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

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Basic information

Entry
Database: PDB / ID: 4oqb
TitleStructure of Human PARP-1 bound to a DNA double strand break in complex with (2Z)-2-{4-[2-(morpholin-4-yl)ethoxy]benzylidene}-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 / 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 / negative regulation of transcription elongation by RNA polymerase II / macrophage differentiation / 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 / enzyme activator activity / Downregulation of SMAD2/3:SMAD4 transcriptional 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 / ubiquitin protein ligase binding / DNA damage response / 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, regulatory domain / Poly(ADP-ribose) Polymerase; domain 1 / Poly [ADP-ribose] polymerase / PADR1 domain / PADR1 domain superfamily / : / PADR1 domain, zinc ribbon fold / PADR1, N-terminal helical domain ...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 / 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. / 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-2UT / DNA / DNA (> 10) / Poly [ADP-ribose] polymerase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.362 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 1.4Sep 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)191,74611
Polymers191,0906
Non-polymers6565
Water00
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)104,0617
Polymers103,5354
Non-polymers5253
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)65.100, 113.080, 296.230
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: _ / Refine code: _

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-2UT / (2Z)-2-{4-[2-(morpholin-4-yl)ethoxy]benzylidene}-3-oxo-2,3-dihydro-1-benzofuran-7-carboxamide


Mass: 394.420 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H22N2O5
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: 2.85 Å3/Da / Density % sol: 56.89 %
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: 3.362→50 Å / Num. all: 32044 / Num. obs: 31785
Reflection shellHighest resolution: 3.362 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: 3.362→20 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.912 / SU B: 165.478 / SU ML: 1.034 / Cross valid method: THROUGHOUT / ESU R Free: 0.75 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.34904 1625 5.1 %RANDOM
Rwork0.32171 ---
obs0.32306 30120 98.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 213.836 Å2
Baniso -1Baniso -2Baniso -3
1--3.04 Å20 Å20 Å2
2--4.09 Å20 Å2
3----1.05 Å2
Refinement stepCycle: LAST / Resolution: 3.362→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10666 1060 33 0 11759
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.01912142
X-RAY DIFFRACTIONr_bond_other_d0.0010.0211134
X-RAY DIFFRACTIONr_angle_refined_deg0.7681.88216612
X-RAY DIFFRACTIONr_angle_other_deg0.8593.00125767
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.37251350
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.46824.828464
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.93152014
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.3971544
X-RAY DIFFRACTIONr_chiral_restr0.0590.21772
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02112897
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022645
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_it0.83811.0625420
X-RAY DIFFRACTIONr_mcbond_other0.83811.0635421
X-RAY DIFFRACTIONr_mcangle_it1.59916.5896757
X-RAY DIFFRACTIONr_mcangle_other1.59916.5896757
X-RAY DIFFRACTIONr_scbond_it0.35310.6896722
X-RAY DIFFRACTIONr_scbond_other0.35310.696723
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.77616.0159840
X-RAY DIFFRACTIONr_long_range_B_refined3.29486.59613569
X-RAY DIFFRACTIONr_long_range_B_other3.29586.58813567
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)
11A51230
12D51230
21A75960
22D75960
31C285720.02
32F285720.02
41M19990.14
42N19990.14
LS refinement shellResolution: 3.362→3.447 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.526 117 -
Rwork0.525 2114 -
obs--96.66 %
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)
15.8038-2.9625-1.64241.8417-0.52766.58610.6565-0.18580.4938-0.35520.0834-0.0704-0.53440.0395-0.740.3612-0.1538-0.13860.756-0.40831.6707-19.085669.01937.5576
24.4724-2.21431.16863.7442-0.70553.1229-0.173-1.18860.50490.34720.14260.83141.8918-0.32810.03041.4269-0.22460.13391.2918-0.41650.9753-26.429151.449220.9226
30.3529-0.2327-0.61381.65751.74833.1306-0.0553-0.38350.0125-0.40880.02910.0970.72260.44820.02621.39880.2596-0.16830.893-0.24710.9668-5.134434.6101-25.9204
410.65571.7642-0.14710.68421.05414.10420.16731.04040.6973-0.0210.09570.1906-0.84650.6162-0.2630.8742-0.2196-0.04441.81820.1970.713451.715978.472372.9985
51.79582.10312.18364.98480.82085.53120.14291.276-0.0874-0.4724-0.2147-0.04311.69711.60710.07180.76920.19860.11153.1209-0.41030.113858.880360.299560.4024
62.04550.1922-0.99481.9064-0.7253.2618-0.12830.9859-0.78751.12820.21910.21660.0774-0.6266-0.09081.5441-0.01650.04840.5411-0.1391.204237.413244.8007107.6194
75.89881.7917.01430.70672.73411.2574-0.342-0.2603-0.6254-0.10290.2322-0.1272-0.47550.24340.10981.02490.0265-0.07021.3151-0.12920.925916.3862.859640.8521
86.8390.11653.55460.02220.08052.402-0.2112-0.1974-0.81760.05250.13590.0477-0.71850.08350.07530.98010.079-0.18491.3293-0.16711.065814.998562.860141.0744
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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