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- PDB-2l4e: NMR structure of the UBA domain of S. cerevisiae Dcn1 -

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Basic information

Entry
Database: PDB / ID: 2l4e
TitleNMR structure of the UBA domain of S. cerevisiae Dcn1
ComponentsDefective in cullin neddylation protein 1
KeywordsPROTEIN BINDING / UBA / ubiquitin binding / neddylation
Function / homology
Function and homology information


ubiquitin-like protein binding / protein neddylation / ubiquitin conjugating enzyme binding / cullin family protein binding / ubiquitin ligase complex / protein-macromolecule adaptor activity
Similarity search - Function
Potentiating neddylation domain / Defective-in-cullin neddylation protein / DCN1-like, PONY binding domain / Cullin binding / DCUN1 domain profile. / : / UBA-like domain / UBA-like domain / Ubiquitin-associated (UBA) domain / UBA-like superfamily ...Potentiating neddylation domain / Defective-in-cullin neddylation protein / DCN1-like, PONY binding domain / Cullin binding / DCUN1 domain profile. / : / UBA-like domain / UBA-like domain / Ubiquitin-associated (UBA) domain / UBA-like superfamily / Helicase, Ruva Protein; domain 3 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Defective in cullin neddylation protein 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / molecular dynamics
Model detailslowest energy, model 1
AuthorsBurschowsky, D. / Rudolf, F. / Mattle, D. / Peter, M. / Wider, G.
CitationJournal: To be Published
Title: Structural analysis of the ubiquitin-associated domain (UBA) of yeast Dcn1 in complex with ubiquitin
Authors: Burschowsky, D. / Rudolf, F. / Mattle, D. / Peter, M. / Wider, G.
History
DepositionOct 5, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 5, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2020Group: Data collection / Database references / Other
Category: pdbx_database_status / pdbx_nmr_software ...pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name ..._pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.2Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Defective in cullin neddylation protein 1


Theoretical massNumber of molelcules
Total (without water)6,9251
Polymers6,9251
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 / 40structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Defective in cullin neddylation protein 1


Mass: 6924.632 Da / Num. of mol.: 1 / Fragment: UBA domain (UNP residues 6-62)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: DCN1, DCN1 YLR128W, L3111, YLR128W / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 Star / References: UniProt: Q12395

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D HNCA
1213D CBCA(CO)NH
1313D (H)CCH-TOCSY
1423D 1H-15N NOESY
1513D 1H-13C NOESY
1613D 1H-13Caro NOESY
1722D 1H-15N HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.6 mM [U-80% 13C; U-90% 15N] Dcn1-UBA, 15 mM potassium phosphate, 110 mM potassium phosphate, 2 mM DTT-4, 2 mM CHAPS, 0.05 % sodium azide, 95% H2O/5% D2O95% H2O/5% D2O
20.55 mM [U-90% 15N] Dcn1-UBA, 15 mM potassium phosphate, 110 mM potassium phosphate, 2 mM DTT, 2 mM CHAPS, 0.05 % sodium azide, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.6 mMDcn1-UBA-1[U-80% 13C; U-90% 15N]1
15 mMpotassium phosphate-21
110 mMpotassium phosphate-31
2 mMDTT-41
2 mMCHAPS-51
0.05 %sodium azide-61
0.55 mMDcn1-UBA-7[U-90% 15N]2
15 mMpotassium phosphate-82
110 mMpotassium phosphate-92
2 mMDTT-102
2 mMCHAPS-112
0.05 %sodium azide-122
Sample conditionsIonic strength: 157 / pH: 6.15 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker DRXBrukerDRX6002
Bruker DRXBrukerDRX7503
Bruker AvanceBrukerAVANCE9004

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Processing

NMR software
NameVersionDeveloperClassification
Unio081.0.4Herrmannchemical shift assignment
Unio081.0.4Herrmannpeak picking
Amber9Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmrefinement
CYANA2Guntert, Mumenthaler and Wuthrichstructure solution
XwinNMRBruker Biospincollection
XwinNMRBruker Biospinprocessing
TopSpin2Bruker Biospinprocessing
CARA1.8.4Kellerdata analysis
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 40 / Conformers submitted total number: 20

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