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- PDB-2ko3: Nedd8 solution structure -

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Basic information

Entry
Database: PDB / ID: 2ko3
TitleNedd8 solution structure
ComponentsNEDD8
KeywordsSIGNALING PROTEIN / Nedd8 / Isopeptide bond / Nucleus / Ubl conjugation pathway
Function / homology
Function and homology information


regulation of proteolysis / protein neddylation / TGF-beta receptor signaling activates SMADs / anatomical structure morphogenesis / Iron uptake and transport / protein modification process / modification-dependent protein catabolic process / protein localization / protein tag activity / UCH proteinases ...regulation of proteolysis / protein neddylation / TGF-beta receptor signaling activates SMADs / anatomical structure morphogenesis / Iron uptake and transport / protein modification process / modification-dependent protein catabolic process / protein localization / protein tag activity / UCH proteinases / Cargo recognition for clathrin-mediated endocytosis / Neddylation / ubiquitin-dependent protein catabolic process / ubiquitin protein ligase binding / regulation of transcription by RNA polymerase II / proteolysis / extracellular exosome / nucleoplasm / nucleus / cytosol
Similarity search - Function
Nedd8-like ubiquitin / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin domain signature. / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. ...Nedd8-like ubiquitin / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin domain signature. / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsChoi, Y.S. / Jeon, Y.H. / Cheong, C.
CitationJournal: Febs Lett. / Year: 2009
Title: 60th residues of ubiquitin and Nedd8 are located out of E2-binding surfaces, but are important for K48 ubiquitin-linkage.
Authors: Choi, Y.S. / Jeon, Y.H. / Ryu, K.S. / Cheong, C.
History
DepositionSep 9, 2009Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Nov 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NEDD8


Theoretical massNumber of molelcules
Total (without water)8,5741
Polymers8,5741
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein NEDD8 / / Ubiquitin-like protein Nedd8 / Neddylin / Neural precursor cell expressed developmentally down- ...Ubiquitin-like protein Nedd8 / Neddylin / Neural precursor cell expressed developmentally down-regulated protein 8 / NEDD-8


Mass: 8573.978 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NEDD8 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15843

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D HNCA
1413D HN(CO)CA
1513D CBCA(CO)NH
1613D HN(CA)CB
1713D HBHA(CO)NH
1813D H(CCO)NH
1913D (H)CCH-COSY
11013D (H)CCH-TOCSY
11113D 1H-13C NOESY
11213D 1H-15N NOESY

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Sample preparation

DetailsContents: 1 mM [U-100% 13C; U-100% 15N] Nedd8-1, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
SampleConc.: 1 mM / Component: Nedd8-1 / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsIonic strength: 200 / pH: 7.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE9001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR softwareName: CNS / Developer: Brunger, Adams, Clore, Gros, Nilges and Read / Classification: 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: 20 / Conformers submitted total number: 20 / Representative conformer: 1

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