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- PDB-5ixf: Solution structure of the STAM2 SH3 with AMSH derived peptide complex -

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Basic information

Entry
Database: PDB / ID: 5ixf
TitleSolution structure of the STAM2 SH3 with AMSH derived peptide complex
Components
  • STAM-binding protein
  • Signal transducing adapter molecule 2
KeywordsSIGNALING PROTEIN / STAM2 / SH3 / endosome / traffic / AMSH
Function / homology
Function and homology information


ESCRT-0 complex / negative regulation of hippocampal neuron apoptotic process / hippocampal neuron apoptotic process / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases / deubiquitinase activity / membrane fission / multivesicular body assembly / negative regulation of Ras protein signal transduction / metal-dependent deubiquitinase activity ...ESCRT-0 complex / negative regulation of hippocampal neuron apoptotic process / hippocampal neuron apoptotic process / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases / deubiquitinase activity / membrane fission / multivesicular body assembly / negative regulation of Ras protein signal transduction / metal-dependent deubiquitinase activity / protein K63-linked deubiquitination / K63-linked deubiquitinase activity / cleavage furrow / cell surface receptor signaling pathway via JAK-STAT / RHOU GTPase cycle / mitotic cytokinesis / endocytic vesicle / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein deubiquitination / Endosomal Sorting Complex Required For Transport (ESCRT) / phosphatidylinositol binding / InlB-mediated entry of Listeria monocytogenes into host cell / ubiquitin binding / macroautophagy / EGFR downregulation / Negative regulation of MET activity / Metalloprotease DUBs / metallopeptidase activity / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / early endosome membrane / early endosome / Ub-specific processing proteases / endosome / protein domain specific binding / intracellular membrane-bounded organelle / positive regulation of cell population proliferation / signal transduction / proteolysis / extracellular exosome / nucleoplasm / nucleus / metal ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
STAM2, SH3 domain / : / : / STAMBP/STALP-like, MPN domain / USP8 dimerisation domain / USP8 dimerisation domain / VHS domain / VHS domain / VHS domain profile. / Domain present in VPS-27, Hrs and STAM ...STAM2, SH3 domain / : / : / STAMBP/STALP-like, MPN domain / USP8 dimerisation domain / USP8 dimerisation domain / VHS domain / VHS domain / VHS domain profile. / Domain present in VPS-27, Hrs and STAM / Ubiquitin interaction motif / ENTH/VHS / Ubiquitin-interacting motif. / Ubiquitin interacting motif / Ubiquitin-interacting motif (UIM) domain profile. / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / SH3 Domains / JAB/MPN domain / JAB1/MPN/MOV34 metalloenzyme domain / MPN domain / MPN domain profile. / 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
STAM-binding protein / Signal transducing adapter molecule 2 / STAM-binding protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsHologne, M. / Cantrelle, F.X. / Trivelli, X. / Walker, O.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-14-OHRI-0006-01 France
CitationJournal: J.Mol.Biol. / Year: 2016
Title: NMR Reveals the Interplay among the AMSH SH3 Binding Motif, STAM2, and Lys63-Linked Diubiquitin.
Authors: Hologne, M. / Cantrelle, F.X. / Riviere, G. / Guilliere, F. / Trivelli, X. / Walker, O.
History
DepositionMar 23, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jun 19, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Signal transducing adapter molecule 2
B: STAM-binding protein


Theoretical massNumber of molelcules
Total (without water)13,9032
Polymers13,9032
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1360 Å2
ΔGint-4 kcal/mol
Surface area6060 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Signal transducing adapter molecule 2 / STAM-2 / Hrs-binding protein


Mass: 12465.770 Da / Num. of mol.: 1 / Fragment: SH3 domain, residues 196-263
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: STAM2, HBP / Plasmid: pETM60 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: O75886
#2: Protein/peptide STAM-binding protein


Mass: 1437.705 Da / Num. of mol.: 1 / Fragment: SBM motif, UNP residues 228-241 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: C9JK83, UniProt: O95630*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D 1H-15N NOESY
121isotropic13D 1H-13C NOESY aliphatic
131isotropic13D 1H-13C NOESY aromatic
141isotropic13D HNCO
151isotropic13D HNCA
161isotropic13D HN(CO)CA
171isotropic13D C(CO)NH
181isotropic13D H(CCO)NH
191isotropic13D CBCA(CO)NH
1101isotropic13D HN(CA)CB

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Sample preparation

DetailsType: solution
Contents: 250 uM [U-13C; U-15N] UIM-SH3, 250 uM SBM motif of AMSH, 20 mM sodium phosphate, 0.02 % sodium azide, 90% H2O/10% D2O
Label: 13C_15N_sample / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
250 uMUIM-SH3[U-13C; U-15N]1
250 uMSBM motif of AMSHnatural abundance1
20 mMsodium phosphatenatural abundance1
0.02 %sodium azidenatural abundance1
Sample conditionsDetails: no details / Ionic strength: 20 mM / Label: conditions_1 / pH: 6.8 / Pressure: 1 atm / Temperature: 293 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 900 MHz

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Processing

NMR software
NameDeveloperClassification
HADDOCKBonvinstructure calculation
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRViewJohnson, One Moon Scientificpeak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: simulated annealing / Software ordinal: 5 / Details: no details
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 10

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