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- PDB-1zw7: Elimination of the C-cap in Ubiquitin Structure, Dynamics and The... -

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Basic information

Entry
Database: PDB / ID: 1zw7
TitleElimination of the C-cap in Ubiquitin Structure, Dynamics and Thermodynamic Consequences
ComponentsUbiquitin
KeywordsSTRUCTURAL PROTEIN / Dynamics / Thermodynamics
Function / homology
Function and homology information


: / : / : / : / : / Regulation of TP53 Degradation / Josephin domain DUBs / RAS processing / Regulation of PTEN localization / ER Quality Control Compartment (ERQC) ...: / : / : / : / : / Regulation of TP53 Degradation / Josephin domain DUBs / RAS processing / Regulation of PTEN localization / ER Quality Control Compartment (ERQC) / UCH proteinases / Pexophagy / Interleukin-1 signaling / Aggrephagy / Peroxisomal protein import / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / ABC-family proteins mediated transport / Metalloprotease DUBs / Endosomal Sorting Complex Required For Transport (ESCRT) / E3 ubiquitin ligases ubiquitinate target proteins / Translesion Synthesis by POLH / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Termination of translesion DNA synthesis / Negative regulators of DDX58/IFIH1 signaling / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of PTEN stability and activity / KEAP1-NFE2L2 pathway / CDK-mediated phosphorylation and removal of Cdc6 / Neddylation / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Formation of TC-NER Pre-Incision Complex / Major pathway of rRNA processing in the nucleolus and cytosol / Orc1 removal from chromatin / MAPK6/MAPK4 signaling / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / Gap-filling DNA repair synthesis and ligation in TC-NER / Formation of a pool of free 40S subunits / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Antigen processing: Ubiquitination & Proteasome degradation / L13a-mediated translational silencing of Ceruloplasmin expression / Dual incision in TC-NER / ribosomal large subunit export from nucleus / Ub-specific processing proteases / ribosomal large subunit assembly / modification-dependent protein catabolic process / protein tag activity / ribosome biogenesis / cytosolic large ribosomal subunit / cytoplasmic translation / protein ubiquitination / structural constituent of ribosome / ubiquitin protein ligase binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin-like (UB roll) / Ubiquitin family ...Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Polyubiquitin / Ubiquitin-60S ribosomal protein L40
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / Structure calculations were performed using CNS version 1.0 on an SGI platform. The refinement protocol for annealing involved torsion angle heating (100 K, 1000 steps), cooling in torsion (100 K, 5000 steps), cartesian space (1000 K, 10,000 steps).
AuthorsErmolenko, D.N. / Dangi, B. / Gronenborn, A.M. / Makhatadze, G.I.
CitationJournal: Biophys.Chem. / Year: 2007
Title: Elimination of the C-cap in ubiquitin-structure, dynamics and thermodynamic consequences.
Authors: Ermolenko, D.N. / Dangi, B. / Gvritishvili, A. / Gronenborn, A.M. / Makhatadze, G.I.
History
DepositionJun 3, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ubiquitin


Theoretical massNumber of molelcules
Total (without water)9,1771
Polymers9,1771
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)21 / 50back calculated data agree with experimental NOESY spectrum
RepresentativeModel #1

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Components

#1: Protein Ubiquitin


Mass: 9177.356 Da / Num. of mol.: 1 / Mutation: R42E, E34P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: UBI1, RPL40A / Production host: Escherichia coli (E. coli) / Keywords: Yeast Ubiquitin mutant / References: UniProt: P61864, UniProt: P0CG63*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1111H-15N HSQC
1213D HN(CA)CB
131CBCA(CO)NH
141HNCA
151HNCO
161HBHA(CO)NH

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Sample preparation

DetailsContents: 1-2 mM of appropriately labeled mutant ubiquitin / Solvent system: 30 mM acetate buffer, pH 5.0
Sample conditionsIonic strength: 30 mM actate / pH: 5 / Pressure: Ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX5001
Bruker DMXBrukerDMX6002

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Processing

NMR software
NameVersionDeveloperClassification
CNS1BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE-KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU,READ,RICE,SIMONSON,WARRENstructure solution
CNS1BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE-KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU,READ,RICE,SIMONSON,WARRENrefinement
RefinementMethod: Structure calculations were performed using CNS version 1.0 on an SGI platform. The refinement protocol for annealing involved torsion angle heating (100 K, 1000 steps), cooling in torsion ...Method: Structure calculations were performed using CNS version 1.0 on an SGI platform. The refinement protocol for annealing involved torsion angle heating (100 K, 1000 steps), cooling in torsion (100 K, 5000 steps), cartesian space (1000 K, 10,000 steps).
Software ordinal: 1
NMR ensembleConformer selection criteria: back calculated data agree with experimental NOESY spectrum
Conformers calculated total number: 50 / Conformers submitted total number: 21

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