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- PDB-2jt4: Solution Structure of the Sla1 SH3-3-Ubiquitin Complex -

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Basic information

Entry
Database: PDB / ID: 2jt4
TitleSolution Structure of the Sla1 SH3-3-Ubiquitin Complex
Components
  • Cytoskeleton assembly control protein SLA1
  • Ubiquitin
KeywordsSIGNALING PROTEIN / endocytosis / monoubiquitin signaling / ubiquitin-binding motif / SH3 / ubiquitin / Actin-binding / Cytoplasm / Cytoskeleton / Phosphorylation / SH3 domain / DNA damage / DNA repair / Nucleus / Ubl conjugation
Function / homology
Function and homology information


actin cytoskeleton-regulatory complex / SLAC complex / cargo adaptor activity / : / : / Metalloprotease DUBs / : / : / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Regulation of PTEN localization ...actin cytoskeleton-regulatory complex / SLAC complex / cargo adaptor activity / : / : / Metalloprotease DUBs / : / : / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Regulation of PTEN localization / ER Quality Control Compartment (ERQC) / Interleukin-1 signaling / Negative regulators of DDX58/IFIH1 signaling / E3 ubiquitin ligases ubiquitinate target proteins / Translesion Synthesis by POLH / Translesion synthesis by POLK / Translesion synthesis by POLI / : / UCH proteinases / Regulation of PTEN stability and activity / Aggrephagy / Regulation of TP53 Degradation / Translesion synthesis by REV1 / CDK-mediated phosphorylation and removal of Cdc6 / actin cortical patch assembly / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Endosomal Sorting Complex Required For Transport (ESCRT) / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Peroxisomal protein import / Orc1 removal from chromatin / ABC-family proteins mediated transport / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / regulation of Arp2/3 complex-mediated actin nucleation / MAPK6/MAPK4 signaling / negative regulation of Arp2/3 complex-mediated actin nucleation / actin cortical patch / Antigen processing: Ubiquitination & Proteasome degradation / regulation of actin filament polymerization / cellular bud neck / mating projection tip / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / Formation of TC-NER Pre-Incision Complex / Ub-specific processing proteases / Dual incision in TC-NER / Major pathway of rRNA processing in the nucleolus and cytosol / 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) / L13a-mediated translational silencing of Ceruloplasmin expression / ribosomal large subunit export from nucleus / ubiquitin binding / cell wall organization / modification-dependent protein catabolic process / protein tag activity / endocytosis / ribosomal large subunit assembly / ribosome biogenesis / actin binding / cell cortex / cytoplasmic translation / cytosolic large ribosomal subunit / protein ubiquitination / endosome membrane / structural constituent of ribosome / ubiquitin protein ligase binding / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
SLA1 homology domain 1, SHD1 / Sla1, first SH3 domain / Sla1, third SH3 domain / SLA1 homology domain 1, SHD1 / Variant SH3 domain / SH3 Domains / Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily ...SLA1 homology domain 1, SHD1 / Sla1, first SH3 domain / Sla1, third SH3 domain / SLA1 homology domain 1, SHD1 / Variant SH3 domain / SH3 Domains / Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Sterile alpha motif/pointed domain superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / SH3 domain / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin domain signature. / Src homology 3 domains / SH3 type barrels. / Ubiquitin-like (UB roll) / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / Ubiquitin-like domain superfamily / Roll / Roll / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Polyubiquitin / Actin cytoskeleton-regulatory complex protein SLA1 / Ubiquitin-60S ribosomal protein L40
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing
AuthorsHe, Y. / Radhakrishnan, I.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Structural Basis for Ubiquitin Recognition by SH3 Domains
Authors: He, Y. / Hicke, L. / Radhakrishnan, I.
History
DepositionJul 18, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 650HELIX DETERMINATION METHOD: AUTHOR The authors state that these records reflect consensus start and ...HELIX DETERMINATION METHOD: AUTHOR The authors state that these records reflect consensus start and end residues in the 20 NMR models.
Remark 700SHEET DETERMINATION METHOD: AUTHOR The authors state that these records reflect consensus start and ...SHEET DETERMINATION METHOD: AUTHOR The authors state that these records reflect consensus start and end residues in the 20 NMR models.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytoskeleton assembly control protein SLA1
B: Ubiquitin


Theoretical massNumber of molelcules
Total (without water)16,7482
Polymers16,7482
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 / 80structures with the least restraint energies, restraint violations and rms deviations from ideal covalent geometry
RepresentativeModel #1closest to the average

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Components

#1: Protein Cytoskeleton assembly control protein SLA1


Mass: 8179.383 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SLA1 / Production host: Escherichia coli (E. coli) / References: UniProt: P32790
#2: Protein Ubiquitin /


Mass: 8568.769 Da / Num. of mol.: 1 / Fragment: SH3 domain sequence database residues 350-420
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: UBI1, RPL40A / Production host: Escherichia coli (E. coli) / 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 HN(CA)CB
1223D HN(CA)CB
1313D C(CO)NH-TOCSY
1423D C(CO)NH-TOCSY
1513D HNCO
1623D HNCO
1713D H(CCO)NH-TOCSY
1823D H(CCO)NH-TOCSY
1913D 15N-edited NOESY
11023D 15N-edited NOESY
11133D (H)CCH-COSY
11243D (H)CCH-COSY
11333D (H)CCH-TOCSY
11443D (H)CCH-TOCSY
11533D 13C-edited NOESY
11643D 13C-edited NOESY
11713D 13C-filtered, 13C-edited NOESY
11823D 13C-filtered, 13C-edited NOESY
11932D 15N,13C-double-half-filtered NOESY
12042D 15N,13C-double-half-filtered NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.9 mM [U-98% 13C; U-98% 15N] SH3, 0.9 mM ubiquitin, 90% H2O/10% D2O90% H2O/10% D2O
20.9 mM [U-98% 13C; U-98% 15N] ubiquitin, 0.9 mM SH3, 90% H2O/10% D2O90% H2O/10% D2O
30.9 mM [U-98% 13C; U-98% 15N] SH3, 0.9 mM ubiquitin, 100% D2O100% D2O
40.9 mM [U-98% 13C; U-98% 15N] ubiquitin, 0.9 mM SH3, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.9 mMentity_1[U-98% 13C; U-98% 15N]1
0.9 mMentity_21
0.9 mMentity_2[U-98% 13C; U-98% 15N]2
0.9 mMentity_12
0.9 mMentity_1[U-98% 13C; U-98% 15N]3
0.9 mMentity_23
0.9 mMentity_2[U-98% 13C; U-98% 15N]4
0.9 mMentity_14
Sample conditionsIonic strength: 20 / pH: 6 / Pressure: ambient / Temperature: 318 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
VNMRVariancollection
FelixAccelrys Software Inc.processing
FelixAccelrys Software Inc.data analysis
NMRViewJohnson, One Moon Scientificdata analysis
NMRViewJohnson, One Moon Scientificchemical shift assignment
ARIALinge, O'Donoghue and Nilgesrefinement
ARIALinge, O'Donoghue and Nilgesstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
RefinementMethod: torsion angle dynamics, simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least 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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