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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 / : / : / : / : / : / RND2 GTPase cycle / Regulation of TP53 Degradation ...actin cytoskeleton-regulatory complex / SLAC complex / cargo adaptor activity / : / : / : / : / : / RND2 GTPase cycle / Regulation of TP53 Degradation / RHOQ GTPase cycle / Josephin domain DUBs / RAS processing / Regulation of PTEN localization / ER Quality Control Compartment (ERQC) / UCH proteinases / PINK1-PRKN Mediated Mitophagy / Pexophagy / Interleukin-1 signaling / Aggrephagy / actin cortical patch assembly / Regulation of pyruvate metabolism / Peroxisomal protein import / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / ABC-family proteins mediated transport / Metalloprotease DUBs / Endosomal Sorting Complex Required For Transport (ESCRT) / regulation of Arp2/3 complex-mediated actin nucleation / negative regulation of Arp2/3 complex-mediated actin nucleation / E3 ubiquitin ligases ubiquitinate target proteins / actin cortical patch / regulation of actin filament polymerization / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / cellular bud neck / Translesion Synthesis by POLH / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / mating projection tip / Termination of translesion DNA synthesis / Negative regulators of DDX58/IFIH1 signaling / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of PTEN stability and activity / CDK-mediated phosphorylation and removal of Cdc6 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Major pathway of rRNA processing in the nucleolus and cytosol / KEAP1-NFE2L2 pathway / Neddylation / Formation of TC-NER Pre-Incision Complex / Orc1 removal from chromatin / MAPK6/MAPK4 signaling / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Formation of a pool of free 40S subunits / Gap-filling DNA repair synthesis and ligation in TC-NER / Antigen processing: Ubiquitination & Proteasome degradation / L13a-mediated translational silencing of Ceruloplasmin expression / Dual incision in TC-NER / ribosomal large subunit export from nucleus / Ub-specific processing proteases / ubiquitin binding / cell wall organization / modification-dependent protein catabolic process / endocytosis / protein tag activity / peroxisome / ribosome biogenesis / actin binding / cell cortex / ribosomal large subunit assembly / cytoplasmic translation / cytosolic large ribosomal subunit / endosome membrane / protein ubiquitination / 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 / : / SH3 type barrels. / Src homology 3 domains / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin-like (UB roll) / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / 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
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
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
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 / 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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