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- PDB-3fog: Crystal structure of the PX domain of sorting nexin-17 (SNX17) -

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Basic information

Entry
Database: PDB / ID: 3fog
TitleCrystal structure of the PX domain of sorting nexin-17 (SNX17)
ComponentsSorting nexin-17
KeywordsPROTEIN TRANSPORT / helix / Structural Genomics / Structural Genomics Consortium / SGC / Cytoplasm / Endosome / Phosphoprotein / Transport
Function / homology
Function and homology information


cardiac septum development / coronary vasculature development / endocytic recycling / aorta development / endosomal transport / low-density lipoprotein particle receptor binding / cholesterol catabolic process / regulation of endocytosis / phosphatidylinositol binding / receptor-mediated endocytosis ...cardiac septum development / coronary vasculature development / endocytic recycling / aorta development / endosomal transport / low-density lipoprotein particle receptor binding / cholesterol catabolic process / regulation of endocytosis / phosphatidylinositol binding / receptor-mediated endocytosis / kidney development / intracellular protein transport / cytoplasmic vesicle / early endosome / endosome membrane / endosome / signaling receptor binding / intracellular membrane-bounded organelle / Golgi apparatus / signal transduction / protein-containing complex / membrane / cytosol
Similarity search - Function
Sorting nexin-17 / SNX17, atypical FERM-like domain / Sorting nexin-17/31, FERM domain / : / : / Sorting Nexin 17 FERM C-terminal domain / Sortin nexin 17/31, FERM domain, F2 lobe / Sortin nexin 17/27/31, FERM domain, F1 lobe / SNX17/27/31 / Phox-like domain ...Sorting nexin-17 / SNX17, atypical FERM-like domain / Sorting nexin-17/31, FERM domain / : / : / Sorting Nexin 17 FERM C-terminal domain / Sortin nexin 17/31, FERM domain, F2 lobe / Sortin nexin 17/27/31, FERM domain, F1 lobe / SNX17/27/31 / Phox-like domain / PX Domain / Ras-associating (RA) domain profile. / Ras-associating (RA) domain / PhoX homologous domain, present in p47phox and p40phox. / PX domain profile. / PX domain / Phox homology / PX domain superfamily / PH-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsWisniewska, M. / Tresaugues, L. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. ...Wisniewska, M. / Tresaugues, L. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, A. / Johansson, I. / Karlberg, T. / Kotenyova, T. / Lehtio, L. / Moche, M. / Nilsson, M.E. / Nordlund, P. / Nyman, T. / Persson, C. / Sagemark, J. / Siponen, M.I. / Thorsell, A.G. / Van Den Berg, S. / Weigelt, J. / Welin, M. / Wikstrom, M. / Schueler, H. / Structural Genomics Consortium (SGC)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of the PX domain of sorting nexin-17 (SNX17)
Authors: Wisniewska, M. / Tresaugues, L. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / ...Authors: Wisniewska, M. / Tresaugues, L. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, A. / Johansson, I. / Karlberg, T. / Kotenyova, T. / Lehtio, L. / Moche, M. / Nilsson, M.E. / Nordlund, P. / Nyman, T. / Persson, C. / Sagemark, J. / Siponen, M.I. / Thorsell, A.G. / Van Den Berg, S. / Weigelt, J. / Welin, M. / Wikstrom, M. / Schueler, H.
History
DepositionDec 30, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 27, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sorting nexin-17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,2772
Polymers13,2541
Non-polymers231
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)89.890, 89.890, 39.260
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321

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Components

#1: Protein Sorting nexin-17 / / SNX17


Mass: 13253.858 Da / Num. of mol.: 1 / Fragment: residues 1-115
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNX17, KIAA0064 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15036
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.24 Å3/Da / Density % sol: 61.98 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20% PEG 3350, 0.2M sodium fluoride, 0.1M bis-Tris propane, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 22, 2008
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. all: 4674 / Num. obs: 4633 / % possible obs: 99.1 %
Reflection shellResolution: 2.8→2.87 Å / % possible all: 98.7

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Processing

Software
NameVersionClassification
MxCuBEdata collection
MOLREPphasing
PHENIX(phenix.refine)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XTE

1xte


Resolution: 2.8→29.423 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.743 / SU ML: 0.38 / σ(F): 1.99 / Phase error: 30.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.279 464 10.02 %
Rwork0.23 4169 -
obs0.235 4633 99.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.415 Å2 / ksol: 0.327 e/Å3
Displacement parametersBiso max: 128.81 Å2 / Biso mean: 71.594 Å2 / Biso min: 41.08 Å2
Baniso -1Baniso -2Baniso -3
1-4.216 Å2-0 Å2-0 Å2
2--4.216 Å20 Å2
3----8.433 Å2
Refinement stepCycle: LAST / Resolution: 2.8→29.423 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms818 0 1 0 819
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006838
X-RAY DIFFRACTIONf_angle_d0.9941134
X-RAY DIFFRACTIONf_chiral_restr0.069123
X-RAY DIFFRACTIONf_plane_restr0.005149
X-RAY DIFFRACTIONf_dihedral_angle_d17.248306
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3 / % reflection obs: 99 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.8001-3.20480.39221510.31771355
3.2048-4.03610.31491520.23591373
4.0361-29.4250.23261610.20071441

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