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- PDB-1zc1: Ufd1 exhibits the AAA-ATPase fold with two distinct ubiquitin int... -

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Basic information

Entry
Database: PDB / ID: 1zc1
TitleUfd1 exhibits the AAA-ATPase fold with two distinct ubiquitin interaction sites
ComponentsUbiquitin fusion degradation protein 1
KeywordsPROTEIN TURNOVER / Ufd1 / double-psi-beta-barrel
Function / homology
Function and homology information


Doa10p ubiquitin ligase complex / DNA replication termination / cytoplasm protein quality control by the ubiquitin-proteasome system / Hrd1p ubiquitin ligase ERAD-L complex / RQC complex / protein localization to vacuole / mitochondria-associated ubiquitin-dependent protein catabolic process / nonfunctional rRNA decay / Translesion Synthesis by POLH / VCP-NPL4-UFD1 AAA ATPase complex ...Doa10p ubiquitin ligase complex / DNA replication termination / cytoplasm protein quality control by the ubiquitin-proteasome system / Hrd1p ubiquitin ligase ERAD-L complex / RQC complex / protein localization to vacuole / mitochondria-associated ubiquitin-dependent protein catabolic process / nonfunctional rRNA decay / Translesion Synthesis by POLH / VCP-NPL4-UFD1 AAA ATPase complex / replisome / ribosome-associated ubiquitin-dependent protein catabolic process / retrograde protein transport, ER to cytosol / KEAP1-NFE2L2 pathway / Neddylation / polyubiquitin modification-dependent protein binding / ERAD pathway / rescue of stalled ribosome / ubiquitin binding / positive regulation of protein localization to nucleus / proteasome-mediated ubiquitin-dependent protein catabolic process / nucleus / cytosol
Similarity search - Function
Ubiquitin fusion degradation protein UFD1, N-terminal domain / Ubiquitin fusion degradation protein Ufd1-like / Ufd1-like, Nn domain / Ubiquitin fusion degradation protein UFD1 / Vcp-like ATPase; Chain A, domain 2 - #10 / Vcp-like ATPase; Chain A, domain 2 / Barwin-like endoglucanases / Roll / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Ubiquitin fusion degradation protein 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / simulated annealing
AuthorsPark, S. / Isaacson, R. / Kim, H.T. / Silver, P.A. / Wagner, G.
CitationJournal: Structure / Year: 2005
Title: Ufd1 Exhibits the AAA-ATPase Fold with Two Distinct Ubiquitin Interaction Sites
Authors: Park, S. / Isaacson, R. / Kim, H.T. / Silver, P.A. / Wagner, G.
History
DepositionApr 10, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 650 HELIX DETERMINATION METHOD: AUTHOR DETERMINED
Remark 700 SHEET The automatically generated beta sheet naming in this pdb file is slightly different from ... SHEET The automatically generated beta sheet naming in this pdb file is slightly different from those in the citation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ubiquitin fusion degradation protein 1


Theoretical massNumber of molelcules
Total (without water)23,2501
Polymers23,2501
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Ubiquitin fusion degradation protein 1 / UB fusion protein 1 / Polymerase-interacting protein 3


Mass: 23249.686 Da / Num. of mol.: 1 / Fragment: N domain, residues 1-208
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: UFD1, PIP3 / Production host: Escherichia coli (E. coli) / References: UniProt: P53044

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

DetailsContents: 0.2mM Ufd1 / Solvent system: 50mM Phosphate, 20mM NaCl,pH6.0
SampleConc.: 0.2 mM / Component: UFD1
Sample conditionsIonic strength: 20 mM Phosphate 50mM NaCl / pH: 6.0 / Pressure: 1 atm / Temperature: 307 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 DRXBrukerDRX5001
Varian INOVAVarianINOVA7502

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Processing

NMR software
NameVersionDeveloperClassification
CNS1Brunger, A.structure solution
CNS1Brunger, A.refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 15

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