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- PDB-6q00: TDP2 UBA Domain Bound to Ubiquitin at 0.85 Angstroms Resolution, ... -

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Basic information

Entry
Database: PDB / ID: 6q00
TitleTDP2 UBA Domain Bound to Ubiquitin at 0.85 Angstroms Resolution, Crystal Form 1
Components
  • Tyrosyl-DNA phosphodiesterase 2
  • Ubiquitin
KeywordsSIGNALING PROTEIN/HYDROLASE / TDP2 / DNA Damage Response / Cell Signaling / post-translational modification / Topoisomerase 2 / SIGNALING PROTEIN / SIGNALING PROTEIN-HYDROLASE complex
Function / homology
Function and homology information


tyrosyl-RNA phosphodiesterase activity / 5'-tyrosyl-DNA phosphodiesterase activity / nuclease activity / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / aggresome / neuron development / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora ...tyrosyl-RNA phosphodiesterase activity / 5'-tyrosyl-DNA phosphodiesterase activity / nuclease activity / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / aggresome / neuron development / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / Downregulation of ERBB4 signaling / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Pexophagy / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / VLDLR internalisation and degradation / Downregulation of ERBB2:ERBB3 signaling / NF-kB is activated and signals survival / NRIF signals cell death from the nucleus / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / Translesion synthesis by REV1 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by POLK / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / Josephin domain DUBs / Regulation of activated PAK-2p34 by proteasome mediated degradation / InlB-mediated entry of Listeria monocytogenes into host cell / IKK complex recruitment mediated by RIP1 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Autodegradation of Cdh1 by Cdh1:APC/C / TNFR1-induced NF-kappa-B signaling pathway / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / SCF-beta-TrCP mediated degradation of Emi1 / TCF dependent signaling in response to WNT / NIK-->noncanonical NF-kB signaling / Regulation of NF-kappa B signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR2 non-canonical NF-kB pathway / NOTCH3 Activation and Transmission of Signal to the Nucleus / activated TAK1 mediates p38 MAPK activation / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / Negative regulators of DDX58/IFIH1 signaling / Deactivation of the beta-catenin transactivating complex / Degradation of DVL / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of signaling by CBL / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Fanconi Anemia Pathway / Hh mutants are degraded by ERAD / Negative regulation of FGFR3 signaling / Recognition of DNA damage by PCNA-containing replication complex / Peroxisomal protein import / Degradation of AXIN / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Regulation of TNFR1 signaling / Degradation of GLI1 by the proteasome / Activation of NF-kappaB in B cells / Negative regulation of FGFR2 signaling / Nonhomologous End-Joining (NHEJ) / Defective CFTR causes cystic fibrosis / Termination of translesion DNA synthesis / Hedgehog ligand biogenesis / EGFR downregulation / Negative regulation of FGFR4 signaling / Stabilization of p53
Similarity search - Function
UBA-like domain / Endonuclease/exonuclease/phosphatase / Endonuclease/Exonuclease/phosphatase family / Endonuclease/exonuclease/phosphatase superfamily / UBA-like superfamily / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin domain signature. / Ubiquitin family / Ubiquitin homologues ...UBA-like domain / Endonuclease/exonuclease/phosphatase / Endonuclease/Exonuclease/phosphatase family / Endonuclease/exonuclease/phosphatase superfamily / UBA-like superfamily / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin domain signature. / Ubiquitin family / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
: / Tyrosyl-DNA phosphodiesterase 2 / Polyubiquitin-C
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 0.85 Å
AuthorsSchellenberg, M.J. / Krahn, J.M. / Williams, R.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)1Z01ES102765 United States
CitationJournal: Nucleic Acids Res. / Year: 2020
Title: Ubiquitin stimulated reversal of topoisomerase 2 DNA-protein crosslinks by TDP2.
Authors: Schellenberg, M.J. / Appel, C.D. / Riccio, A.A. / Butler, L.R. / Krahn, J.M. / Liebermann, J.A. / Cortes-Ledesma, F. / Williams, R.S.
History
DepositionAug 1, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2020Provider: repository / Type: Initial release
Revision 1.1May 13, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 24, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ubiquitin
B: Tyrosyl-DNA phosphodiesterase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6994
Polymers13,6202
Non-polymers782
Water4,197233
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1490 Å2
ΔGint-4 kcal/mol
Surface area6970 Å2
Unit cell
Length a, b, c (Å)48.742, 48.742, 50.421
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Ubiquitin /


Mass: 8576.831 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBC / Plasmid: pet15 / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG48
#2: Protein/peptide Tyrosyl-DNA phosphodiesterase 2 / hTDP2 / 5'-tyrosyl-DNA phosphodiesterase / 5'-Tyr-DNA phosphodiesterase / ETS1-associated protein 2 ...hTDP2 / 5'-tyrosyl-DNA phosphodiesterase / 5'-Tyr-DNA phosphodiesterase / ETS1-associated protein 2 / ETS1-associated protein II / EAPII / TRAF and TNF receptor-associated protein / Tyrosyl-RNA phosphodiesterase / VPg unlinkase


Mass: 5043.624 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TDP2, EAP2, TTRAP, AD-022 / Plasmid: pMCSG9 / Production host: Escherichia coli (E. coli)
References: UniProt: O95551, Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 233 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.2 Å3/Da / Density % sol: 44.06 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 10 mM Tris, 200 mM Potassium Formate, 14% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.8266 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Apr 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8266 Å / Relative weight: 1
ReflectionResolution: 0.85→50 Å / Num. obs: 202939 / % possible obs: 99.6 % / Redundancy: 16.1 % / Biso Wilson estimate: 10.64 Å2 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.009 / Rrim(I) all: 0.049 / Χ2: 1.022 / Net I/σ(I): 15.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. unique obsCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
0.85-0.868.650670.5740.4430.99897.8
0.86-0.8811.350290.7280.3471.02198.3
0.88-0.913.851190.8420.2581.01999.20.9330.968
0.9-0.9214.551250.9060.20.99999.20.7420.769
0.92-0.9414.551090.9440.1491.01899.60.5550.575
0.94-0.9614.651420.9650.1161.03699.70.4340.449
0.96-0.9814.751360.9810.0861.02999.70.3210.332
0.98-1.0114.751330.9880.0671.02999.70.2480.257
1.01-1.0414.851500.9920.0511.02699.90.1910.197
1.04-1.0714.851340.9960.0391.02499.90.1440.149
1.07-1.111551950.9970.0311.03299.90.1140.119
1.11-1.151551200.9980.0241.0261000.0890.093
1.15-1.2115.151610.9990.0190.9921000.0720.075
1.21-1.2715.251670.9990.0171.0151000.0650.067
1.27-1.3515.351820.9990.0161.0311000.0610.063
1.35-1.4515.451410.9990.0141.0241000.0530.054
1.45-1.615.551990.9990.0111.0181000.0430.044
1.6-1.8315.5517710.011.0151000.0370.039
1.83-2.312952250.9990.0111.02899.90.0640.065
2.31-5034.3528210.0081.031000.0420.043

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
HKL-2000data collection
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: SAD / Resolution: 0.85→28.453 Å / FOM work R set: 0.9456 / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 10.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1118 10141 5 %
Rwork0.0949 192788 -
obs0.0958 202929 99.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 49.83 Å2 / Biso mean: 14.6 Å2 / Biso min: 6.61 Å2
Refinement stepCycle: final / Resolution: 0.85→28.453 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms954 0 2 310 1266
Biso mean--14.65 22.33 -
Num. residues----121
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0151278
X-RAY DIFFRACTIONf_angle_d1.4691750
X-RAY DIFFRACTIONf_chiral_restr0.09190
X-RAY DIFFRACTIONf_plane_restr0.009248
X-RAY DIFFRACTIONf_dihedral_angle_d16.06513
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
0.8502-0.85980.3142910.2961617295
0.8598-0.870.26633670.267634198
0.87-0.88060.25993670.242626098
0.8806-0.89170.24313840.2225637699
0.8917-0.90340.22193290.1967642099
0.9034-0.91580.17513440.1756638699
0.9158-0.92890.17153500.1558636399
0.9289-0.94280.15013430.1464642199
0.9428-0.95750.14612920.1299648399
0.9575-0.97320.1253520.1159639599
0.9732-0.990.10783530.1048640599
0.99-1.0080.09563070.09656426100
1.008-1.02740.10333390.08936513100
1.0274-1.04830.0923460.08056393100
1.0483-1.07110.09423280.07286460100
1.0711-1.09610.08213620.06996465100
1.0961-1.12350.0873300.06556436100
1.1235-1.15380.07653670.06186428100
1.1538-1.18780.07753090.05996535100
1.1878-1.22610.06983060.066482100
1.2261-1.270.07363290.06016435100
1.27-1.32080.08413510.06756462100
1.3208-1.38090.08543660.06986451100
1.3809-1.45370.0943270.07096420100
1.4537-1.54480.0873270.07066498100
1.5448-1.66410.08983320.07816496100
1.6641-1.83150.0953340.08816457100
1.8315-2.09640.10873080.08876511100
2.0964-2.6410.10283450.09646433100
2.641-28.4530.13823560.11516465100

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