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- PDB-8sx2: PARP4 catalytic domain bound to EB47 -

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Basic information

Entry
Database: PDB / ID: 8sx2
TitlePARP4 catalytic 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: 2.95 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,5954
Polymers74,5202
Non-polymers1,0752
Water66737
1
A: Protein mono-ADP-ribosyltransferase PARP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7972
Polymers37,2601
Non-polymers5381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Protein mono-ADP-ribosyltransferase PARP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7972
Polymers37,2601
Non-polymers5381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.905, 72.265, 160.978
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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: 37259.855 Da / Num. of mol.: 2
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-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: isolated from a natural source / Formula: C24H27N9O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 2.42 Å3/Da / Density % sol: 49.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 23% PEG3350, 0.1 M Bis-Tris pH 6.5, 0.2 M MgCl2, and 600 uM 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: 1.1158 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 3, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1158 Å / Relative weight: 1
ReflectionResolution: 2.95→65.93 Å / Num. obs: 29266 / % possible obs: 100 % / Redundancy: 14.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.203 / Rpim(I) all: 0.056 / Rrim(I) all: 0.211 / Χ2: 1.06 / Net I/σ(I): 11.6
Reflection shellResolution: 2.95→3.13 Å / % possible obs: 100 % / Redundancy: 14.6 % / Rmerge(I) obs: 2.235 / Num. measured all: 36612 / Num. unique obs: 2510 / CC1/2: 0.541 / Rpim(I) all: 0.6 / Rrim(I) all: 2.316 / Χ2: 0.89 / 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: 2.95→19.99 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 0.63 / Phase error: 30.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2616 1553 5.31 %
Rwork0.2153 --
obs0.2178 29266 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.95→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4856 0 78 37 4971
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065026
X-RAY DIFFRACTIONf_angle_d1.0996796
X-RAY DIFFRACTIONf_dihedral_angle_d13.2711957
X-RAY DIFFRACTIONf_chiral_restr0.06793
X-RAY DIFFRACTIONf_plane_restr0.004906
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.95-3.040.3721320.34582536X-RAY DIFFRACTION100
3.05-3.150.35951190.32172534X-RAY DIFFRACTION100
3.15-3.280.42731550.30952549X-RAY DIFFRACTION100
3.28-3.430.33421270.272506X-RAY DIFFRACTION100
3.43-3.610.31211510.24192506X-RAY DIFFRACTION100
3.61-3.830.29591540.21792522X-RAY DIFFRACTION100
3.83-4.130.28161350.20642517X-RAY DIFFRACTION100
4.13-4.530.2371460.17972512X-RAY DIFFRACTION100
4.54-5.180.19521490.16652520X-RAY DIFFRACTION100
5.18-6.490.22541390.21682499X-RAY DIFFRACTION100
6.49-19.990.22141460.19162512X-RAY DIFFRACTION99
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)
12.42730.89450.75221.5941.14492.2793-0.0528-0.41030.9565-0.0809-0.13520.1734-0.1409-0.1361-00.8637-0.05610.02020.9301-0.07361.0998-45.256124.189827.7987
22.5121-1.2562-0.66051.04580.63791.84850.2146-0.36511.086-0.41970.2866-0.3975-0.62540.7232-00.9591-0.12640.20640.9278-0.07171.0891-19.655821.961623.5131
34.1451-1.0923-1.5421.79422.11574.10310.15750.75920.7673-0.7862-0.0005-0.0465-0.82060.17040.00041.0868-0.11910.03490.88330.17521.0047-27.331119.803814.7851
40.2886-0.22320.81690.1938-0.68762.42140.13520.0696-0.02210.14260.09340.05830.18560.06060.00050.80490.01720.07140.75880.00510.712812.0091-21.779930.2841
51.65450.67820.22192.7588-0.2430.715-0.1325-0.2691-0.6386-0.0907-0.1041-0.3090.16160.2703-00.77430.05830.00180.8596-0.00860.661212.4829-17.944321.0662
63.3179-1.1135-0.85843.4587-1.472.27030.1513-0.5306-0.23270.145-0.22010.76210.2611-0.3806-00.6412-0.01250.06210.7296-0.05580.5408-12.1861-15.038620.3187
72.4622-1.0319-0.09626.2394-1.66963.00950.05410.36770.0036-0.4828-0.1217-0.00080.09670.0818-00.5967-0.06850.04020.7262-0.04340.495-4.8563-9.954911.5384
80.35690.4840.4230.69810.62090.5545-0.20061.0796-1.04130.6618-0.1106-0.09680.1273-1.219600.84090.0494-0.05841.2501-0.10251.0721-32.538230.450556.3623
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'B' and resid 262 through 394)
2X-RAY DIFFRACTION2chain 'B' and (resid 395 through 432 )
3X-RAY DIFFRACTION3chain 'B' and (resid 433 through 566 )
4X-RAY DIFFRACTION4chain 'A' and (resid 243 through 309 )
5X-RAY DIFFRACTION5chain 'A' and (resid 310 through 394 )
6X-RAY DIFFRACTION6chain 'A' and (resid 395 through 432 )
7X-RAY DIFFRACTION7chain 'A' and (resid 433 through 563 )
8X-RAY DIFFRACTION8(chain 'B' and resid 243 through 261)

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