[English] 日本語
Yorodumi
- PDB-9dfp: PARP4 BRCT domain K23/24Q mutant -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9dfp
TitlePARP4 BRCT domain K23/24Q mutant
ComponentsProtein mono-ADP-ribosyltransferase PARP4
KeywordsTRANSFERASE / PARP family / ADP-ribosyltransferase / marylation / vault
Function / homology
Function and homology information


Nicotinamide salvage / Maturation of nucleoprotein / Maturation of nucleoprotein / NAD+-protein-aspartate ADP-ribosyltransferase activity / NAD+-protein-glutamate ADP-ribosyltransferase activity / NAD+-protein mono-ADP-ribosyltransferase activity / NAD+ poly-ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / nucleotidyltransferase activity / spindle microtubule ...Nicotinamide salvage / Maturation of nucleoprotein / Maturation of nucleoprotein / NAD+-protein-aspartate ADP-ribosyltransferase activity / NAD+-protein-glutamate ADP-ribosyltransferase activity / NAD+-protein mono-ADP-ribosyltransferase activity / NAD+ poly-ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / nucleotidyltransferase activity / spindle microtubule / protein modification process / inflammatory response / response to xenobiotic stimulus / ribonucleoprotein complex / DNA repair / DNA damage response / enzyme binding / DNA binding / extracellular exosome / nucleoplasm / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
Protein mono-ADP-ribosyltransferase PARP4 / VIT domain / Vault protein inter-alpha-trypsin domain / VIT domain profile. / Vault protein Inter-alpha-Trypsin domain / Poly(ADP-ribose) polymerase, regulatory domain superfamily / Poly(ADP-ribose) polymerase, regulatory domain / PARP alpha-helical domain profile. / von Willebrand factor type A domain / BRCA1 C Terminus (BRCT) domain ...Protein mono-ADP-ribosyltransferase PARP4 / VIT domain / Vault protein inter-alpha-trypsin domain / VIT domain profile. / Vault protein Inter-alpha-Trypsin domain / Poly(ADP-ribose) polymerase, regulatory domain superfamily / Poly(ADP-ribose) polymerase, regulatory domain / PARP alpha-helical domain profile. / von Willebrand factor type A domain / 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 / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / BRCT domain profile. / BRCT domain / BRCT domain superfamily / von Willebrand factor A-like domain superfamily
Similarity search - Domain/homology
Protein mono-ADP-ribosyltransferase PARP4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsFrigon, L. / Pascal, J.M.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)PJT153295 Canada
CitationJournal: J.Biol.Chem. / Year: 2025
Title: Crystal structure and mutagenesis of a nucleic acid-binding BRCT domain in human PARP4.
Authors: Frigon, L. / Pascal, J.M.
History
DepositionAug 30, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 28, 2025Provider: repository / Type: Initial release
Revision 1.1Jun 18, 2025Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein mono-ADP-ribosyltransferase PARP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,8062
Polymers11,7101
Non-polymers961
Water1,76598
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)114.664, 114.664, 114.664
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number196
Space group name H-MF23
Components on special symmetry positions
IDModelComponents
11A-337-

HOH

21A-348-

HOH

31A-372-

HOH

41A-385-

HOH

51A-393-

HOH

61A-396-

HOH

-
Components

#1: Protein Protein mono-ADP-ribosyltransferase PARP4 / 193 kDa vault protein / ADP-ribosyltransferase diphtheria toxin-like 4 / ARTD4 / PARP- ...193 kDa vault protein / ADP-ribosyltransferase diphtheria toxin-like 4 / ARTD4 / PARP-related/IalphaI-related H5/proline-rich / PH5P / Poly [ADP-ribose] polymerase 4 / PARP-4 / Vault poly(ADP-ribose) polymerase / VPARP


Mass: 11709.556 Da / Num. of mol.: 1 / Mutation: K23Q,K24Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PARP4, ADPRTL1, KIAA0177, PARPL / Production host: Escherichia coli (E. coli)
References: UniProt: Q9UKK3, Transferases; Glycosyltransferases; Pentosyltransferases
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.68 Å3/Da / Density % sol: 54.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 27% PEG3350, 0.2M ammonium sulfate and 0.1M sodium acetate pH 4.6

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1.2 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 2, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2 Å / Relative weight: 1
ReflectionResolution: 1.92→20 Å / Num. obs: 9666 / % possible obs: 99.9 % / Redundancy: 8.7 % / CC1/2: 1 / Net I/σ(I): 23.7
Reflection shellResolution: 1.92→1.97 Å / Redundancy: 8.5 % / Num. unique obs: 656 / CC1/2: 0.621 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
Aimlessdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.92→19.39 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.946 / SU B: 7.375 / SU ML: 0.11 / Cross valid method: THROUGHOUT / ESU R: 0.138 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21934 470 4.9 %RANDOM
Rwork0.17527 ---
obs0.17751 9185 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.769 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.92→19.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms768 0 5 98 871
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.012825
X-RAY DIFFRACTIONr_bond_other_d0.0010.016797
X-RAY DIFFRACTIONr_angle_refined_deg1.211.8121118
X-RAY DIFFRACTIONr_angle_other_deg0.4311.7971838
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.852599
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.93853
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.0910156
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0640.2121
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02968
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02198
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_it1.512.611387
X-RAY DIFFRACTIONr_mcbond_other1.5092.611387
X-RAY DIFFRACTIONr_mcangle_it2.0944.677486
X-RAY DIFFRACTIONr_mcangle_other2.0934.683487
X-RAY DIFFRACTIONr_scbond_it2.2873.01438
X-RAY DIFFRACTIONr_scbond_other2.262.95435
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.7425.281626
X-RAY DIFFRACTIONr_long_range_B_refined8.00527.68952
X-RAY DIFFRACTIONr_long_range_B_other7.84926.24926
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.921→1.97 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 28 -
Rwork0.263 660 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 13.2926 Å / Origin y: 3.2461 Å / Origin z: 25.269 Å
111213212223313233
T0.0126 Å2-0.012 Å2-0.0223 Å2-0.0392 Å20.028 Å2--0.0576 Å2
L7.0601 °20.4827 °2-1.8021 °2-2.2474 °2-0.135 °2--3.9018 °2
S-0.0555 Å °-0.3473 Å °-0.0278 Å °-0.0142 Å °-0.0782 Å °-0.1032 Å °0.0407 Å °-0.0288 Å °0.1337 Å °

+
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