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- PDB-8swz: PARP4 ART domain bound to EB47 -

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Basic information

Entry
Database: PDB / ID: 8swz
TitlePARP4 ART domain bound to EB47
ComponentsProtein mono-ADP-ribosyltransferase PARP4
KeywordsTRANSFERASE / PARP family / ADP-ribosyltransferase / marylation / vault
Function / homology
Function and homology information


regulation of telomerase activity / Nicotinamide salvaging / Maturation of nucleoprotein / Maturation of nucleoprotein / NAD+-protein ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / NAD+ ADP-ribosyltransferase activity / nucleotidyltransferase activity / protein modification process / spindle microtubule ...regulation of telomerase activity / Nicotinamide salvaging / Maturation of nucleoprotein / Maturation of nucleoprotein / NAD+-protein ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / NAD+ ADP-ribosyltransferase activity / nucleotidyltransferase activity / protein modification process / spindle microtubule / response to xenobiotic stimulus / inflammatory response / ribonucleoprotein complex / DNA repair / DNA damage response / enzyme binding / DNA binding / extracellular exosome / nucleoplasm / membrane / nucleus / 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
Chem-UHB / Protein mono-ADP-ribosyltransferase PARP4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsFrigon, L. / Pascal, J.M.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)PJT153295 Canada
CitationJournal: Nucleic Acids Res. / Year: 2023
Title: Structural and biochemical analysis of the PARP1-homology region of PARP4/vault PARP.
Authors: Frigon, L. / Pascal, J.M.
History
DepositionMay 19, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 8, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Dec 20, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)87,2027
Polymers85,9423
Non-polymers1,2594
Water63135
1
A: Protein mono-ADP-ribosyltransferase PARP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2773
Polymers28,6471
Non-polymers6302
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein mono-ADP-ribosyltransferase PARP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2773
Polymers28,6471
Non-polymers6302
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Protein mono-ADP-ribosyltransferase PARP4


Theoretical massNumber of molelcules
Total (without water)28,6471
Polymers28,6471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)116.848, 150.859, 104.613
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-718-

HOH

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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: 28647.484 Da / Num. of mol.: 3
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: 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.: 2 / Source method: obtained synthetically / Formula: C24H27N9O6 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 35 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.68 Å3/Da / Density % sol: 54.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20% PEG3350, 0.2M sodium citrate tribasic dihydrate, 800uM EB47

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.12 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12 Å / Relative weight: 1
ReflectionResolution: 3→69.24 Å / Num. obs: 35783 / % possible obs: 100 % / Redundancy: 14.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.031 / Rrim(I) all: 0.118 / Χ2: 1 / Net I/σ(I): 18.2
Reflection shellResolution: 3→3.18 Å / % possible obs: 99.9 % / Redundancy: 14.5 % / Rmerge(I) obs: 2.022 / Num. measured all: 43823 / Num. unique obs: 3020 / CC1/2: 0.521 / Rpim(I) all: 0.547 / Rrim(I) all: 2.096 / Χ2: 0.83 / Net I/σ(I) obs: 1.4

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimlessdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→69.24 Å / SU ML: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0.36 / Phase error: 29.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2483 1854 5.18 %
Rwork0.2034 --
obs0.2058 35783 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→69.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5655 0 90 35 5780
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115859
X-RAY DIFFRACTIONf_angle_d1.5597928
X-RAY DIFFRACTIONf_dihedral_angle_d14.4892237
X-RAY DIFFRACTIONf_chiral_restr0.102912
X-RAY DIFFRACTIONf_plane_restr0.0151035
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.080.42331240.33562684X-RAY DIFFRACTION100
3.08-3.170.35391450.33362570X-RAY DIFFRACTION100
3.17-3.270.30481500.29182622X-RAY DIFFRACTION100
3.27-3.390.29471400.26482576X-RAY DIFFRACTION100
3.39-3.530.32581690.24362602X-RAY DIFFRACTION100
3.53-3.690.32351180.24782628X-RAY DIFFRACTION100
3.69-3.880.26171400.21022621X-RAY DIFFRACTION100
3.88-4.120.22811340.1962624X-RAY DIFFRACTION100
4.13-4.440.25991420.17692587X-RAY DIFFRACTION100
4.44-4.890.24191430.16912627X-RAY DIFFRACTION100
4.89-5.60.24231330.19242600X-RAY DIFFRACTION100
5.6-7.050.29871470.23312622X-RAY DIFFRACTION100
7.05-69.240.1791690.16222566X-RAY DIFFRACTION100
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)
15.13130.96360.97163.1438-4.62918.205-0.05531.07650.25980.5529-0.214-0.866-0.95360.22860.25840.63410.0253-0.02750.9533-0.20520.781414.3574-38.666753.4076
22.02091.3643-1.73282.8132-1.36332.47520.2647-0.2502-0.0823-0.0374-0.06050.18890.11150.1222-0.22240.974-0.0533-0.16590.91720.00741.036514.5667-9.035232.454
30.09710.46850.23074.76412.52821.3433-0.5443-0.03631.28121.26541.24980.19960.055-0.3309-0.6461.44260.316-0.2051.17760.43671.261657.871141.509918.8151
43.76231.0522-0.4763.8921-1.06772.8384-0.009-0.1487-0.1191-0.3501-0.5066-0.51290.42260.87760.43770.71730.14190.10260.9590.15570.755649.269816.8399.1367
52.7445-1.4758-0.86282.09911.515.45240.0319-0.4733-0.1063-0.16920.2535-0.0719-0.24660.6533-0.24470.8268-0.20860.08840.9536-0.06050.900726.625528.82845.3554
61.40052.9542-0.00236.7412-0.24430.1018-1.02210.36761.10841.15890.5917-0.34121.12440.43070.53312.02870.26420.08511.2734-0.15362.025522.939153.467930.7112
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 316 through 335)
2X-RAY DIFFRACTION2(chain 'A' and resid 336 through 570)
3X-RAY DIFFRACTION3(chain 'B' and resid 316 through 335)
4X-RAY DIFFRACTION4(chain 'B' and resid 336 through 570)
5X-RAY DIFFRACTION5(chain 'C' and resid 336 through 570)
6X-RAY DIFFRACTION6(chain 'C' and resid 316 through 335)

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