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- PDB-4xhu: The complex structure of Timeless_PAB and PARP-1_catalytic domain -

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Basic information

Entry
Database: PDB / ID: 4xhu
TitleThe complex structure of Timeless_PAB and PARP-1_catalytic domain
Components
  • Poly [ADP-ribose] polymerase 1
  • Protein timeless homolog
KeywordsTRANSFERASE/REPLICATION / DNA damage response / TRANSFERASE-REPLICATION complex
Function / homology
Function and homology information


cellular response to bleomycin / detection of abiotic stimulus / replication fork arrest / cell cycle phase transition / cellular response to cisplatin / NAD+-histone H2BS6 serine ADP-ribosyltransferase activity / NAD+-histone H3S10 serine ADP-ribosyltransferase activity / NAD+-histone H2BE35 glutamate ADP-ribosyltransferase activity / regulation of base-excision repair / positive regulation of myofibroblast differentiation ...cellular response to bleomycin / detection of abiotic stimulus / replication fork arrest / cell cycle phase transition / cellular response to cisplatin / NAD+-histone H2BS6 serine ADP-ribosyltransferase activity / NAD+-histone H3S10 serine ADP-ribosyltransferase activity / NAD+-histone H2BE35 glutamate ADP-ribosyltransferase activity / regulation of base-excision repair / positive regulation of myofibroblast differentiation / negative regulation of ATP biosynthetic process / NAD+-protein-tyrosine ADP-ribosyltransferase activity / NAD+-protein-histidine ADP-ribosyltransferase activity / carbohydrate biosynthetic process / positive regulation of single strand break repair / regulation of circadian sleep/wake cycle, non-REM sleep / vRNA Synthesis / negative regulation of adipose tissue development / NAD+-protein-serine ADP-ribosyltransferase activity / NAD DNA ADP-ribosyltransferase activity / cellular response to hydroxyurea / NAD+-protein-aspartate ADP-ribosyltransferase activity / NAD+-protein-glutamate ADP-ribosyltransferase activity / mitochondrial DNA metabolic process / DNA ADP-ribosylation / regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / DNA replication checkpoint signaling / entrainment of circadian clock / signal transduction involved in regulation of gene expression / positive regulation of necroptotic process / regulation of catalytic activity / ATP generation from poly-ADP-D-ribose / replication fork reversal / transcription regulator activator activity / HDR through MMEJ (alt-NHEJ) / replication fork protection complex / positive regulation of DNA-templated transcription, elongation / positive regulation of double-strand break repair / positive regulation of intracellular estrogen receptor signaling pathway / NAD+ ADP-ribosyltransferase / cellular response to zinc ion / negative regulation of telomere maintenance via telomere lengthening / protein auto-ADP-ribosylation / positive regulation of mitochondrial depolarization / response to aldosterone / mitochondrial DNA repair / branching morphogenesis of an epithelial tube / negative regulation of cGAS/STING signaling pathway / protein poly-ADP-ribosylation / positive regulation of cardiac muscle hypertrophy / negative regulation of transcription elongation by RNA polymerase II / nuclear replication fork / NAD+-protein ADP-ribosyltransferase activity / site of DNA damage / R-SMAD binding / positive regulation of SMAD protein signal transduction / macrophage differentiation / protein autoprocessing / decidualization / Transferases; Glycosyltransferases; Pentosyltransferases / positive regulation of double-strand break repair via homologous recombination / NAD+-protein poly-ADP-ribosyltransferase activity / POLB-Dependent Long Patch Base Excision Repair / SUMOylation of DNA damage response and repair proteins / nucleosome binding / protein localization to chromatin / negative regulation of innate immune response / telomere maintenance / nucleotidyltransferase activity / mitochondrion organization / transforming growth factor beta receptor signaling pathway / cellular response to nerve growth factor stimulus / morphogenesis of an epithelium / nuclear estrogen receptor binding / response to gamma radiation / protein-DNA complex / Downregulation of SMAD2/3:SMAD4 transcriptional activity / DNA Damage Recognition in GG-NER / lung development / protein modification process / regulation of circadian rhythm / Dual Incision in GG-NER / Formation of Incision Complex in GG-NER / histone deacetylase binding / positive regulation of protein localization to nucleus / circadian rhythm / cellular response to amyloid-beta / cellular response to insulin stimulus / regulation of protein localization / cellular response to UV / NAD binding / double-strand break repair / nuclear envelope / site of double-strand break / Processing of DNA double-strand break ends / cellular response to oxidative stress / positive regulation of canonical NF-kappaB signal transduction / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / transcription by RNA polymerase II
Similarity search - Function
Timeless, C-terminal / Timeless PAB domain / Timeless / Poly(ADP-ribose) polymerase, regulatory domain / Timeless, N-terminal / Timeless protein / Poly(ADP-ribose) Polymerase; domain 1 / : / PADR1, N-terminal helical domain / PADR1 domain profile. ...Timeless, C-terminal / Timeless PAB domain / Timeless / Poly(ADP-ribose) polymerase, regulatory domain / Timeless, N-terminal / Timeless protein / Poly(ADP-ribose) Polymerase; domain 1 / : / PADR1, N-terminal helical domain / PADR1 domain profile. / Poly [ADP-ribose] polymerase / PADR1 domain / PADR1 domain superfamily / PADR1 domain, zinc ribbon fold / PADR1 / Zinc finger poly(ADP-ribose) polymerase (PARP)-type signature. / Zinc finger, PARP-type superfamily / Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region / Zinc finger poly(ADP-ribose) polymerase (PARP)-type profile. / Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region / Zinc finger, PARP-type / 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 / 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 / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Alpha-Beta Complex / Up-down Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Poly [ADP-ribose] polymerase 1 / Protein timeless homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.089 Å
AuthorsXie, S. / Qian, C.
Funding support Hong Kong, 2items
OrganizationGrant numberCountry
General Research Council776313 Hong Kong
General Research Council775712 Hong Kong
CitationJournal: Mol.Cell / Year: 2015
Title: Timeless Interacts with PARP-1 to Promote Homologous Recombination Repair.
Authors: Xie, S. / Mortusewicz, O. / Ma, H.T. / Herr, P. / Poon, R.R. / Helleday, T. / Qian, C.
History
DepositionJan 6, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 30, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2015Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list / refine
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _refine.pdbx_method_to_determine_struct

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Poly [ADP-ribose] polymerase 1
D: Protein timeless homolog
A: Poly [ADP-ribose] polymerase 1
B: Protein timeless homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,89611
Polymers103,3704
Non-polymers5277
Water4,468248
1
C: Poly [ADP-ribose] polymerase 1
D: Protein timeless homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0206
Polymers51,6852
Non-polymers3354
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2300 Å2
ΔGint-9 kcal/mol
Surface area19560 Å2
MethodPISA
2
A: Poly [ADP-ribose] polymerase 1
B: Protein timeless homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8765
Polymers51,6852
Non-polymers1913
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2150 Å2
ΔGint-20 kcal/mol
Surface area20000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.364, 98.416, 116.900
Angle α, β, γ (deg.)90.00, 113.19, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 2 types, 4 molecules CADB

#1: Protein Poly [ADP-ribose] polymerase 1 / PARP-1 / ADP-ribosyltransferase diphtheria toxin-like 1 / ARTD1 / NAD(+) ADP-ribosyltransferase 1 / ...PARP-1 / ADP-ribosyltransferase diphtheria toxin-like 1 / ARTD1 / NAD(+) ADP-ribosyltransferase 1 / ADPRT 1 / Poly[ADP-ribose] synthase 1


Mass: 40164.969 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 661-1014
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PARP1, ADPRT, PPOL / Production host: Escherichia coli (E. coli) / References: UniProt: P09874, NAD+ ADP-ribosyltransferase
#2: Protein Protein timeless homolog / hTIM


Mass: 11519.938 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 1000-1098
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TIMELESS, TIM, TIM1, TIMELESS1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UNS1

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Non-polymers , 4 types, 255 molecules

#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 248 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.76 Å3/Da / Density % sol: 55.44 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6
Details: 200mM sodium acetate 100mM calcium cacodylate 15% PEG8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97907 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 23, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97907 Å / Relative weight: 1
ReflectionResolution: 2.089→25.1 Å / Num. obs: 62689 / % possible obs: 99.6 % / Redundancy: 3.2 % / Rmerge F obs: 0.07 / Rsym value: 0.458 / Net I/σ(I): 15.9
Reflection shellResolution: 2.05→2.09 Å / % possible obs: 100 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.458 / Mean I/σ(I) obs: 3 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XHT

4xht


Resolution: 2.089→25.096 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2105 1984 3.3 %
Rwork0.1825 60143 -
obs0.1834 60143 98.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.089→25.096 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6519 0 33 248 6800
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086744
X-RAY DIFFRACTIONf_angle_d1.0639123
X-RAY DIFFRACTIONf_dihedral_angle_d15.3822519
X-RAY DIFFRACTIONf_chiral_restr0.0431041
X-RAY DIFFRACTIONf_plane_restr0.0051169
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.089-2.14120.30541450.24044011X-RAY DIFFRACTION95
2.1412-2.19910.26271350.21394227X-RAY DIFFRACTION100
2.1991-2.26380.23881520.20234237X-RAY DIFFRACTION100
2.2638-2.33680.28641400.1954206X-RAY DIFFRACTION100
2.3368-2.42020.21481430.19334211X-RAY DIFFRACTION100
2.4202-2.51710.20931420.20144218X-RAY DIFFRACTION100
2.5171-2.63150.24611510.20134182X-RAY DIFFRACTION100
2.6315-2.77010.23661380.20254241X-RAY DIFFRACTION100
2.7701-2.94340.21211390.20184239X-RAY DIFFRACTION100
2.9434-3.17020.25081460.1984258X-RAY DIFFRACTION100
3.1702-3.48850.20651380.18344209X-RAY DIFFRACTION100
3.4885-3.99160.18761450.16654146X-RAY DIFFRACTION98
3.9916-5.02230.16491450.14564023X-RAY DIFFRACTION94
5.0223-25.09770.21711250.18943751X-RAY DIFFRACTION87
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)
11.5902-0.1350.14742.1069-1.13222.6573-0.0911-0.15290.26970.031-0.099-0.4785-0.01880.31410.18870.29440.0246-0.02360.3678-0.01450.479254.183322.3133157.5558
22.63740.7341-0.67453.7219-1.38612.5371-0.09510.05210.3934-0.11610.08-0.0586-0.0986-0.32620.02660.32140.0221-0.00570.37660.01950.303340.171427.4566146.671
34.68461.25961.26884.20531.48220.77830.16380.49950.7590.40340.14980.64590.2892-0.333-0.30720.5876-0.1210.01410.7076-0.01670.499437.89958.2018127.1525
42.6585-0.2468-0.752.021-0.57755.5393-0.5167-0.2254-0.53950.8471-0.10920.13020.6792-0.05360.51011.1313-0.1139-0.00770.4384-0.05310.712739.0663-3.4246132.4883
50.57120.76640.53161.72772.43554.87660.22350.2411-0.04040.66590.3283-0.05931.37970.3133-0.26150.8057-0.0544-0.00550.4673-0.01410.36344.27467.2829137.5632
62.22910.74751.27582.78831.7464.0155-0.50670.7567-0.2137-0.14860.66820.03090.84790.8459-0.3090.7576-0.09750.07040.7861-0.14790.434445.68812.1662120.8234
72.28440.4081.33921.90770.59331.80890.054-0.66340.19770.4944-0.2471-0.14030.15770.10910.17690.44860.04790.00540.4716-0.01950.384482.630312.5248137.9261
83.7992-0.76260.88831.16420.19931.4804-0.17990.07770.51240.1385-0.0358-0.2701-0.15010.3590.24630.4895-0.0073-0.08870.5530.00950.491993.140718.8079135.0669
92.1106-0.4639-0.26473.47980.07572.84150.0122-0.123-0.15630.1022-0.15690.49180.3783-0.12270.13270.3447-0.02320.03950.3130.02670.425368.75875.6136124.6299
101.5373-0.1918-0.17033.7384-0.13731.9854-0.01420.12230.1077-0.3155-0.1087-0.16660.10950.14840.11380.30950.04640.01120.34690.0460.33778.471111.2806115.6215
112.74060.146-1.06133.1276-0.10883.8371-0.25340.1694-0.1347-0.35070.41640.07470.1735-0.0987-0.18780.4485-0.0391-0.03350.38060.01990.453656.828236.2476109.6067
122.1607-0.17180.20893.38390.0082.1279-0.2571-0.01530.0480.1242-0.0626-0.79930.05230.07680.27250.48650.021-0.07290.3650.01150.585466.296235.7418114.208
132.2849-2.3522-0.21162.44420.19130.0887-0.3801-0.42410.13130.51760.3304-0.2501-0.2081-0.187-0.04260.44260.0985-0.07480.36850.01790.430960.822635.5658120.7373
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN C AND (RESID 665 THROUGH 820 )
2X-RAY DIFFRACTION2CHAIN C AND (RESID 821 THROUGH 1009 )
3X-RAY DIFFRACTION3CHAIN D AND (RESID 21 THROUGH 62 )
4X-RAY DIFFRACTION4CHAIN D AND (RESID 63 THROUGH 72 )
5X-RAY DIFFRACTION5CHAIN D AND (RESID 73 THROUGH 87 )
6X-RAY DIFFRACTION6CHAIN D AND (RESID 88 THROUGH 103 )
7X-RAY DIFFRACTION7CHAIN A AND (RESID 661 THROUGH 721 )
8X-RAY DIFFRACTION8CHAIN A AND (RESID 728 THROUGH 778 )
9X-RAY DIFFRACTION9CHAIN A AND (RESID 779 THROUGH 875 )
10X-RAY DIFFRACTION10CHAIN A AND (RESID 876 THROUGH 1012 )
11X-RAY DIFFRACTION11CHAIN B AND (RESID 15 THROUGH 41 )
12X-RAY DIFFRACTION12CHAIN B AND (RESID 42 THROUGH 71 )
13X-RAY DIFFRACTION13CHAIN B AND (RESID 72 THROUGH 103 )

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