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- PDB-2enm: Solution structure of the SH3 domain from mouse sorting nexin-9 -

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Basic information

Entry
Database: PDB / ID: 2enm
TitleSolution structure of the SH3 domain from mouse sorting nexin-9
ComponentsSorting nexin-9
KeywordsENDOCYTOSIS / SH3-like barrel / Protein transport / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


lipid tube assembly / plasma membrane tubulation / 1-phosphatidylinositol binding / Arp2/3 complex binding / Golgi Associated Vesicle Biogenesis / cleavage furrow formation / Clathrin-mediated endocytosis / positive regulation of membrane protein ectodomain proteolysis / clathrin-coated vesicle / endosomal transport ...lipid tube assembly / plasma membrane tubulation / 1-phosphatidylinositol binding / Arp2/3 complex binding / Golgi Associated Vesicle Biogenesis / cleavage furrow formation / Clathrin-mediated endocytosis / positive regulation of membrane protein ectodomain proteolysis / clathrin-coated vesicle / endosomal transport / positive regulation of actin filament polymerization / mitotic cytokinesis / positive regulation of protein kinase activity / extrinsic component of cytoplasmic side of plasma membrane / ruffle / phosphatidylinositol binding / receptor-mediated endocytosis / positive regulation of GTPase activity / intracellular protein transport / cytoplasmic vesicle membrane / trans-Golgi network / endocytosis / cytoplasmic vesicle / protein-containing complex assembly / ubiquitin protein ligase binding / protein homodimerization activity / identical protein binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Sorting nexin-9 / SNX9, SH3 domain / Sorting nexin-9, BAR domain / Sorting nexin-9, PX domain / Sorting nexin 9 family / Sorting nexin protein, WASP-binding domain / WASP-binding domain of Sorting nexin protein / PhoX homologous domain, present in p47phox and p40phox. / PX domain profile. / PX domain ...Sorting nexin-9 / SNX9, SH3 domain / Sorting nexin-9, BAR domain / Sorting nexin-9, PX domain / Sorting nexin 9 family / Sorting nexin protein, WASP-binding domain / WASP-binding domain of Sorting nexin protein / PhoX homologous domain, present in p47phox and p40phox. / PX domain profile. / PX domain / Phox homology / PX domain superfamily / AH/BAR domain superfamily / SH3 Domains / 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
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsWakabayashi, M. / Kurosaki, C. / Yoshida, M. / Hayashi, F. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of the SH3 domain from mouse sorting nexin-9
Authors: Wakabayashi, M. / Kurosaki, C. / Yoshida, M. / Hayashi, F. / Yokoyama, S.
History
DepositionMar 28, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 2, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 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 1.3May 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: Sorting nexin-9


Theoretical massNumber of molelcules
Total (without water)8,0391
Polymers8,0391
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 / 100structures with the least restraint violations, target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Sorting nexin-9


Mass: 8038.771 Da / Num. of mol.: 1 / Fragment: SH3 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Description: cell free protein synthesis / Gene: Snx9 / Plasmid: P060130-11 / References: UniProt: Q91VH2

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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 13C-separated NOESY

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Sample preparation

DetailsContents: 1.14mM 13C, 15N-laveled protein; 20mM d-Tris-HCl (pH7.0); 100mM NaCl; d-DTT; 0.02% NaN3; 10% D2O, 90% H2O
Solvent system: 10% D2O, 90% H2O
Sample conditionsIonic strength: 120mM / pH: 7.0 / Pressure: ambient / Temperature: 296 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
JEOL ECAJEOLECA7001
Varian INOVAVarianINOVA9002

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Processing

NMR software
NameVersionDeveloperClassification
Delta NMR4.3.2JEOLcollection
VNMR6.1CVariancollection
NMRPipe20031121Delagio,F.processing
NMRView5.0.4Johnson,B.A.data analysis
KUJIRA0.9815Kobayashi,N.data analysis
CYANA2.0.17Guntert,P.structure solution
CYANA2.0.17Guntert,P.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations, target function
Conformers calculated total number: 100 / Conformers submitted total number: 20

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