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- PDB-5vzm: Solution NMR structure of human Rev1 (932-1039) in complex with u... -

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Basic information

Entry
Database: PDB / ID: 5vzm
TitleSolution NMR structure of human Rev1 (932-1039) in complex with ubiquitin
Components
  • DNA repair protein REV1
  • Ubiquitin
KeywordsPROTEIN BINDING / Translesion DNA synthesis / DNA repair / DNA replication / Rev1 / ubiquitin / PCNA
Function / homology
Function and homology information


deoxycytidyl transferase activity / hypothalamus gonadotrophin-releasing hormone neuron development / Evasion by RSV of host interferon responses / female meiosis I / positive regulation of protein monoubiquitination / mitochondrion transport along microtubule / fat pad development / error-free translesion synthesis / female gonad development / seminiferous tubule development ...deoxycytidyl transferase activity / hypothalamus gonadotrophin-releasing hormone neuron development / Evasion by RSV of host interferon responses / female meiosis I / positive regulation of protein monoubiquitination / mitochondrion transport along microtubule / fat pad development / error-free translesion synthesis / female gonad development / seminiferous tubule development / male meiosis I / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / error-prone translesion synthesis / energy homeostasis / regulation of neuron apoptotic process / regulation of proteasomal protein catabolic process / response to UV / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Signaling by ALK fusions and activated point 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 / neuron projection morphogenesis / 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 / regulation of mitochondrial membrane potential / 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 / positive regulation of protein ubiquitination / 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
Similarity search - Function
DNA repair protein Rev1, C-terminal / Rev1, C-terminal domain superfamily / : / DNA repair protein REV1 C-terminal domain / HUWE1/Rev1, ubiquitin binding region / Ubiquitin binding region / DNA repair protein Rev1 / DNApol eta/Rev1, HhH motif / BRCA1 C Terminus (BRCT) domain / DNA polymerase, Y-family, little finger domain ...DNA repair protein Rev1, C-terminal / Rev1, C-terminal domain superfamily / : / DNA repair protein REV1 C-terminal domain / HUWE1/Rev1, ubiquitin binding region / Ubiquitin binding region / DNA repair protein Rev1 / DNApol eta/Rev1, HhH motif / BRCA1 C Terminus (BRCT) domain / DNA polymerase, Y-family, little finger domain / impB/mucB/samB family C-terminal domain / UmuC domain / DNA polymerase, Y-family, little finger domain superfamily / impB/mucB/samB family / UmuC domain profile. / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin domain signature. / Ubiquitin family / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / Ubiquitin-like domain superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
Polyubiquitin-B / DNA repair protein REV1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsCui, G. / Botuyan, M.V. / Mer, G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)CA132878 United States
CitationJournal: J. Mol. Biol. / Year: 2018
Title: Structural Basis for the Interaction of Mutasome Assembly Factor REV1 with Ubiquitin.
Authors: Cui, G. / Botuyan, M.V. / Mer, G.
History
DepositionMay 29, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 4, 2018Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Data collection
Category: pdbx_audit_support / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ubiquitin
B: DNA repair protein REV1


Theoretical massNumber of molelcules
Total (without water)20,5622
Polymers20,5622
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Ubiquitin /


Mass: 8576.831 Da / Num. of mol.: 1 / Fragment: UNP residues 1-76
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Plasmid: pRSUb / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0CG47
#2: Protein DNA repair protein REV1 / / Alpha integrin-binding protein 80 / AIBP80 / Rev1-like terminal deoxycytidyl transferase


Mass: 11985.354 Da / Num. of mol.: 1 / Fragment: UNP residues 933-1040
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: REV1, REV1L / Plasmid: pTEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9UBZ9, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic12D 1H-13C HSQC
131isotropic12D 1H-13C HSQC aromatic
141isotropic13D HN(CA)CB
151isotropic13D CBCA(CO)NH
161isotropic13D HNCO
171isotropic13D HN(CA)CO
181isotropic13D HBHA(CO)NH
191isotropic13D H(CCO)NH
1111isotropic13D (H)CC(CO)NH
1281isotropic13D (H)CCH-TOCSY
1121isotropic13D 1H-15N TOCSY
1131isotropic13D 1H-15N NOESY
1141isotropic13D 1H-13C NOESY
1151isotropic13D 1H-13C NOESY aromatic
2162isotropic12D 1H-15N HSQC
2172isotropic12D 1H-13C HSQC
2182isotropic12D 1H-13C HSQC aromatic
2192isotropic13D HN(CA)CB
2202isotropic13D CBCA(CO)NH
2212isotropic13D HNCO
2222isotropic13D HN(CA)CO
2232isotropic13D HBHA(CO)NH
2242isotropic13D H(CCO)NH
2262isotropic13D (H)CC(CO)NH
2272isotropic13D (H)CCH-TOCSY
2292isotropic13D 1H-15N TOCSY
2302isotropic13D 1H-15N NOESY
2312isotropic13D 1H-13C NOESY
2322isotropic13D 1H-13C NOESY aromatic
2332isotropic113C,15N-filetered/edited NOESY
2343isotropic12D 1H-15N HSQC
2353isotropic12D 1H-13C HSQC
2363isotropic13D 1H-15N NOESY
2373isotropic13D 1H-13C NOESY
2383isotropic113C,15N-filetered/edited NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11 mM [U-100% 13C; U-100% 15N] Ubiquitin, 20 mM Sodium phosphate buffer, 90% H2O/10% D2OSample_190% H2O/10% D2O
solution21 mM [U-100% 13C; U-100% 15N] Rev1, 3 mM Ubiquitin, 50 mM Sodium phosphate buffer, 90% H2O/10% D2OSample_290% H2O/10% D2O
solution33 mM Rev1, 1 mM [U-100% 13C; U-100% 15N] Ubiquitin, 50 mM Sodium phosphate buffer, 90% H2O/10% D2OSample_390% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMUbiquitin[U-100% 13C; U-100% 15N]1
20 mMSodium phosphate buffernatural abundance1
1 mMRev1[U-100% 13C; U-100% 15N]2
3 mMUbiquitinnatural abundance2
50 mMSodium phosphate buffernatural abundance2
3 mMRev1natural abundance3
1 mMUbiquitin[U-100% 13C; U-100% 15N]3
50 mMSodium phosphate buffernatural abundance3
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
120 mM sodium phosphate mMConditions_17.0 1 atm303 K
250 mM sodium phosphate mMConditions_26.8 1 atm303 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 700 MHz

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
NMRViewJohnson, One Moon Scientificdata analysis
SANEDuggan, Legge, Dyson & Wrightchemical shift assignment
TALOSCornilescu, Delaglio and Baxdata analysis
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
RefinementMethod: simulated annealing / Software ordinal: 8
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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