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- PDB-2mxc: Solution structure of the full length sorting nexin 3 -

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Basic information

Entry
Database: PDB / ID: 2mxc
TitleSolution structure of the full length sorting nexin 3
ComponentsSorting nexin-3
KeywordsPROTEIN TRANSPORT / PI3P / SNX3 / membrane / endosome
Function / homology
Function and homology information


negative regulation of early endosome to late endosome transport / late endosome to Golgi transport / protein to membrane docking / negative regulation of protein transport / membrane invagination / WNT ligand biogenesis and trafficking / intralumenal vesicle formation / retromer complex binding / retromer complex / phosphatidylinositol-5-phosphate binding ...negative regulation of early endosome to late endosome transport / late endosome to Golgi transport / protein to membrane docking / negative regulation of protein transport / membrane invagination / WNT ligand biogenesis and trafficking / intralumenal vesicle formation / retromer complex binding / retromer complex / phosphatidylinositol-5-phosphate binding / negative regulation of viral entry into host cell / early phagosome / endocytic recycling / phosphatidylinositol-3-phosphate binding / regulation of Wnt signaling pathway / phosphatidylinositol-4-phosphate binding / phosphatidylinositol-3,5-bisphosphate binding / negative regulation of phagocytosis / clathrin-coated vesicle / response to bacterium / negative regulation of protein catabolic process / positive regulation of neuron projection development / protein transport / early endosome membrane / protein phosphatase binding / early endosome / endosome membrane / Ub-specific processing proteases / extracellular exosome / cytosol / cytoplasm
Similarity search - Function
Vertebrate SNX3, PX domain / : / Phox-like domain / PX Domain / PhoX homologous domain, present in p47phox and p40phox. / PX domain profile. / PX domain / Phox homology / PX domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
Model detailsclosest to the average, model1
AuthorsLenoir, M.M.L. / Rajesh, S.S.R. / Gruenberg, J.J.G. / Overduin, M.M.O. / Kaur, J.J.K.
CitationJournal: Nat Commun / Year: 2018
Title: Phosphorylation of conserved phosphoinositide binding pocket regulates sorting nexin membrane targeting.
Authors: Lenoir, M. / Ustunel, C. / Rajesh, S. / Kaur, J. / Moreau, D. / Gruenberg, J. / Overduin, M.
History
DepositionDec 20, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 4, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.3May 15, 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-3


Theoretical massNumber of molelcules
Total (without water)19,9481
Polymers19,9481
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 lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Sorting nexin-3 / Protein SDP3


Mass: 19947.605 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNX3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O60493

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR / Details: The solution structure of SNX3
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC/HMQC
1213D HNCA
1313D HN(CO)CA
1413D HNCO
1513D CBCA(CO)NH
1613D HN(CA)CB
1713D HNCO
1813D HN(CA)CO
1913D (H)CCH-TOCSY
11013D 1H-13C NOESY
11113D 1H-15N NOESY
11212D 1H-13C HSQC

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Sample preparation

DetailsContents: 0.5 mM [U-100% 13C; U-100% 15N] SNX3FL, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
SampleConc.: 0.5 mM / Component: SNX3FL-1 / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsIonic strength: 0.1 / pH: 6.5 / Pressure: 1.000 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian UnityInova / Manufacturer: Varian / Model: UnityInova / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CcpNmr Analysis2.2CCPNchemical shift calculation
CcpNmr Analysis2.2CCPNdata analysis
CcpNmr Analysis2.2CCPNstructure solution
CcpNmr Analysis2.2Linge, O'Donoghue and Nilgeschemical shift calculation
CcpNmr Analysis2.2Linge, O'Donoghue and Nilgesdata analysis
CcpNmr Analysis2.2Linge, O'Donoghue and Nilgesstructure solution
CcpNmr Analysis2.2CCPNchemical shift calculation
CcpNmr Analysis2.2CCPNdata analysis
CcpNmr Analysis2.2CCPNstructure solution
CcpNmr Analysis2.2Linge, O'Donoghue and Nilgeschemical shift calculation
CcpNmr Analysis2.2Linge, O'Donoghue and Nilgesdata analysis
CcpNmr Analysis2.2Linge, O'Donoghue and Nilgesstructure solution
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
ARIArefinement
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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