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

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Basic information

Entry
Database: PDB / ID: 4opx
TitleStructure of Human PARP-1 bound to a DNA double strand break in complex with (2R)-5-fluoro-2-methyl-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


positive regulation of myofibroblast differentiation / regulation of base-excision repair / negative regulation of ATP biosynthetic process / NAD+-protein-tyrosine ADP-ribosyltransferase activity / NAD+-protein-histidine ADP-ribosyltransferase activity / 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 ...positive regulation of myofibroblast differentiation / regulation of base-excision repair / negative regulation of ATP biosynthetic process / NAD+-protein-tyrosine ADP-ribosyltransferase activity / NAD+-protein-histidine ADP-ribosyltransferase activity / 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 / NAD+-histone H2BS6 serine ADP-ribosyltransferase activity / NAD+-histone H3S10 serine ADP-ribosyltransferase activity / regulation of catalytic activity / negative regulation of adipose tissue development / NAD DNA 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 / positive regulation of necroptotic process / replication fork reversal / ATP generation from poly-ADP-D-ribose / 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 / NAD+-protein-aspartate ADP-ribosyltransferase activity / mitochondrial DNA repair / protein poly-ADP-ribosylation / response to aldosterone / negative regulation of cGAS/STING signaling pathway / NAD+-histone H2BE35 glutamate ADP-ribosyltransferase activity / NAD+-histone H2BE2 glutamate ADP-ribosyltransferase activity / NAD+-histone H2BE18 glutamate ADP-ribosyltransferase activity / positive regulation of mitochondrial depolarization / positive regulation of cardiac muscle hypertrophy / NAD+-protein mono-ADP-ribosyltransferase activity / nuclear replication fork / R-SMAD binding / site of DNA damage / negative regulation of transcription elongation by RNA polymerase II / protein autoprocessing / NAD+ poly-ADP-ribosyltransferase activity / macrophage differentiation / Transferases; Glycosyltransferases; Pentosyltransferases / decidualization / positive regulation of SMAD protein signal transduction / POLB-Dependent Long Patch Base Excision Repair / positive regulation of double-strand break repair via homologous recombination / SUMOylation of DNA damage response and repair proteins / nucleosome binding / protein localization to chromatin / telomere maintenance / nucleotidyltransferase activity / transforming growth factor beta receptor signaling pathway / negative regulation of innate immune response / nuclear estrogen receptor binding / mitochondrion organization / response to gamma radiation / 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 / cellular response to amyloid-beta / NAD binding / cellular response to UV / nuclear envelope / double-strand break repair / regulation of protein localization / site of double-strand break / 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 / damaged DNA binding / transcription by RNA polymerase II / chromosome, telomeric region / 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 / nucleolus / chromatin / 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 / 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-2UR / DNA / DNA (> 10) / Poly [ADP-ribose] polymerase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.314 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 6, 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)191,54711
Polymers191,0906
Non-polymers4575
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)103,8617
Polymers103,5354
Non-polymers3263
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)65.150, 112.910, 295.290
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-2UR / (2R)-5-fluoro-2-methyl-2,3-dihydro-1-benzofuran-7-carboxamide


Mass: 195.190 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H10FNO2
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: 2.84 Å3/Da / Density % sol: 56.72 %
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, 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: 3.313→50 Å / Num. all: 33300 / Num. obs: 33077
Reflection shellHighest resolution: 3.313 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: 3.314→20 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.92 / SU B: 131.214 / SU ML: 0.842 / Cross valid method: THROUGHOUT / ESU R Free: 0.673 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.3248 1683 5.1 %RANDOM
Rwork0.30275 ---
obs0.30383 31353 98.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 205.025 Å2
Baniso -1Baniso -2Baniso -3
1-0.94 Å20 Å20 Å2
2--5.4 Å20 Å2
3----6.34 Å2
Refinement stepCycle: LAST / Resolution: 3.314→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10666 1060 18 0 11744
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.01912125
X-RAY DIFFRACTIONr_bond_other_d0.0010.0211122
X-RAY DIFFRACTIONr_angle_refined_deg0.7661.88216590
X-RAY DIFFRACTIONr_angle_other_deg0.8593.00125739
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.36151350
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.29524.828464
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.948152014
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.3121544
X-RAY DIFFRACTIONr_chiral_restr0.0590.21772
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02112819
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022639
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_it0.78711.3815418
X-RAY DIFFRACTIONr_mcbond_other0.78711.3815417
X-RAY DIFFRACTIONr_mcangle_it1.50517.0686757
X-RAY DIFFRACTIONr_mcangle_other1.50517.0686758
X-RAY DIFFRACTIONr_scbond_it0.32110.9656707
X-RAY DIFFRACTIONr_scbond_other0.32110.9656708
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.71616.4259818
X-RAY DIFFRACTIONr_long_range_B_refined3.0188.90313549
X-RAY DIFFRACTIONr_long_range_B_other3.0188.90513550
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)
11A51310
12D51310
21A76240
22D76240
31C286260.02
32F286260.02
41M19920.14
42N19920.14
LS refinement shellResolution: 3.314→3.398 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.45 113 -
Rwork0.443 2169 -
obs--96.65 %
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)
14.8848-2.8006-2.42333.2898-1.03885.09850.3683-0.20930.3199-0.2230.11360.1599-0.59790.3351-0.48190.5321-0.1666-0.1850.4249-0.26251.4592-18.643468.75567.5046
22.1488-1.8377-0.50483.29510.59433.2489-0.1927-0.46310.40750.34440.11520.46980.7434-0.08780.07750.3869-0.1940.10730.9267-0.23871.0149-26.268151.292220.8742
31.4925-0.2244-0.2711.09121.69732.9053-0.2401-0.1167-0.0065-0.13730.26540.09670.25350.661-0.02531.26760.1715-0.09110.5429-0.08540.8224-4.967534.2834-25.8638
41.5505-0.1788-0.17491.14542.30975.27680.00150.47740.1605-0.35590.06360.1177-1.07741.0962-0.06510.8657-0.3475-0.24132.24110.08210.633651.315678.56972.981
51.15761.47971.27472.19351.01773.7866-0.09030.5346-0.0409-0.17670.00940.03330.46421.02260.08090.34020.31650.09622.5982-0.35350.274758.795160.501760.3028
63.3170.1020.54351.6409-1.243.1654-0.15851.1919-1.19731.17160.2916-0.05920.1286-0.4337-0.13311.6034-0.04810.03780.5674-0.37751.139937.564944.7362107.4062
74.19050.48493.80150.08050.66475.8974-0.1369-0.4778-0.14550.03120.0312-0.00480.0696-0.13150.10560.92940.0023-0.30411.2478-0.0990.788616.453662.751540.8814
84.78170.19644.31680.03020.16995.8877-0.3068-0.68340.0184-0.0816-0.08820.1355-0.2589-0.33820.3950.91560.0666-0.3211.0301-0.18120.957715.109362.778741.0976
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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