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- PDB-5woe: Solution structure of the sorting nexin 25 phox-homology domain -

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Basic information

Entry
Database: PDB / ID: 5woe
TitleSolution structure of the sorting nexin 25 phox-homology domain
ComponentsSorting nexin-25
KeywordsTRANSPORT PROTEIN / endosome / Mdm1 / PX domain / PXA domain / PXC domain / RGS domain / sorting nexin / SNX / SNX13 / SNX14 / SNX19 / SNX25
Function / homology
Function and homology information


: / receptor catabolic process / type I transforming growth factor beta receptor binding / phosphatidylinositol binding / negative regulation of transforming growth factor beta receptor signaling pathway / protein transport / endosome membrane / intracellular membrane-bounded organelle
Similarity search - Function
Sorting nexin-25 / SNX25, PX domain / Phox-associated domain / Sorting nexin, C-terminal / PXA domain / Sorting nexin C terminal / PXA domain profile. / Domain associated with PX domains / PhoX homologous domain, present in p47phox and p40phox. / Regulator of G protein signaling domain ...Sorting nexin-25 / SNX25, PX domain / Phox-associated domain / Sorting nexin, C-terminal / PXA domain / Sorting nexin C terminal / PXA domain profile. / Domain associated with PX domains / PhoX homologous domain, present in p47phox and p40phox. / Regulator of G protein signaling domain / PX domain profile. / PX domain / Phox homology / PX domain superfamily / RGS domain / RGS domain profile. / Regulator of G protein signalling domain / RGS domain superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsChin, Y.K.Y. / Mas, C. / Mobli, M. / Collins, B.M.
CitationJournal: Nat Commun / Year: 2019
Title: Classification of the human phox homology (PX) domains based on their phosphoinositide binding specificities.
Authors: Chandra, M. / Chin, Y.K. / Mas, C. / Feathers, J.R. / Paul, B. / Datta, S. / Chen, K.E. / Jia, X. / Yang, Z. / Norwood, S.J. / Mohanty, B. / Bugarcic, A. / Teasdale, R.D. / Henne, W.M. / ...Authors: Chandra, M. / Chin, Y.K. / Mas, C. / Feathers, J.R. / Paul, B. / Datta, S. / Chen, K.E. / Jia, X. / Yang, Z. / Norwood, S.J. / Mohanty, B. / Bugarcic, A. / Teasdale, R.D. / Henne, W.M. / Mobli, M. / Collins, B.M.
History
DepositionAug 1, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / pdbx_nmr_software / pdbx_nmr_spectrometer
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 / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.2Jun 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 1.3May 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-25


Theoretical massNumber of molelcules
Total (without water)14,2451
Polymers14,2451
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8000 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Sorting nexin-25


Mass: 14245.309 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNX25, MSTP043 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H3E2

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111anisotropic13D HNCO
121anisotropic13D CBCA(CO)NH
131anisotropic13D HN(CA)CB
141anisotropic13D HBHA(CO)NH
151anisotropic12D 1H-15N HSQC
161anisotropic13D 1H-15N NOESY
181anisotropic13D 1H-13C NOESY aliphatic
171anisotropic13D 1H-13C NOESY aromatic

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Sample preparation

DetailsType: solution
Contents: 0.8 mM [U-99% 13C; U-99% 15N] SNX25, 20 mM HEPES, 100 mM NaCl, 2 mM DTT, 90% H2O/10% D2O
Label: Apo / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMSNX25[U-99% 13C; U-99% 15N]1
20 mMHEPESnatural abundance1
100 mMNaClnatural abundance1
2 mMDTTnatural abundance1
Sample conditionsIonic strength: 100 mM / Label: 1 / pH: 7 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

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

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Processing

NMR software
NameDeveloperClassification
AnalysisCCPNchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
Rowland NMR ToolKitGregory P. Mullen NMR Structural Biology Facility University of Connecticut Health Centerprocessing
TopSpinBruker Biospincollection
CYANAGuntert, Mumenthaler and Wuthrichrefinement
AnalysisCCPNpeak picking
RefinementMethod: torsion angle dynamics / Software ordinal: 5
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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