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- PDB-2g3q: Solution Structure of Ede1 UBA-ubiquitin complex -

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Basic information

Entry
Database: PDB / ID: 2g3q
TitleSolution Structure of Ede1 UBA-ubiquitin complex
Components
  • Protein YBL047C
  • Ubiquitin
KeywordsENDOCYTOSIS/SIGNALING PROTEIN / endocytosis / monoubiquitin signaling / solution structure / UBA domain / ubiquitin-binding motif / ENDOCYTOSIS-SIGNALING PROTEIN COMPLEX
Function / homology
Function and homology information


G alpha (12/13) signalling events / CDC42 GTPase cycle / Clathrin-mediated endocytosis / : / : / : / : / : / actin cortical patch organization / Regulation of TP53 Degradation ...G alpha (12/13) signalling events / CDC42 GTPase cycle / Clathrin-mediated endocytosis / : / : / : / : / : / actin cortical patch organization / Regulation of TP53 Degradation / RHOQ GTPase cycle / Josephin domain DUBs / Cargo recognition for clathrin-mediated endocytosis / RHOU GTPase cycle / 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) / actin cortical patch / clathrin coat of coated pit / cellular bud tip / E3 ubiquitin ligases ubiquitinate target proteins / Translesion Synthesis by POLH / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / cellular bud neck / mating projection tip / 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 / endosomal transport / 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 / Major pathway of rRNA processing in the nucleolus and cytosol / Formation of TC-NER Pre-Incision Complex / Orc1 removal from chromatin / MAPK6/MAPK4 signaling / positive regulation of cytokinesis / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / Formation of a pool of free 40S subunits / Gap-filling DNA repair synthesis and ligation in TC-NER / 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 / endoplasmic reticulum unfolded protein response / ubiquitin binding / ribosomal large subunit assembly / modification-dependent protein catabolic process / endocytosis / protein tag activity / regulation of protein localization / ribosome biogenesis / cytosolic large ribosomal subunit / cytoplasmic translation / protein ubiquitination / structural constituent of ribosome / cadherin binding / ubiquitin protein ligase binding / calcium ion binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Cytoskeletal-regulatory complex EF hand / EH domain profile. / Eps15 homology domain / EH domain / Ubiquitin-associated (UBA) domain / UBA/TS-N domain / Ubiquitin associated domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily ...Cytoskeletal-regulatory complex EF hand / EH domain profile. / Eps15 homology domain / EH domain / Ubiquitin-associated (UBA) domain / UBA/TS-N domain / Ubiquitin associated domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily / Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Helicase, Ruva Protein; domain 3 / EF-hand, calcium binding motif / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / Ubiquitin-like (UB roll) / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Polyubiquitin / EH domain-containing and endocytosis protein 1 / Ubiquitin-60S ribosomal protein L40
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / Torsion angle dynamics, simulated annealing
AuthorsSwanson, K.A. / Hicke, L. / Radhakrishnan, I.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Structural Basis for Monoubiquitin Recognition by the Ede1 UBA Domain.
Authors: Swanson, K.A. / Hicke, L. / Radhakrishnan, I.
History
DepositionFeb 20, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 650HELIX DETERMINATION METHOD: AUTHOR

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein YBL047C
B: Ubiquitin


Theoretical massNumber of molelcules
Total (without water)13,2562
Polymers13,2562
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)20 / 80The submitted conformers are the 20 structures with the lowest restraint energies, restraint violations, and RMS deviations from ideal covalent geometry
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide Protein YBL047C


Mass: 4687.109 Da / Num. of mol.: 1 / Fragment: Ede1 UBA, Residues 1339-1381
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: Ede1 / Plasmid: pET30 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): Bl21 / References: UniProt: P34216
#2: Protein Ubiquitin


Mass: 8568.769 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: pET30 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): Bl21 / 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
1113D 15N-separated NOESY
1223D 13C-separated NOESY
1333D 15N-separated NOESY
1443D 13C-separated NOESY
1523D 13C-separated 12C-edited NOESY
1643D 13C-separated 12C-edited NOESY
NMR detailsText: Additional experiments: 2D Double half filtered NOESY was performed for both D2O and H2O samples

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM 15N,13C-labeled Ede1 UBA; 1mM Ubiquitin; 20mM phosphate buffer (pH 6.0), 2mM DTT, 0.2% NaN3, 90% H2O, 10% D2O90% H2O/10% D2O
21mM 15N,13C-labeled Ede1 UBA; 1mM Ubiquitin; 20mM phosphate buffer (pH 6.0), 2mM DTT, 0.2% NaN3, 100% D2O100% D2O
31mM Ede1 UBA; 1mM 15N,13C-labeled Ubiquitin; 20mM phosphate buffer (pH 6.0), 2mM DTT, 0.2% NaN3, 90% H2O, 10% D2O90% H2O/10% D2O
41mM Ede1 UBA; 1mM 15N,13C-labeled Ubiquitin; 20mM phosphate buffer (pH 6.0), 2mM DTT, 0.2% NaN3, 100% D2O100% D2O
Sample conditionsIonic strength: 20mM Sodium Phosphate / pH: 6.0 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.1Brunger et al.refinement
ARIA1.2Linge and Nilgesrefinement
Felix98Accelrysdata analysis
RefinementMethod: Torsion angle dynamics, simulated annealing / Software ordinal: 1
Details: THE STRUCTURES ARE BASED ON A TOTAL OF 2489 DISTANCE RESTRAINTS, INCLUDING 2489 NOE-DERIVED DISTANCE RESTRAINTS [2069 UNAMBIGUOUS AND 420 AMBIGUOUS RESTRAINTS], 74 HYDROGEN BONDING DISTANCE ...Details: THE STRUCTURES ARE BASED ON A TOTAL OF 2489 DISTANCE RESTRAINTS, INCLUDING 2489 NOE-DERIVED DISTANCE RESTRAINTS [2069 UNAMBIGUOUS AND 420 AMBIGUOUS RESTRAINTS], 74 HYDROGEN BONDING DISTANCE RESTRAINTS, AND 161 TORSION ANGLE RESTRAINTS.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: The submitted conformers are the 20 structures with the lowest restraint energies, restraint violations, and RMS deviations from ideal covalent geometry
Conformers calculated total number: 80 / Conformers submitted total number: 20

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