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- PDB-5f0k: Structure of VPS35 N terminal region -

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Basic information

Entry
Database: PDB / ID: 5f0k
TitleStructure of VPS35 N terminal region
ComponentsVacuolar protein sorting-associated protein 35Vacuole
KeywordsPROTEIN TRANSPORT / retromer / sorting nexin
Function / homology
Function and homology information


positive regulation of locomotion involved in locomotory behavior / neurotransmitter receptor transport, endosome to plasma membrane / negative regulation of protein localization / regulation of postsynapse assembly / mitochondrion-derived vesicle / negative regulation of protein homooligomerization / regulation of dendritic spine maintenance / tubular endosome / mitochondrion to lysosome vesicle-mediated transport / positive regulation of Wnt protein secretion ...positive regulation of locomotion involved in locomotory behavior / neurotransmitter receptor transport, endosome to plasma membrane / negative regulation of protein localization / regulation of postsynapse assembly / mitochondrion-derived vesicle / negative regulation of protein homooligomerization / regulation of dendritic spine maintenance / tubular endosome / mitochondrion to lysosome vesicle-mediated transport / positive regulation of Wnt protein secretion / regulation of terminal button organization / retromer, cargo-selective complex / vesicle-mediated transport in synapse / WNT ligand biogenesis and trafficking / negative regulation of late endosome to lysosome transport / negative regulation of lysosomal protein catabolic process / positive regulation of dopamine receptor signaling pathway / positive regulation of dopamine biosynthetic process / dopaminergic synapse / mitochondrial fragmentation involved in apoptotic process / regulation of protein metabolic process / retromer complex / neurotransmitter receptor transport, endosome to postsynaptic membrane / protein localization to endosome / regulation of synapse maturation / voluntary musculoskeletal movement / transcytosis / endocytic recycling / positive regulation of protein localization to cell periphery / retrograde transport, endosome to Golgi / regulation of mitochondrion organization / positive regulation of mitochondrial fission / lysosome organization / regulation of presynapse assembly / D1 dopamine receptor binding / regulation of macroautophagy / intracellular protein transport / modulation of chemical synaptic transmission / protein destabilization / regulation of protein stability / negative regulation of inflammatory response / Wnt signaling pathway / positive regulation of canonical Wnt signaling pathway / positive regulation of protein catabolic process / late endosome / presynapse / postsynaptic density / lysosome / early endosome / endosome membrane / endosome / neuron projection / lysosomal membrane / negative regulation of gene expression / neuronal cell body / glutamatergic synapse / positive regulation of gene expression / perinuclear region of cytoplasm / extracellular exosome / cytosol
Similarity search - Function
Vacuolar protein sorting-associated protein 35 / Vacuolar protein sorting-associated protein 35, C-terminal / Vacuolar protein sorting-associated protein 35 / Armadillo-type fold
Similarity search - Domain/homology
Vacuolar protein sorting-associated protein 35
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.074 Å
AuthorsLucas, M. / Gershlick, D. / Vidaurrazaga, A. / Rojas, A.L. / Bonifacino, J.S. / Hierro, A.
Funding support Spain, 3items
OrganizationGrant numberCountry
Carlos III Health InstituteBFU2014-59759-R Spain
Basque GovernmentPI2011-26 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: PDBE / Processing site: PDBE
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2016Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Vacuolar protein sorting-associated protein 35
B: Vacuolar protein sorting-associated protein 35
C: Vacuolar protein sorting-associated protein 35
D: Vacuolar protein sorting-associated protein 35
E: Vacuolar protein sorting-associated protein 35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)268,62232
Polymers266,4415
Non-polymers2,18027
Water32418
1
A: Vacuolar protein sorting-associated protein 35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7878
Polymers53,2881
Non-polymers4987
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Vacuolar protein sorting-associated protein 35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7857
Polymers53,2881
Non-polymers4966
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Vacuolar protein sorting-associated protein 35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,6995
Polymers53,2881
Non-polymers4104
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Vacuolar protein sorting-associated protein 35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,6596
Polymers53,2881
Non-polymers3705
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Vacuolar protein sorting-associated protein 35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,6936
Polymers53,2881
Non-polymers4045
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)200.700, 108.600, 167.900
Angle α, β, γ (deg.)90.000, 125.500, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 5 molecules ABCDE

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


Mass: 53288.270 Da / Num. of mol.: 5 / 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

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Non-polymers , 5 types, 45 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O

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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: 2.8 Å3/Da / Density % sol: 56 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.6 / Details: 1.7 M AmSO4, 2% PEG 1000, 0.1 M Hepes pH 7.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97903 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 31, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97903 Å / Relative weight: 1
ReflectionNumber: 245225 / Rmerge(I) obs: 0.071 / Χ2: 2.95 / D res high: 2.79 Å / D res low: 50 Å / Num. obs: 137337 / % possible obs: 95.8
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obsIDRmerge(I) obs
12.4950144310.017
8.8312.49276710.014
7.218.83358210.018
6.257.21429610.036
5.596.25485410.044
5.15.59543310.039
4.725.1585210.037
4.424.72640610.04
4.164.42678310.044
3.954.16714710.065
3.773.95751010.095
3.613.77777110.141
3.463.61813110.207
3.343.46855210.211
3.233.34883010.313
3.123.23908210.43
3.033.12950810.591
2.943.03965610.881
2.872.941003111.184
2.792.87970311.465
ReflectionResolution: 2.95→50 Å / Num. obs: 62588 / % possible obs: 98.6 % / Redundancy: 2.3 % / Biso Wilson estimate: 53.87 Å2 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.05 / Rrim(I) all: 0.081 / Χ2: 1.042 / Net I/av σ(I): 14.61 / Net I/σ(I): 10.4 / Num. measured all: 141769
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.95-3.062.30.65662280.6970.520.8411.01298.7
3.06-3.182.20.46361910.8070.3690.5951.05898.6
3.18-3.322.20.29862450.9050.2380.3831.05998.8
3.32-3.52.30.19862540.9490.1580.2551.04298.6
3.5-3.722.20.1462410.9630.1130.1811.0398.8
3.72-42.30.09762560.9790.0780.1251.0598.9
4-4.412.30.06662580.9870.0530.0851.02598.6
4.41-5.042.30.05362790.9920.0430.0691.01598.6
5.04-6.352.30.04863180.9930.0390.0621.06298.9
6.35-502.30.02963180.9980.0240.0381.06797.4

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Processing

Software
NameVersionClassification
PHENIXrefinement
HKL-2000data collection
SCALEPACKdata scaling
PDB_EXTRACT3.15data extraction
BUCCANEERmodel building
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 3.074→47.914 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 26.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2553 2724 4.99 %RANDOM
Rwork0.2058 51828 --
obs0.2084 54552 99.53 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 187.17 Å2 / Biso mean: 63.8509 Å2 / Biso min: 5.27 Å2
Refinement stepCycle: final / Resolution: 3.074→47.914 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17455 0 312 18 17785
Biso mean--66.15 27.35 -
Num. residues----2158
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00417824
X-RAY DIFFRACTIONf_angle_d0.62524011
X-RAY DIFFRACTIONf_chiral_restr0.0372805
X-RAY DIFFRACTIONf_plane_restr0.0033038
X-RAY DIFFRACTIONf_dihedral_angle_d14.27610985
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.074-3.12990.35391380.29212485262392
3.1299-3.19010.31671400.264226982838100
3.1901-3.25520.32751190.233527532872100
3.2552-3.3260.30581110.22527562867100
3.326-3.40330.30171690.215126822851100
3.4033-3.48840.29411600.205227362896100
3.4884-3.58270.28791600.217927082868100
3.5827-3.68810.29661310.239727532884100
3.6881-3.80710.30431250.21427412866100
3.8071-3.94310.22791660.189226862852100
3.9431-4.10090.24751520.181727532905100
4.1009-4.28740.21121380.173327122850100
4.2874-4.51330.23131390.166527602899100
4.5133-4.79580.2441410.169627362877100
4.7958-5.16570.21481510.174227662917100
5.1657-5.68480.22421400.201527492889100
5.6848-6.50570.24491320.24427542886100
6.5057-8.18980.27561540.23827892943100
8.1898-47.92010.20941580.194528112969100

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