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- PDB-6v88: Solution NMR structure of Dictyostelium discoideum Skp1A (truncat... -

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Basic information

Entry
Database: PDB / ID: 6v88
TitleSolution NMR structure of Dictyostelium discoideum Skp1A (truncated) dimer
ComponentsSCF ubiquitin ligase complex protein SKP1a
KeywordsPROTEIN BINDING / Ubiquitin ligase E3 SCF complex Skp1
Function / homology
Function and homology information


cytoplasmic SCF ubiquitin ligase complex / : / : / Orc1 removal from chromatin / Cyclin D associated events in G1 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Neddylation / Iron uptake and transport / Antigen processing: Ubiquitination & Proteasome degradation / sorocarp development ...cytoplasmic SCF ubiquitin ligase complex / : / : / Orc1 removal from chromatin / Cyclin D associated events in G1 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Neddylation / Iron uptake and transport / Antigen processing: Ubiquitination & Proteasome degradation / sorocarp development / F-box domain binding / WD40-repeat domain binding / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / cullin family protein binding / cell cortex / protein ubiquitination / identical protein binding / nucleus / cytoplasm
Similarity search - Function
SKP1 component, dimerisation / S-phase kinase-associated protein 1 / SKP1-like, dimerisation domain superfamily / Skp1 family, dimerisation domain / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family ...SKP1 component, dimerisation / S-phase kinase-associated protein 1 / SKP1-like, dimerisation domain superfamily / Skp1 family, dimerisation domain / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / SKP1/BTB/POZ domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
SCF ubiquitin ligase complex protein SKP1a
Similarity search - Component
Biological speciesDictyostelium discoideum (eukaryote)
MethodSOLUTION NMR / simulated annealing
AuthorsKim, H.W. / Eletsky, A. / West, C.M.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)RO1GM037539 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM084383 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41GM103390 United States
CitationJournal: Biochemistry / Year: 2020
Title: Skp1 Dimerization Conceals Its F-Box Protein Binding Site.
Authors: Kim, H.W. / Eletsky, A. / Gonzalez, K.J. / van der Wel, H. / Strauch, E.M. / Prestegard, J.H. / West, C.M.
History
DepositionDec 10, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2020Provider: repository / Type: Initial release
Revision 1.1May 6, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Mar 16, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.3Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _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

Downloads & links

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Assembly

Deposited unit
A: SCF ubiquitin ligase complex protein SKP1a
B: SCF ubiquitin ligase complex protein SKP1a


Theoretical massNumber of molelcules
Total (without water)25,9982
Polymers25,9982
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: assay for oligomerization, Sedimentation velocity
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1490 Å2
ΔGint-11 kcal/mol
Surface area12610 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein SCF ubiquitin ligase complex protein SKP1a / Glycoprotein FP21 isoform A


Mass: 12998.891 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dictyostelium discoideum (eukaryote) / Gene: fpaA, fp21A, fpa1, fpa1A, skp1A, DDB_G0269230 / Production host: Escherichia coli (E. coli) / References: UniProt: P52285

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D [15N, 1H]-HSQC
121isotropic12D [13C, 1H] CT-HSQC aliphatic
131isotropic12D [13C, 1H] CT-HSQC aromatic
141isotropic13D 13C/15N-edited [1H,1H] NOESY
151isotropic13D TROSY-HN(CA)CB
161isotropic13D (H)CCH-COSY aromatic
171isotropic13D (H)CCH-COSY aliphatic
181isotropic13D (H)CCH-TOCSY aliphatic
191isotropic23D 13C/15N-filtered 13C/15N-edited [1H,1H] NOESY
1141isotropic23D CBCA(CO)NH
1131isotropic23D HBHA(CO)NH
1121isotropic23D HNCO
1151isotropic23D (HCA)CONH
1111isotropic22D long-range [15N, 1H]-HSQC

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Sample preparation

DetailsType: solution
Contents: 0.5 mM [U-90% 13C; U-90% 15N] DDSkp1, 50 mM MES, 50 mM NaCl, 5 mM DTT, 0.05 % sodium azide, 90% H2O/10% D2O
Label: 15N_13C_DDSkp1 / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMDDSkp1[U-90% 13C; U-90% 15N]1
50 mMMESnatural abundance1
50 mMNaClnatural abundance1
5 mMDTTnatural abundance1
0.05 %sodium azidenatural abundance1
Sample conditionsIonic strength: 50 mM / Label: DDSkp1 / pH: 6.0 / Pressure: 1 atm / Temperature: 308 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE NEOBrukerAVANCE NEO8001
Agilent VNMRSAgilentVNMRS6002

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospinprocessing
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CARAKeller and Wuthrichdata analysis
CARAKeller and Wuthrichchemical shift assignment
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CARAKeller and Wuthrichpeak picking
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
TopSpinBruker Biospincollection
VNMRVariancollection
TALOSCornilescu, Delaglio and Baxdata analysis
PSVSBhattacharya and Montelionedata analysis
RefinementMethod: simulated annealing / Software ordinal: 12 / Details: Refinement in explicit water bath
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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