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- PDB-2hbp: Solution Structure of Sla1 Homology Domain 1 -

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Basic information

Entry
Database: PDB / ID: 2hbp
TitleSolution Structure of Sla1 Homology Domain 1
ComponentsCytoskeleton assembly control protein SLA1
KeywordsENDOCYTOSIS / PROTEIN BINDING / Sla1 / SHD1 / NPFx(1 / 2)D
Function / homology
Function and homology information


actin cytoskeleton-regulatory complex / SLAC complex / cargo adaptor activity / RND2 GTPase cycle / RHOQ GTPase cycle / actin cortical patch assembly / regulation of Arp2/3 complex-mediated actin nucleation / negative regulation of Arp2/3 complex-mediated actin nucleation / actin cortical patch / regulation of actin filament polymerization ...actin cytoskeleton-regulatory complex / SLAC complex / cargo adaptor activity / RND2 GTPase cycle / RHOQ GTPase cycle / actin cortical patch assembly / regulation of Arp2/3 complex-mediated actin nucleation / negative regulation of Arp2/3 complex-mediated actin nucleation / actin cortical patch / regulation of actin filament polymerization / cellular bud neck / mating projection tip / ubiquitin binding / cell wall organization / endocytosis / actin binding / cell cortex / endosome membrane / identical protein binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
SLA1 homology domain 1 / SLA1 homology domain 1, SHD1 / Sla1, first SH3 domain / Sla1, third SH3 domain / SLA1 homology domain 1, SHD1 / Variant SH3 domain / Sterile alpha motif/pointed domain superfamily / SH3 domain / SH3 type barrels. / Src homology 3 domains ...SLA1 homology domain 1 / SLA1 homology domain 1, SHD1 / Sla1, first SH3 domain / Sla1, third SH3 domain / SLA1 homology domain 1, SHD1 / Variant SH3 domain / Sterile alpha motif/pointed domain superfamily / SH3 domain / SH3 type barrels. / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Roll / Mainly Beta
Similarity search - Domain/homology
Actin cytoskeleton-regulatory complex protein SLA1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / simulated annealing
AuthorsOverduin, M. / Mahadev, R.K.
CitationJournal: Embo J. / Year: 2007
Title: Structure of Sla1p homology domain 1 and interaction with the NPFxD endocytic internalization motif.
Authors: Mahadev, R.K. / Di Pietro, S.M. / Olson, J.M. / Piao, H.L. / Payne, G.S. / Overduin, M.
History
DepositionJun 14, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytoskeleton assembly control protein SLA1


Theoretical massNumber of molelcules
Total (without water)7,4531
Polymers7,4531
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 / 200structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Cytoskeleton assembly control protein SLA1


Mass: 7452.612 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

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D-15N/13C-EDITED NOESY

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Sample preparation

DetailsContents: 0.5mM 15N, 13C labelled SHD1, 1mM unlabeled YNENPFSDPIK peptide. PBS buffer pH 6.7, 1mM d-DTT, 1mM NaN3
Solvent system: 90% H2O, 10% D20
Sample conditionspH: 6.7 / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameClassification
NMRPipeprocessing
Sparkyprocessing
CNSrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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