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- PDB-5kes: Solution structure of the yeast Ddi1 HDD domain -

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Basic information

Entry
Database: PDB / ID: 5kes
TitleSolution structure of the yeast Ddi1 HDD domain
ComponentsDNA damage-inducible protein 1
KeywordsUNKNOWN FUNCTION / helical bundles / DNA repair
Function / homology
Function and homology information


proteasome regulatory particle binding / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / protein secretion / polyubiquitin modification-dependent protein binding / vesicle-mediated transport / SNARE binding / positive regulation of DNA replication / ubiquitin binding / protein-macromolecule adaptor activity ...proteasome regulatory particle binding / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / protein secretion / polyubiquitin modification-dependent protein binding / vesicle-mediated transport / SNARE binding / positive regulation of DNA replication / ubiquitin binding / protein-macromolecule adaptor activity / ubiquitin-dependent protein catabolic process / aspartic-type endopeptidase activity / plasma membrane / cytoplasm
Similarity search - Function
DNA damage inducible protein 1 ubiquitin-like domain / Aspartic peptidase, DDI1-type / Aspartyl protease / UBA/TS-N domain / Ubiquitin associated domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily / Peptidase A2A, retrovirus, catalytic / Aspartic peptidase domain superfamily
Similarity search - Domain/homology
DNA damage-inducible protein 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / simulated annealing
AuthorsTrempe, J.-F. / Ratcliffe, C. / Veverka, V. / Saskova, K. / Gehring, K.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: Sci Rep / Year: 2016
Title: Structural studies of the yeast DNA damage-inducible protein Ddi1 reveal domain architecture of this eukaryotic protein family.
Authors: Trempe, J.F. / Saskova, K.G. / Siva, M. / Ratcliffe, C.D. / Veverka, V. / Hoegl, A. / Menade, M. / Feng, X. / Shenker, S. / Svoboda, M. / Kozisek, M. / Konvalinka, J. / Gehring, K.
History
DepositionJun 10, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Structure summary / Category: entity / pdbx_audit_support
Item: _entity.pdbx_number_of_molecules / _pdbx_audit_support.funding_organization
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Data collection
Category: pdbx_audit_support / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.3Jun 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 1.4May 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: DNA damage-inducible protein 1


Theoretical massNumber of molelcules
Total (without water)13,3101
Polymers13,3101
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9490 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein DNA damage-inducible protein 1 / v-SNARE-master 1


Mass: 13309.941 Da / Num. of mol.: 1 / Fragment: residues 86-196
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: DDI1, VSM1, YER143W / Plasmid: pGEX-6P1 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K12 / References: UniProt: P40087

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
112isotropic12D 1H-15N het NOE
122isotropic12D 1H-15N HSQC-IPAP
232anisotropic12D 1H-15N HSQC-IPAP
141isotropic13D CBCA(CO)NH
151isotropic13D HN(CA)CB
161isotropic23D 15N/1H NOESY-HSQC
171isotropic23D 13C/1H HSQC-NOESY
182isotropic12D 1H-15N HSQC
191isotropic22D 1H-15N HSQC

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.5 mM [U-13C; U-15N] Ddi1 86-196, 90% H2O/10% D2O15N13C_sample90% H2O/10% D2O
solution20.5 mM [U-15N] Ddi1 86-196, 90% H2O/10% D2O15N_sample90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMDdi1 86-196-1[U-13C; U-15N]1
0.5 mMDdi1 86-196-2[U-15N]2
Sample conditions
Conditions-IDDetailsIonic strengthLabelpHPressure (kPa)Temperature (K)
110 mM HEPES 50 mM NaCl pH 6.5 with NaOH110 mMiso6.5 1 atm303 K
210 mM HEPES 50 mM NaCl pH 6.5 with NaOH 10 mg/mL Pf1 phage added110 mMPf16.5 1 atm303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker AVANCEBrukerAVANCE6001RT probe
Bruker AVANCEBrukerAVANCE8502cryoprobe

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Processing

NMR software
NameVersionDeveloperClassification
XPLOR-NIH2.4C.D. Schwieters, J.J. Kuszewski, N. Tjandra, and G.M. Clorestructure calculation
XPLOR-NIH2.4C.D. Schwieters, J.J. Kuszewski, N. Tjandra, and G.M. Clorerefinement
SparkyGoddardchemical shift assignment
TALOSCornilescu, Delaglio and Baxdata analysis
CYANAGuntert, Mumenthaler and Wuthrichchemical shift assignment
ModuleM. Blackledgedata analysis
RefinementMethod: simulated annealing / Software ordinal: 6
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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