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- PDB-2i4k: Solution Structure of the PX domain of Sorting Nexin 1 -

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Basic information

Entry
Database: PDB / ID: 2i4k
TitleSolution Structure of the PX domain of Sorting Nexin 1
ComponentsSorting nexin-1
KeywordsPROTEIN TRANSPORT / 3-Stranded Beta sheet / 3 alpha helices / proline rich loop
Function / homology
Function and homology information


retromer, tubulation complex / lamellipodium morphogenesis / leptin receptor binding / early endosome to Golgi transport / retromer complex / transferrin receptor binding / retrograde transport, endosome to Golgi / epidermal growth factor receptor binding / phosphatidylinositol binding / intracellular protein transport ...retromer, tubulation complex / lamellipodium morphogenesis / leptin receptor binding / early endosome to Golgi transport / retromer complex / transferrin receptor binding / retrograde transport, endosome to Golgi / epidermal growth factor receptor binding / phosphatidylinositol binding / intracellular protein transport / insulin receptor binding / receptor internalization / lamellipodium / early endosome membrane / vesicle / lysosome / endosome membrane / endosome / cadherin binding / protein heterodimerization activity / intracellular membrane-bounded organelle / Golgi apparatus / protein homodimerization activity / protein-containing complex / identical protein binding / membrane / cytoplasm / cytosol
Similarity search - Function
Sorting nexin, N-terminal / Sorting nexin-1 / Sorting Nexin 1, PX domain / Sorting nexin, N-terminal domain / Sorting nexin Vps5-like, C-terminal / Vps5 C terminal like / Phox-like domain / PX Domain / PhoX homologous domain, present in p47phox and p40phox. / PX domain profile. ...Sorting nexin, N-terminal / Sorting nexin-1 / Sorting Nexin 1, PX domain / Sorting nexin, N-terminal domain / Sorting nexin Vps5-like, C-terminal / Vps5 C terminal like / Phox-like domain / PX Domain / PhoX homologous domain, present in p47phox and p40phox. / PX domain profile. / PX domain / Phox homology / PX domain superfamily / AH/BAR domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics, simulated annealing, torsion angle dynamics
AuthorsWatson, M.J. / Zhong, Q. / Lazar, C.S. / Hounslow, A.M. / Gill, G.N. / Waltho, J.P.
CitationJournal: Mol.Cell.Biol. / Year: 2005
Title: Determinants of the Endosomal Localization of Sorting Nexin 1
Authors: Zhong, Q. / Watson, M.J. / Lazar, C.S. / Hounslow, A.M. / Waltho, J.P. / Gill, G.N.
History
DepositionAug 22, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 19, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name
Revision 1.4Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.5May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sorting nexin-1


Theoretical massNumber of molelcules
Total (without water)14,7021
Polymers14,7021
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Sorting nexin-1 / SNX1


Mass: 14701.784 Da / Num. of mol.: 1 / Fragment: Phox homology (PX) domain (Residues 142-269)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNX1 / Plasmid: pTYB11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 CodonplusRIL / References: UniProt: Q13596

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 3D 13C/15N-separated NOESY

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Sample preparation

DetailsContents: 1mM SNX1-PX U-15N;U-13C 20mM Phosphate pH6.5 0.1M NaCL 10mM NaN3 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 0.1M NaCl / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX8001
Bruker DRXBrukerDRX6002
Bruker DRXBrukerDRX5003

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5Brukercollection
Felix2000Accelrysprocessing
Felix2000Accelrysdata analysis
CNS1.1Brungerstructure solution
CNS1.1Brungerrefinement
RefinementMethod: molecular dynamics, simulated annealing, torsion angle dynamics
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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