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- PDB-4av1: Crystal structure of the human PARP-1 DNA binding domain in compl... -

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Basic information

Entry
Database: PDB / ID: 4av1
TitleCrystal structure of the human PARP-1 DNA binding domain in complex with DNA
Components
  • 5'-D(*AP*AP*GP*TP*GP*TP*TP*GP*CP*AP*TP*TP)-3'
  • 5'-D(*TP*AP*AP*TP*GP*CP*AP*AP*CP*AP*CP*TP)-3'
  • POLY [ADP-RIBOSE] POLYMERASE 1
KeywordsTRANSFERASE / PARP1 / DNA-BINDING DOMAIN / DBD / DNA REPAIR / CANCER / POLY- ADP(RIBOSYL)ATION
Function / homology
Function and homology information


positive regulation of myofibroblast differentiation / regulation of base-excision repair / NAD+-histone H2BS6 serine ADP-ribosyltransferase activity / NAD+-histone H3S10 serine ADP-ribosyltransferase activity / NAD+-histone H2BE35 glutamate ADP-ribosyltransferase activity / negative regulation of ATP biosynthetic process / NAD+-protein-tyrosine ADP-ribosyltransferase activity / NAD+-protein-histidine ADP-ribosyltransferase activity / regulation of circadian sleep/wake cycle, non-REM sleep / vRNA Synthesis ...positive regulation of myofibroblast differentiation / regulation of base-excision repair / NAD+-histone H2BS6 serine ADP-ribosyltransferase activity / NAD+-histone H3S10 serine ADP-ribosyltransferase activity / NAD+-histone H2BE35 glutamate ADP-ribosyltransferase activity / negative regulation of ATP biosynthetic process / NAD+-protein-tyrosine ADP-ribosyltransferase activity / NAD+-protein-histidine ADP-ribosyltransferase activity / regulation of circadian sleep/wake cycle, non-REM sleep / vRNA Synthesis / positive regulation of single strand break repair / carbohydrate biosynthetic process / NAD+-protein-serine ADP-ribosyltransferase activity / regulation of catalytic 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 / HDR through MMEJ (alt-NHEJ) / positive regulation of DNA-templated transcription, elongation / signal transduction involved in regulation of gene expression / 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 / positive regulation of intracellular estrogen receptor signaling pathway / negative regulation of cGAS/STING signaling pathway / NAD+-protein-glutamate ADP-ribosyltransferase activity / response to aldosterone / positive regulation of mitochondrial depolarization / positive regulation of cardiac muscle hypertrophy / NAD+-protein mono-ADP-ribosyltransferase activity / R-SMAD binding / nuclear replication fork / negative regulation of transcription elongation by RNA polymerase II / protein autoprocessing / site of DNA damage / macrophage differentiation / NAD+ poly-ADP-ribosyltransferase activity / decidualization / Transferases; Glycosyltransferases; Pentosyltransferases / 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 / 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 / Downregulation of SMAD2/3:SMAD4 transcriptional activity / cellular response to nerve growth factor stimulus / DNA Damage Recognition in GG-NER / protein-DNA complex / protein modification process / positive regulation of protein localization to nucleus / Dual Incision in GG-NER / histone deacetylase binding / Formation of Incision Complex in GG-NER / 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 / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II / damaged DNA binding / positive regulation of canonical NF-kappaB signal transduction / 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 / 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 / PADR1 domain / PADR1 domain superfamily / : / PADR1 domain, zinc ribbon fold / PADR1, N-terminal helical domain / PADR1 domain profile. / PADR1 ...Zinc finger, PARP-type / first zn-finger domain of poly(adp-ribose) polymerase-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. / 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 / DNA (> 10) / Poly [ADP-ribose] polymerase 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsAli, A.A.E. / Timinszky, G. / Arribas-Bosacoma, R. / Kozlowski, M. / Hassa, P.O. / Hassler, M. / Ladurner, A.G. / Pearl, L.H. / Oliver, A.W.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2012
Title: The Zinc-Finger Domains of Parp1 Cooperate to Recognise DNA Strand-Breaks
Authors: Ali, A.A.E. / Timinszky, G. / Arribas-Bosacoma, R. / Kozlowski, M. / Hassa, P.O. / Hassler, M. / Ladurner, A.G. / Pearl, L.H. / Oliver, A.W.
History
DepositionMay 23, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 13, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 18, 2012Group: Other
Revision 1.2May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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
X: 5'-D(*AP*AP*GP*TP*GP*TP*TP*GP*CP*AP*TP*TP)-3'
Y: 5'-D(*TP*AP*AP*TP*GP*CP*AP*AP*CP*AP*CP*TP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,95910
Polymers107,6986
Non-polymers2624
Water79344
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area650 Å2
ΔGint-1.6 kcal/mol
Surface area27630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)163.978, 59.504, 61.582
Angle α, β, γ (deg.)90.00, 101.18, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 6:14 OR RESSEQ 16:40 OR RESSEQ 47:59 OR RESSEQ 64:75 )
211CHAIN C AND (RESSEQ 6:14 OR RESSEQ 16:40 OR RESSEQ 47:59 OR RESSEQ 64:75 )
112CHAIN B AND (RESSEQ 109:140 OR RESSEQ 155:202 )
212CHAIN D AND (RESSEQ 109:140 OR RESSEQ 155:202 )

NCS ensembles :
ID
1
2

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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: 25093.754 Da / Num. of mol.: 4 / Fragment: DNA-BINDING DOMAIN, RESIDUES 5-202
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Description: HUMAN CDNA LIBRARY / Plasmid: PSTREP-B / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: P09874, NAD+ ADP-ribosyltransferase
#2: DNA chain 5'-D(*AP*AP*GP*TP*GP*TP*TP*GP*CP*AP*TP*TP)-3'


Mass: 3692.426 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#3: DNA chain 5'-D(*TP*AP*AP*TP*GP*CP*AP*AP*CP*AP*CP*TP)-3'


Mass: 3630.406 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 3.15 Å3/Da / Density % sol: 60.62 % / Description: NONE
Crystal growDetails: 50 MM MES PH 6.5, 6% W/V PEG 1500, 5 MM DTT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 25, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.77→44.35 Å / Num. obs: 9910 / % possible obs: 92.2 % / Redundancy: 3.54 % / Biso Wilson estimate: 51.92 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 4.43
Reflection shellResolution: 3.1→3.27 Å / Redundancy: 3.62 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 1.51 / % possible all: 95.3

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: B-FORM DNA DUPLEX GENERATED IN COOT

Resolution: 3.1→44.353 Å / SU ML: 0.45 / σ(F): 1.38 / Phase error: 26.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2487 457 4.6 %
Rwork0.2295 --
obs0.2305 9863 91.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.662 Å2 / ksol: 0.323 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-9.203 Å20 Å22.8652 Å2
2--1.8003 Å20 Å2
3----11.0033 Å2
Refinement stepCycle: LAST / Resolution: 3.1→44.353 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2802 486 4 44 3336
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013436
X-RAY DIFFRACTIONf_angle_d0.6644715
X-RAY DIFFRACTIONf_dihedral_angle_d16.0011293
X-RAY DIFFRACTIONf_chiral_restr0.059494
X-RAY DIFFRACTIONf_plane_restr0.002523
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A462X-RAY DIFFRACTIONPOSITIONAL
12C462X-RAY DIFFRACTIONPOSITIONAL0.068
21B623X-RAY DIFFRACTIONPOSITIONAL
22D623X-RAY DIFFRACTIONPOSITIONAL0.056
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.54840.30831530.25333175X-RAY DIFFRACTION94
3.5484-4.470.22721460.21353157X-RAY DIFFRACTION92
4.47-44.35730.22491580.21663074X-RAY DIFFRACTION89

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