[English] 日本語
Yorodumi
- PDB-4xhu: The complex structure of Timeless_PAB and PARP-1_catalytic domain -

+
Open data


ID or keywords:

Loading...

-
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 / cellular response to cisplatin / cell cycle phase transition / NAD+-histone H2BS6 serine ADP-ribosyltransferase activity / NAD+-histone H3S10 serine ADP-ribosyltransferase activity / NAD+-histone H2BE35 glutamate ADP-ribosyltransferase activity / positive regulation of myofibroblast differentiation / regulation of base-excision repair ...cellular response to bleomycin / detection of abiotic stimulus / replication fork arrest / cellular response to cisplatin / cell cycle phase transition / NAD+-histone H2BS6 serine ADP-ribosyltransferase activity / NAD+-histone H3S10 serine ADP-ribosyltransferase activity / NAD+-histone H2BE35 glutamate ADP-ribosyltransferase activity / positive regulation of myofibroblast differentiation / regulation of base-excision repair / negative regulation of ATP biosynthetic process / NAD+-protein-tyrosine ADP-ribosyltransferase activity / NAD+-protein-histidine ADP-ribosyltransferase activity / positive regulation of single strand break repair / regulation of circadian sleep/wake cycle, non-REM sleep / vRNA Synthesis / carbohydrate biosynthetic process / NAD+-protein-serine ADP-ribosyltransferase activity / regulation of catalytic activity / negative regulation of adipose tissue development / NAD DNA ADP-ribosyltransferase activity / cellular response to hydroxyurea / NAD+-protein-aspartate ADP-ribosyltransferase activity / NAD+-protein-glutamate ADP-ribosyltransferase activity / DNA ADP-ribosylation / mitochondrial DNA metabolic process / regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / replication fork reversal / signal transduction involved in regulation of gene expression / positive regulation of necroptotic process / DNA replication checkpoint signaling / ATP generation from poly-ADP-D-ribose / transcription regulator activator activity / replication fork protection complex / HDR through MMEJ (alt-NHEJ) / negative regulation of cGAS/STING signaling pathway / positive regulation of DNA-templated transcription, elongation / positive regulation of intracellular estrogen receptor signaling pathway / NAD+ ADP-ribosyltransferase / cellular response to zinc ion / positive regulation of double-strand break repair / negative regulation of telomere maintenance via telomere lengthening / protein auto-ADP-ribosylation / mitochondrial DNA repair / response to aldosterone / branching morphogenesis of an epithelial tube / protein poly-ADP-ribosylation / positive regulation of mitochondrial depolarization / positive regulation of cardiac muscle hypertrophy / nuclear replication fork / negative regulation of transcription elongation by RNA polymerase II / NAD+-protein ADP-ribosyltransferase activity / site of DNA damage / R-SMAD binding / positive regulation of SMAD protein signal transduction / protein autoprocessing / macrophage differentiation / decidualization / NAD+-protein poly-ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / nucleosome binding / POLB-Dependent Long Patch Base Excision Repair / positive regulation of double-strand break repair via homologous recombination / SUMOylation of DNA damage response and repair proteins / negative regulation of innate immune response / protein localization to chromatin / telomere maintenance / nucleotidyltransferase activity / transforming growth factor beta receptor signaling pathway / cellular response to nerve growth factor stimulus / protein-DNA complex / response to gamma radiation / mitochondrion organization / morphogenesis of an epithelium / nuclear estrogen receptor binding / lung development / Downregulation of SMAD2/3:SMAD4 transcriptional activity / DNA Damage Recognition in GG-NER / protein modification process / regulation of circadian rhythm / Dual Incision in GG-NER / histone deacetylase binding / cellular response to insulin stimulus / Formation of Incision Complex in GG-NER / positive regulation of protein localization to nucleus / circadian rhythm / cellular response to amyloid-beta / cellular response to UV / NAD binding / double-strand break repair / nuclear envelope / regulation of protein localization / 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 / damaged DNA binding
Similarity search - Function
Timeless, C-terminal / Timeless PAB domain / Poly(ADP-ribose) polymerase, regulatory domain / Timeless, N-terminal / Timeless / Timeless protein / Poly(ADP-ribose) Polymerase; domain 1 / Poly [ADP-ribose] polymerase / PADR1 domain / PADR1 domain superfamily ...Timeless, C-terminal / Timeless PAB domain / Poly(ADP-ribose) polymerase, regulatory domain / Timeless, N-terminal / Timeless / Timeless protein / Poly(ADP-ribose) Polymerase; domain 1 / Poly [ADP-ribose] polymerase / PADR1 domain / PADR1 domain superfamily / : / PADR1 domain, zinc ribbon fold / PADR1, N-terminal helical domain / PADR1 domain profile. / 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 / : / Poly(ADP-ribose) polymerase, regulatory domain / WGR domain / WGR domain superfamily / WGR domain / WGR domain profile. / 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
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
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

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
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

-
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

-
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 )

+
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