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- PDB-5f0j: Structure of retromer VPS26-VPS35 subunits bound to SNX3 -

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Basic information

Entry
Database: PDB / ID: 5f0j
TitleStructure of retromer VPS26-VPS35 subunits bound to SNX3
Components
  • (Vacuolar protein sorting-associated protein ...) x 2
  • Sorting nexin-3
KeywordsTRANSPORT PROTEIN / protein transport / retromer / sorting nexin
Function / homology
Function and homology information


negative regulation of early endosome to late endosome transport / late endosome to Golgi transport / negative regulation of protein transport / protein to membrane docking / neurotransmitter receptor transport, endosome to plasma membrane / membrane invagination / negative regulation of protein localization / regulation of dendritic spine maintenance / mitochondrion-derived vesicle / negative regulation of protein homooligomerization ...negative regulation of early endosome to late endosome transport / late endosome to Golgi transport / negative regulation of protein transport / protein to membrane docking / neurotransmitter receptor transport, endosome to plasma membrane / membrane invagination / negative regulation of protein localization / regulation of dendritic spine maintenance / mitochondrion-derived vesicle / negative regulation of protein homooligomerization / tubular endosome / regulation of terminal button organization / positive regulation of Wnt protein secretion / mitochondrion to lysosome vesicle-mediated transport / WNT ligand biogenesis and trafficking / retromer, cargo-selective complex / intralumenal vesicle formation / negative regulation of lysosomal protein catabolic process / positive regulation of locomotion involved in locomotory behavior / negative regulation of late endosome to lysosome transport / retromer complex binding / positive regulation of dopamine biosynthetic process / positive regulation of dopamine receptor signaling pathway / phosphatidylinositol-5-phosphate binding / neurotransmitter receptor transport, endosome to postsynaptic membrane / protein localization to endosome / retromer complex / vesicle-mediated transport in synapse / voluntary musculoskeletal movement / mitochondrial fragmentation involved in apoptotic process / transcytosis / host-mediated suppression of symbiont invasion / regulation of protein metabolic process / dopaminergic synapse / early phagosome / regulation of synapse maturation / phosphatidylinositol-3-phosphate binding / endocytic recycling / retrograde transport, endosome to Golgi / phosphatidylinositol-4-phosphate binding / regulation of mitochondrion organization / phosphatidylinositol-3,5-bisphosphate binding / regulation of Wnt signaling pathway / clathrin-coated vesicle / positive regulation of protein localization to cell periphery / negative regulation of phagocytosis / lysosome organization / positive regulation of mitochondrial fission / regulation of postsynapse assembly / regulation of presynapse assembly / regulation of macroautophagy / D1 dopamine receptor binding / response to bacterium / intracellular protein transport / protein destabilization / negative regulation of protein catabolic process / positive regulation of neuron projection development / modulation of chemical synaptic transmission / regulation of protein stability / negative regulation of inflammatory response / Wnt signaling pathway / positive regulation of protein catabolic process / positive regulation of canonical Wnt signaling pathway / late endosome / protein transport / presynapse / vesicle / early endosome membrane / protein phosphatase binding / early endosome / neuron projection / endosome membrane / lysosome / Ub-specific processing proteases / endosome / postsynaptic density / negative regulation of gene expression / lysosomal membrane / neuronal cell body / intracellular membrane-bounded organelle / positive regulation of gene expression / perinuclear region of cytoplasm / glutamatergic synapse / extracellular exosome / cytosol / cytoplasm
Similarity search - Function
Vertebrate SNX3, PX domain / : / Vacuolar protein sorting protein 26 related / Vacuolar protein sorting-associated protein 26 / Vacuolar protein sorting-associated protein 35 / Vacuolar protein sorting-associated protein 35, C-terminal / Vacuolar protein sorting-associated protein 35 / Immunoglobulin-like - #640 / Phox-like domain / PX Domain ...Vertebrate SNX3, PX domain / : / Vacuolar protein sorting protein 26 related / Vacuolar protein sorting-associated protein 26 / Vacuolar protein sorting-associated protein 35 / Vacuolar protein sorting-associated protein 35, C-terminal / Vacuolar protein sorting-associated protein 35 / Immunoglobulin-like - #640 / Phox-like domain / PX Domain / PhoX homologous domain, present in p47phox and p40phox. / PX domain profile. / PX domain / Phox homology / PX domain superfamily / Arrestin-like, C-terminal / Armadillo-type fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Sorting nexin-3 / Vacuolar protein sorting-associated protein 26A / Vacuolar protein sorting-associated protein 35
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsLucas, M. / Gershlick, D. / Vidaurrazaga, A. / Rojas, A.L. / Bonifacino, J.S. / Hierro, A.
Funding support Spain, 3items
OrganizationGrant numberCountry
Carlos III Health InstitutePI11/00121 Spain
Basque GovernmentBFU2014-59759-R Spain
Spanish Ministry of Economy and CompetitivenessBFU2014-59759-R Spain
CitationJournal: Cell / Year: 2016
Title: Structural Mechanism for Cargo Recognition by the Retromer Complex.
Authors: Lucas, M. / Gershlick, D.C. / Vidaurrazaga, A. / Rojas, A.L. / Bonifacino, J.S. / Hierro, A.
History
DepositionNov 27, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Vacuolar protein sorting-associated protein 35
B: Vacuolar protein sorting-associated protein 26A
C: Sorting nexin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,24838
Polymers112,7223
Non-polymers2,52635
Water1,71195
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12350 Å2
ΔGint-25 kcal/mol
Surface area45690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)372.820, 75.580, 57.530
Angle α, β, γ (deg.)90.000, 97.870, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Vacuolar protein sorting-associated protein ... , 2 types, 2 molecules AB

#1: Protein Vacuolar protein sorting-associated protein 35 / hVPS35 / Maternal-embryonic 3 / Vesicle protein sorting 35


Mass: 53288.270 Da / Num. of mol.: 1 / Fragment: Residues 14-470
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VPS35, MEM3, TCCCTA00141 / Plasmid: pGST-Parallel2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q96QK1
#2: Protein Vacuolar protein sorting-associated protein 26A / Vesicle protein sorting 26A / hVPS26


Mass: 40239.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VPS26A, VPS26 / Plasmid: pmr101A / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O75436

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Protein , 1 types, 1 molecules C

#3: Protein Sorting nexin-3 / Protein SDP3


Mass: 19193.814 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNX3 / Plasmid: pHis-MBP-Parallel2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O60493

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Non-polymers , 4 types, 130 molecules

#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 3.56 Å3/Da / Density % sol: 65.46 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.9 M AmSO4, 0.1 M MES pH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97893 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 24, 2014
RadiationMonochromator: Si(111) channel-cut, cryocooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97893 Å / Relative weight: 1
ReflectionResolution: 2.69→57 Å / Num. obs: 85401 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 67.063 Å2 / Rmerge F obs: 0.997 / Rmerge(I) obs: 0.09 / Rrim(I) all: 0.107 / Χ2: 1.064 / Net I/σ(I): 12.09 / Num. measured all: 292428
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.69-2.850.7250.81.514372414049130080.95192.6
2.85-3.040.8740.4752.794537713217131840.56499.8
3.04-3.290.9520.2715.094243912243121900.32299.6
3.29-3.60.9830.1469.33809211343112650.17499.3
3.6-4.020.9910.09814.863451410130100710.11699.4
4.02-4.640.9930.07121.730744900589510.08499.4
4.64-5.680.9940.0624.8126352762975770.07299.3
5.68-7.990.9950.05625.520049590558710.06699.4
7.990.9990.02838.8711137331632840.03399

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Processing

Software
NameVersionClassification
XSCALEdata scaling
REFMAC5.8.0135refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FAU, 2YPS

2fau

2yps


Resolution: 2.7→56.98 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.911 / WRfactor Rfree: 0.246 / WRfactor Rwork: 0.2072 / FOM work R set: 0.8343 / SU B: 11.486 / SU ML: 0.224 / SU R Cruickshank DPI: 0.5345 / SU Rfree: 0.3016 / Cross valid method: FREE R-VALUE / σ(F): 0 / ESU R: 0.534 / ESU R Free: 0.302 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2461 2100 5 %RANDOM
Rwork0.2072 ---
obs0.2091 39941 95.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 150.07 Å2 / Biso mean: 57.454 Å2 / Biso min: 16.35 Å2
Baniso -1Baniso -2Baniso -3
1-0.32 Å20 Å2-0.28 Å2
2--0.17 Å20 Å2
3----0.4 Å2
Refinement stepCycle: final / Resolution: 2.7→56.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7481 0 156 95 7732
Biso mean--67.38 36.07 -
Num. residues----919
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0197741
X-RAY DIFFRACTIONr_bond_other_d0.0010.027595
X-RAY DIFFRACTIONr_angle_refined_deg1.1981.9910400
X-RAY DIFFRACTIONr_angle_other_deg0.879317467
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9535915
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.79124.293375
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.866151406
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7221556
X-RAY DIFFRACTIONr_chiral_restr0.0670.21171
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0218500
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021724
X-RAY DIFFRACTIONr_mcbond_it2.4185.6793672
X-RAY DIFFRACTIONr_mcbond_other2.4175.6783671
X-RAY DIFFRACTIONr_mcangle_it4.1928.5074583
LS refinement shellResolution: 2.698→2.768 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.474 83 -
Rwork0.468 1607 -
all-1690 -
obs--52.93 %

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