[English] 日本語
Yorodumi
- PDB-5dsy: Crystal structure of constitutively active PARP-2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5dsy
TitleCrystal structure of constitutively active PARP-2
ComponentsPoly [ADP-ribose] polymerase 2
KeywordsTRANSFERASE / ADP-ribosyl transferase / PARP / PARP-2
Function / homology
Function and homology information


hippocampal neuron apoptotic process / response to oxygen-glucose deprivation / poly-ADP-D-ribose binding / positive regulation of cell growth involved in cardiac muscle cell development / NAD+-protein-serine ADP-ribosyltransferase activity / NAD DNA ADP-ribosyltransferase activity / NAD+- protein-aspartate ADP-ribosyltransferase activity / NAD+-protein-glutamate ADP-ribosyltransferase activity / DNA ADP-ribosylation / HDR through MMEJ (alt-NHEJ) ...hippocampal neuron apoptotic process / response to oxygen-glucose deprivation / poly-ADP-D-ribose binding / positive regulation of cell growth involved in cardiac muscle cell development / NAD+-protein-serine ADP-ribosyltransferase activity / NAD DNA ADP-ribosyltransferase activity / NAD+- protein-aspartate ADP-ribosyltransferase activity / NAD+-protein-glutamate ADP-ribosyltransferase activity / DNA ADP-ribosylation / HDR through MMEJ (alt-NHEJ) / poly-ADP-D-ribose modification-dependent protein binding / DNA repair-dependent chromatin remodeling / NAD+ ADP-ribosyltransferase / protein auto-ADP-ribosylation / protein poly-ADP-ribosylation / site of DNA damage / NAD+-protein ADP-ribosyltransferase activity / decidualization / Transferases; Glycosyltransferases; Pentosyltransferases / NAD+ ADP-ribosyltransferase activity / POLB-Dependent Long Patch Base Excision Repair / nucleosome binding / extrinsic apoptotic signaling pathway / nucleotidyltransferase activity / DNA Damage Recognition in GG-NER / base-excision repair / Dual Incision in GG-NER / Formation of Incision Complex in GG-NER / double-strand break repair / damaged DNA binding / DNA repair / DNA damage response / chromatin binding / nucleolus / nucleoplasm / nucleus
Similarity search - Function
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 ...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 / Poly(ADP-ribose) polymerase catalytic domain / Poly(ADP-ribose) polymerase, catalytic domain / PARP catalytic domain profile. / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-UHB / Poly [ADP-ribose] polymerase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsRiccio, A.A. / Pascal, J.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM087282 United States
CitationJournal: Mol.Cell / Year: 2015
Title: PARP-1 Activation Requires Local Unfolding of an Autoinhibitory Domain.
Authors: Dawicki-McKenna, J.M. / Langelier, M.F. / DeNizio, J.E. / Riccio, A.A. / Cao, C.D. / Karch, K.R. / McCauley, M. / Steffen, J.D. / Black, B.E. / Pascal, J.M.
History
DepositionSep 17, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Poly [ADP-ribose] polymerase 2
B: Poly [ADP-ribose] polymerase 2
C: Poly [ADP-ribose] polymerase 2
D: Poly [ADP-ribose] polymerase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,8548
Polymers126,7044
Non-polymers2,1504
Water91951
1
A: Poly [ADP-ribose] polymerase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2132
Polymers31,6761
Non-polymers5381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Poly [ADP-ribose] polymerase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2132
Polymers31,6761
Non-polymers5381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Poly [ADP-ribose] polymerase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2132
Polymers31,6761
Non-polymers5381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Poly [ADP-ribose] polymerase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2132
Polymers31,6761
Non-polymers5381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)92.163, 119.900, 120.739
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
Poly [ADP-ribose] polymerase 2 / hPARP-2 / ADP-ribosyltransferase diphtheria toxin-like 2 / ARTD2 / NAD(+) ADP-ribosyltransferase 2 ...hPARP-2 / ADP-ribosyltransferase diphtheria toxin-like 2 / ARTD2 / NAD(+) ADP-ribosyltransferase 2 / ADPRT-2 / Poly[ADP-ribose] synthase 2 / pADPRT-2


Mass: 31675.916 Da / Num. of mol.: 4 / Fragment: unp residues 348-583
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PARP2, ADPRT2, ADPRTL2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UGN5, NAD+ ADP-ribosyltransferase
#2: Chemical
ChemComp-UHB / 2-[4-[(2S,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]carbonylpiperazin-1-yl]-N-(1-oxidanylidene-2,3-dihydroisoindol-4-yl)ethanamide


Mass: 537.528 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C24H27N9O6
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.63 Å3/Da / Density % sol: 53.28 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 2.55-2.65 M NaCl and 0.1 M Tris / PH range: 7.5-8.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1.12 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 29, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 70646 / % possible obs: 98.4 % / Redundancy: 12 % / Net I/σ(I): 11
Reflection shellResolution: 2.68→2.8 Å / Redundancy: 11.5 % / Mean I/σ(I) obs: 1.3 / % possible all: 87.2

-
Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
XDSdata reduction
XDSdata scaling
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KJD

3kjd


Resolution: 2.7→46.54 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.32 / Phase error: 26.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.248 3524 4.99 %
Rwork0.1926 --
obs0.1954 70646 99.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→46.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7880 0 156 51 8087
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.018248
X-RAY DIFFRACTIONf_angle_d1.34911193
X-RAY DIFFRACTIONf_dihedral_angle_d13.6683147
X-RAY DIFFRACTIONf_chiral_restr0.0551204
X-RAY DIFFRACTIONf_plane_restr0.0071541
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6957-2.73260.3733980.33452097X-RAY DIFFRACTION77
2.7326-2.77170.33791540.31322681X-RAY DIFFRACTION100
2.7717-2.8130.3191400.30462749X-RAY DIFFRACTION100
2.813-2.8570.39751430.30452704X-RAY DIFFRACTION100
2.857-2.90380.31521890.30192646X-RAY DIFFRACTION100
2.9038-2.95390.34891310.28422706X-RAY DIFFRACTION100
2.9539-3.00760.31491210.27512706X-RAY DIFFRACTION100
3.0076-3.06540.27841520.24582759X-RAY DIFFRACTION100
3.0654-3.1280.29061390.23132682X-RAY DIFFRACTION100
3.128-3.1960.27191340.23342718X-RAY DIFFRACTION100
3.196-3.27030.31141480.23482720X-RAY DIFFRACTION100
3.2703-3.35210.28711140.22192739X-RAY DIFFRACTION100
3.3521-3.44270.30451470.21872723X-RAY DIFFRACTION100
3.4427-3.54390.32791270.19322730X-RAY DIFFRACTION100
3.5439-3.65830.24691390.18642686X-RAY DIFFRACTION100
3.6583-3.7890.20021370.17372744X-RAY DIFFRACTION100
3.789-3.94060.2551460.17562656X-RAY DIFFRACTION100
3.9406-4.11980.20791420.16862733X-RAY DIFFRACTION100
4.1198-4.33690.17051420.14882706X-RAY DIFFRACTION100
4.3369-4.60840.22931690.14822705X-RAY DIFFRACTION100
4.6084-4.96380.17471210.13132713X-RAY DIFFRACTION100
4.9638-5.46270.22311520.15122709X-RAY DIFFRACTION100
5.4627-6.25150.24271360.17662712X-RAY DIFFRACTION100
6.2515-7.87010.22791640.1842685X-RAY DIFFRACTION100
7.8701-46.54730.19791390.16422713X-RAY DIFFRACTION100

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more