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- PDB-6v3w: Human Poly(ADP-Ribose) Polymerase 12, Catalytic fragment with fou... -

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Basic information

Entry
Database: PDB / ID: 6v3w
TitleHuman Poly(ADP-Ribose) Polymerase 12, Catalytic fragment with four point mutations in complex with RBN-2397
ComponentsProtein mono-ADP-ribosyltransferase PARP12
KeywordsTRANSFERASE / ADP-ribosyltransferase activity
Function / homology
Function and homology information


NAD+-protein-cysteine ADP-ribosyltransferase activity / protein auto-ADP-ribosylation / NAD+-protein ADP-ribosyltransferase activity / NAD+-protein poly-ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / nucleotidyltransferase activity / RNA binding / nucleus / metal ion binding
Similarity search - Function
: / WWE domain / Zinc finger C-x8-C-x5-C-x3-H type (and similar) / WWE domain superfamily / WWE domain / WWE domain profile. / zinc finger / Zinc finger, CCCH-type / Zinc finger C3H1-type profile. / Poly(ADP-ribose) polymerase catalytic domain ...: / WWE domain / Zinc finger C-x8-C-x5-C-x3-H type (and similar) / WWE domain superfamily / WWE domain / WWE domain profile. / zinc finger / Zinc finger, CCCH-type / Zinc finger C3H1-type profile. / Poly(ADP-ribose) polymerase catalytic domain / Poly(ADP-ribose) polymerase, catalytic domain / PARP catalytic domain profile. / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Chem-QO4 / Protein mono-ADP-ribosyltransferase PARP12
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsSwinger, K.K. / Gozgit, J.M. / Vasbinder, M.M. / Wigle, T.J. / Kuntz, K.W.
CitationJournal: Cancer Cell / Year: 2021
Title: PARP7 negatively regulates the type I interferon response in cancer cells and its inhibition triggers antitumor immunity.
Authors: Gozgit, J.M. / Vasbinder, M.M. / Abo, R.P. / Kunii, K. / Kuplast-Barr, K.G. / Gui, B. / Lu, A.Z. / Molina, J.R. / Minissale, E. / Swinger, K.K. / Wigle, T.J. / Blackwell, D.J. / Majer, C.R. ...Authors: Gozgit, J.M. / Vasbinder, M.M. / Abo, R.P. / Kunii, K. / Kuplast-Barr, K.G. / Gui, B. / Lu, A.Z. / Molina, J.R. / Minissale, E. / Swinger, K.K. / Wigle, T.J. / Blackwell, D.J. / Majer, C.R. / Ren, Y. / Niepel, M. / Varsamis, Z.A. / Nayak, S.P. / Bamberg, E. / Mo, J.R. / Church, W.D. / Mady, A.S.A. / Song, J. / Utley, L. / Rao, P.E. / Mitchison, T.J. / Kuntz, K.W. / Richon, V.M. / Keilhack, H.
History
DepositionNov 26, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 18, 2021Group: Database references / Category: citation / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Aug 25, 2021Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Sep 29, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Oct 11, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein mono-ADP-ribosyltransferase PARP12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1743
Polymers22,6151
Non-polymers5592
Water88349
1
A: Protein mono-ADP-ribosyltransferase PARP12
hetero molecules

A: Protein mono-ADP-ribosyltransferase PARP12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3486
Polymers45,2312
Non-polymers1,1184
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_564x,x-y+1,-z-1/61
Buried area1630 Å2
ΔGint-34 kcal/mol
Surface area18840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.466, 80.466, 142.648
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Protein mono-ADP-ribosyltransferase PARP12 / ADP-ribosyltransferase diphtheria toxin-like 12 / ARTD12 / Poly [ADP-ribose] polymerase 12 / PARP- ...ADP-ribosyltransferase diphtheria toxin-like 12 / ARTD12 / Poly [ADP-ribose] polymerase 12 / PARP-12 / Zinc finger CCCH domain-containing protein 1


Mass: 22615.250 Da / Num. of mol.: 1 / Mutation: F570V,A573G,Q577H,Y607F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PARP12, ZC3HDC1 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q9H0J9, Transferases; Glycosyltransferases; Pentosyltransferases
#2: Chemical ChemComp-QO4 / 5-{[(2S)-1-(3-oxo-3-{4-[5-(trifluoromethyl)pyrimidin-2-yl]piperazin-1-yl}propoxy)propan-2-yl]amino}-4-(trifluoromethyl)pyridazin-3(2H)-one / RBN-2397


Mass: 523.432 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H23F6N7O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.95 Å3/Da / Density % sol: 58.27 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 0.2 M Ammonium acetate, 0.1 M Sodium acetate pH 4, 15% w/v PEG 4000

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Data collection

DiffractionMean temperature: 63 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jul 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.04→69.78 Å / Num. obs: 18026 / % possible obs: 99.2 % / Redundancy: 19.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.022 / Rrim(I) all: 0.096 / Net I/σ(I): 18.8
Reflection shellResolution: 2.04→2.15 Å / Redundancy: 18.8 % / Rmerge(I) obs: 1.636 / Num. measured all: 47552 / Num. unique obs: 2534 / CC1/2: 0.903 / Rpim(I) all: 0.384 / Rrim(I) all: 1.681 / Net I/σ(I) obs: 2.8 / % possible all: 98.3

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Processing

Software
NameVersionClassification
Aimless0.6.2data scaling
REFMAC5.8.0257refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PQF

2pqf


Resolution: 2.04→69.78 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.947 / SU B: 12.292 / SU ML: 0.158 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.176 / ESU R Free: 0.166
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2553 918 5.1 %RANDOM
Rwork0.2104 ---
obs0.2127 17084 98.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 142.69 Å2 / Biso mean: 61.258 Å2 / Biso min: 42.38 Å2
Baniso -1Baniso -2Baniso -3
1-0.97 Å20.49 Å20 Å2
2--0.97 Å2-0 Å2
3----3.16 Å2
Refinement stepCycle: final / Resolution: 2.04→69.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1497 0 37 49 1583
Biso mean--66.04 65.34 -
Num. residues----183
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0131680
X-RAY DIFFRACTIONr_bond_other_d0.0010.0181431
X-RAY DIFFRACTIONr_angle_refined_deg1.5921.6692287
X-RAY DIFFRACTIONr_angle_other_deg1.3531.5943329
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1065199
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.46222.81396
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.24115256
X-RAY DIFFRACTIONr_dihedral_angle_4_deg27.99158
X-RAY DIFFRACTIONr_chiral_restr0.0710.2200
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021930
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02395
LS refinement shellResolution: 2.04→2.088 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.371 75 -
Rwork0.329 1212 -
obs--99 %
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)
17.02914.17864.61616.12310.59096.11070.1970.6073-0.0986-0.1526-0.2324-0.54740.03450.90140.03540.14190.0540.0750.20470.08190.1037-9.74917.048-21.151
22.7485-0.3871.15432.6112-0.75776.0995-0.1631-0.02990.44970.1157-0.1884-0.1904-0.58680.72170.35150.0809-0.0693-0.0370.11160.03070.0941-9.97820.241-6.167
34.78383.17193.48972.34450.66113.9813-0.063-0.1415-0.2553-0.1173-0.1441-0.22790.56370.19040.20720.13240.0050.03560.05760.02840.0767-12.4466.2374.363
42.37430.15280.35577.858-1.29338.7410.0053-0.1060.60660.1897-0.33440.4313-0.7958-0.75470.32920.09550.0381-0.02990.1321-0.04930.199-19.65324.325-10.851
510.0456-10.00333.63769.9952-3.65671.4597-0.0505-0.0912-0.16060.01680.15380.266-0.1065-0.4367-0.10320.39540.1688-0.01271.2863-0.10250.4814-33.47220.748-6.564
63.64990.40440.59613.0658-1.17310.25470.12920.14490.4842-0.3442-0.26420.1732-0.122-0.60630.1350.11950.03190.00540.1022-0.00250.0706-21.60918.86-17.521
711.8017-1.0115-2.32146.3073-1.1123.3481-0.02190.02340.01280.2359-0.09260.888-0.1336-0.68340.11450.2242-0.13470.02440.3095-0.09180.1634-29.42112.1580.585
81.84822.4713-4.38084.2455-6.987611.7407-0.16960.3258-0.2246-0.03910.12940.11150.1731-0.39640.04030.2025-0.20350.07890.3025-0.14310.2142-25.9948.3127.074
94.9894.28495.272711.47875.00855.6146-0.1665-0.09320.08-0.87020.09780.1222-0.2455-0.07890.06870.1395-0.08120.02730.1819-0.00370.0301-25.83310.853-6.345
102.06310.64980.30511.3736-1.02669.6932-0.03670.10460.1699-0.05-0.1311-0.0647-0.3810.36830.16780.0841-0.0037-0.01220.03680.03940.0773-15.28721.416-14.799
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A496 - 524
2X-RAY DIFFRACTION2A525 - 551
3X-RAY DIFFRACTION3A552 - 558
4X-RAY DIFFRACTION4A559 - 583
5X-RAY DIFFRACTION5A584 - 594
6X-RAY DIFFRACTION6A595 - 623
7X-RAY DIFFRACTION7A624 - 639
8X-RAY DIFFRACTION8A640 - 652
9X-RAY DIFFRACTION9A653 - 665
10X-RAY DIFFRACTION10A666 - 680

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