription regulator activator activity / : / positive regulation of DNA-templated transcription, elongation / NAD+ ADP-ribosyltransferase / 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 / positive regulation of mitochondrial depolarization / response to aldosterone / mitochondrial DNA repair / negative regulation of cGAS/STING signaling pathway / positive regulation of double-strand break repair via homologous recombination / 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 / macrophage differentiation / protein autoprocessing / decidualization / NAD+ ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / nucleosome binding / POLB-Dependent Long Patch Base Excision Repair / SUMOylation of DNA damage response and repair proteins / protein localization to chromatin / telomere maintenance / negative regulation of innate immune response / nucleotidyltransferase activity / mitochondrion organization / cellular response to nerve growth factor stimulus / transforming growth factor beta receptor signaling pathway / 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 / site of double-strand break / nuclear envelope / cellular response to oxidative stress / positive regulation of canonical NF-kappaB signal transduction / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II / damaged DNA binding / chromosome, telomeric region / nuclear body / DNA repair / innate immune response / negative regulation of DNA-templated transcription / apoptotic process / DNA damage response / chromatin binding / ubiquitin protein ligase binding / chromatin / nucleolus / protein kinase binding / negative regulation of transcription by RNA polymerase II / enzyme binding
Similarity search - Function
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 ...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 / Phosphoenolpyruvate Carboxykinase; domain 3 / 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 / Alpha-Beta Complex / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-2US / DNA / DNA (> 10) / Poly [ADP-ribose] polymerase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.65 Å
AuthorsPascal, J.M. / Steffen, J.D.
CitationJournal: J.Med.Chem. / Year: 2014
Title: Discovery and Structure-Activity Relationship of Novel 2,3-Dihydrobenzofuran-7-carboxamide and 2,3-Dihydrobenzofuran-3(2H)-one-7-carboxamide Derivatives as Poly(ADP-ribose)polymerase-1 Inhibitors.
Authors: Patel, M.R. / Bhatt, A. / Steffen, J.D. / Chergui, A. / Murai, J. / Pommier, Y. / Pascal, J.M. / Trombetta, L.D. / Fronczek, F.R. / Talele, T.T.
History
DepositionFeb 7, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 2, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 9, 2014Group: Database references
Revision 1.2Jul 23, 2014Group: Database references
Revision 1.3Jul 26, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.4Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.5Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_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
C: Poly [ADP-ribose] polymerase 1
D: 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)191,64911
Polymers191,0906
Non-polymers5595
Water0
1
A: 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)103,9637
Polymers103,5354
Non-polymers4283
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: 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)103,6666
Polymers103,5354
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.160, 114.230, 294.240
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
12A
22D
13C
23F
14M
24N

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPALAALAAA6 - 916 - 91
21ASPASPALAALADC6 - 916 - 91
12SERSERPROPROAA224 - 359117 - 252
22SERSERPROPRODC224 - 359117 - 252
13ALAALATHRTHRCB531 - 101114 - 494
23ALAALATHRTHRFD531 - 101114 - 494
14DGDGDCDCME1 - 261 - 26
24DGDGDCDCNF1 - 261 - 26

NCS ensembles :
ID
1
2
3
4

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Components

#1: Protein Poly [ADP-ribose] polymerase 1 / PARP-1 / ADP-ribosyltransferase diphtheria toxin-like 1 / ARTD1 / NAD(+) ADP-ribosyltransferase 1 / ...PARP-1 / ADP-ribosyltransferase diphtheria toxin-like 1 / ARTD1 / NAD(+) ADP-ribosyltransferase 1 / ADPRT 1 / Poly[ADP-ribose] synthase 1


Mass: 30520.051 Da / Num. of mol.: 2 / Fragment: N-terminus (Zn1-Zn3, SEE REMARK 999)
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
#2: Protein Poly [ADP-ribose] polymerase 1 / PARP-1 / ADP-ribosyltransferase diphtheria toxin-like 1 / ARTD1 / NAD(+) ADP-ribosyltransferase 1 / ...PARP-1 / ADP-ribosyltransferase diphtheria toxin-like 1 / ARTD1 / NAD(+) ADP-ribosyltransferase 1 / ADPRT 1 / Poly[ADP-ribose] synthase 1


Mass: 57035.020 Da / Num. of mol.: 2 / Fragment: C-terminus (WGR-CAT, UNP residues 518-1014)
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
#3: DNA chain DNA (26-MER)


Mass: 7990.130 Da / Num. of mol.: 2 / Source method: obtained synthetically
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-2US / (2Z)-2-(2,4-dihydroxybenzylidene)-3-oxo-2,3-dihydro-1-benzofuran-7-carboxamide


Mass: 297.262 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H11NO5
Sequence detailsCHAINS A AND D EACH COMPRISE UNP RESIDUES 1-97 AND 207-366 OF PARP-1 CONNECTED BY A ASP-ILE LINKER.

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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: 2.87 Å3/Da / Density % sol: 57.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25 mM HEPES, 150 mM sodium chloride, 1 mM EDTA, 0.1 mM TCEP, 6.8% PEG3350, 2% ethylene glycol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 28, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 3.65→50 Å / Num. all: 25245 / Num. obs: 24937
Reflection shellHighest resolution: 3.65 Å

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Processing

Software
NameVersionClassification
CBASSdata collection
REFMAC5.7.0032refinement
xia2data reduction
xia2data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4DQY

4dqy


Resolution: 3.65→20 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.911 / SU B: 164.771 / SU ML: 0.998 / Cross valid method: THROUGHOUT / ESU R Free: 0.882 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.33424 1250 5 %RANDOM
Rwork0.29845 ---
obs0.30022 23595 98.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 257.215 Å2
Baniso -1Baniso -2Baniso -3
1--1.03 Å20 Å20 Å2
2--9.67 Å20 Å2
3----8.64 Å2
Refinement stepCycle: LAST / Resolution: 3.65→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10666 1060 26 0 11752
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.01912134
X-RAY DIFFRACTIONr_bond_other_d0.0010.0211123
X-RAY DIFFRACTIONr_angle_refined_deg0.7741.88216603
X-RAY DIFFRACTIONr_angle_other_deg0.863.00125737
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.33851350
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.13124.828464
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.893152014
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.3941544
X-RAY DIFFRACTIONr_chiral_restr0.0590.21772
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02112894
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022644
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_it1.12616.8665420
X-RAY DIFFRACTIONr_mcbond_other1.12616.8665421
X-RAY DIFFRACTIONr_mcangle_it2.11425.2936757
X-RAY DIFFRACTIONr_mcangle_other2.11425.2936757
X-RAY DIFFRACTIONr_scbond_it0.60516.3466714
X-RAY DIFFRACTIONr_scbond_other0.60516.3476715
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.22624.4919831
X-RAY DIFFRACTIONr_long_range_B_refined4.10513556
X-RAY DIFFRACTIONr_long_range_B_other4.10513557
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A51070
12D51070
21A75770
22D75770
31C285010.02
32F285010.02
41M19890.14
42N19890.14
LS refinement shellResolution: 3.65→3.742 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.482 78 -
Rwork0.464 1564 -
obs--94.53 %
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)
16.2703-3.4658-4.11982.47150.792110.23240.33920.25210.4602-0.38990.04540.005-0.7285-0.4369-0.38460.3913-0.1003-0.28390.6078-0.3861.1598-18.805169.597.4726
23.8659-3.4623-0.38373.7221-0.53483.0493-0.4691-0.77620.05420.1230.54090.56481.5417-0.4076-0.07180.8533-0.33140.14511.2474-0.4110.9657-25.994451.968520.8909
30.8392-0.2511-0.56551.57822.46154.2032-0.2044-0.34970.01470.04790.2796-0.04310.70460.567-0.07521.13650.1884-0.1570.7604-0.13940.7276-4.727934.8069-25.9125
49.21232.2499-4.48131.45690.84110.61350.32991.29770.78720.30970.01110.2322-1.04910.8238-0.34110.6647-0.3873-0.13191.9552-0.00690.348451.584380.381972.3722
54.30191.75392.25584.0596-1.07122.73490.18291.7-0.2696-0.1898-0.28350.06090.54091.08150.10050.31850.15790.16572.1895-0.77230.459858.795162.160459.542
61.05670.6364-0.37692.0025-1.29372.0713-0.19870.6632-0.81860.50370.46310.0820.1836-0.5245-0.26450.95320.01190.03510.6489-0.37141.375437.103745.9173106.5225
74.06040.89954.87430.28571.43197.69840.0757-0.16450.09670.2519-0.07930.0751.17660.40080.00360.81070.0021-0.22851.4081-0.33660.814716.638863.966440.4401
87.23290.39532.68730.18110.15011.29070.4486-0.34650.65990.0195-0.57390.22870.7937-0.09750.12531.44810.006-0.39311.7487-0.51230.798815.286864.030340.726
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 91
2X-RAY DIFFRACTION2A224 - 359
3X-RAY DIFFRACTION3C531 - 1011
4X-RAY DIFFRACTION4D6 - 91
5X-RAY DIFFRACTION5D224 - 359
6X-RAY DIFFRACTION6F531 - 1011
7X-RAY DIFFRACTION7M1 - 26
8X-RAY DIFFRACTION8N1 - 26

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