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- PDB-2r17: Functional architecture of the retromer cargo-recognition complex -

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Basic information

Entry
Database: PDB / ID: 2r17
TitleFunctional architecture of the retromer cargo-recognition complex
Components
  • Vacuolar protein sorting-associated protein 29
  • Vacuolar protein sorting-associated protein 35
KeywordsPROTEIN TRANSPORT / Membrane / Phosphorylation
Function / homology
Function and homology information


positive regulation of locomotion involved in locomotory behavior / neurotransmitter receptor transport, endosome to plasma membrane / regulation of postsynapse assembly / mitochondrion-derived vesicle / negative regulation of protein localization / regulation of dendritic spine maintenance / negative regulation of protein homooligomerization / 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 / regulation of postsynapse assembly / mitochondrion-derived vesicle / negative regulation of protein localization / regulation of dendritic spine maintenance / negative regulation of protein homooligomerization / 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 / retromer complex / mitochondrial fragmentation involved in apoptotic process / protein localization to endosome / dopaminergic synapse / neurotransmitter receptor transport, endosome to postsynaptic membrane / regulation of synapse maturation / voluntary musculoskeletal movement / regulation of protein metabolic process / transcytosis / endocytic recycling / retrograde transport, endosome to Golgi / positive regulation of protein localization to cell periphery / 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 / protein destabilization / modulation of chemical synaptic transmission / regulation of protein stability / Wnt signaling pathway / negative regulation of inflammatory response / positive regulation of protein catabolic process / positive regulation of canonical Wnt signaling pathway / late endosome / presynapse / postsynaptic density / lysosome / early endosome / endosome membrane / endosome / neuron projection / lysosomal membrane / negative regulation of gene expression / intracellular membrane-bounded organelle / neuronal cell body / glutamatergic synapse / positive regulation of gene expression / perinuclear region of cytoplasm / extracellular exosome / metal ion binding / cytosol
Similarity search - Function
Vacuolar protein sorting-associated protein 35, helical subcomplex Vps35-C / Vacuolar protein sorting-associated protein 35 / Vacuolar protein sorting-associated protein 35, C-terminal / Vacuolar protein sorting-associated protein 35 / Vacuolar protein sorting-associated protein 29 / Phosphodiesterase MJ0936/Vps29 / Calcineurin-like phosphoesterase domain, lpxH-type / Calcineurin-like phosphoesterase superfamily domain / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 ...Vacuolar protein sorting-associated protein 35, helical subcomplex Vps35-C / Vacuolar protein sorting-associated protein 35 / Vacuolar protein sorting-associated protein 35, C-terminal / Vacuolar protein sorting-associated protein 35 / Vacuolar protein sorting-associated protein 29 / Phosphodiesterase MJ0936/Vps29 / Calcineurin-like phosphoesterase domain, lpxH-type / Calcineurin-like phosphoesterase superfamily domain / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 / Metallo-dependent phosphatase-like / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / 4-Layer Sandwich / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Vacuolar protein sorting-associated protein 35 / Vacuolar protein sorting-associated protein 29
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsHierro, A. / Rojas, A.L. / Rojas, R. / Murthy, N. / Effantin, G. / Kajava, A.V. / Steven, A.C. / Bonifacino, J.S. / Hurley, J.H.
CitationJournal: Nature / Year: 2007
Title: Functional architecture of the retromer cargo-recognition complex.
Authors: Hierro, A. / Rojas, A.L. / Rojas, R. / Murthy, N. / Effantin, G. / Kajava, A.V. / Steven, A.C. / Bonifacino, J.S. / Hurley, J.H.
History
DepositionAug 22, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software

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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 29
B: Vacuolar protein sorting-associated protein 29
C: Vacuolar protein sorting-associated protein 35
D: Vacuolar protein sorting-associated protein 35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,9216
Polymers110,7364
Non-polymers1842
Water88349
1
A: Vacuolar protein sorting-associated protein 29
C: Vacuolar protein sorting-associated protein 35


Theoretical massNumber of molelcules
Total (without water)55,3682
Polymers55,3682
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3250 Å2
MethodPISA
2
B: Vacuolar protein sorting-associated protein 29
D: Vacuolar protein sorting-associated protein 35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,5524
Polymers55,3682
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.250, 128.471, 140.452
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological unit is a dimer. There are 2 biological units in the asymmetric unit (chains A & C and chains B & D)

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Components

#1: Protein Vacuolar protein sorting-associated protein 29 / Vesicle protein sorting 29 / hVPS29 / PEP11


Mass: 20850.480 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VPS29 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9UBQ0
#2: Protein Vacuolar protein sorting-associated protein 35 / Vesicle protein sorting 35 / hVPS35 / Maternal-embryonic 3


Mass: 34517.703 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VPS35, MEM3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q96QK1
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 2.7 Å3/Da / Density % sol: 54.43 %
Crystal growTemperature: 291 K / Method: hanging drop / pH: 8
Details: 20% PEG 3350, 1M NaCl,50mM Tris, pH 8.0, hanging drop, temperature 291K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97926 Å
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 29916 / % possible obs: 98.8 % / Redundancy: 13.5 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 11
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.8-2.99.80.332191.7
2.9-3.0211.70.285198
3.02-3.1512.90.226199.4
3.15-3.3214.10.181199.6
3.32-3.5314.50.139199.7
3.53-3.814.60.101199.7
3.8-4.1814.60.081199.9
4.18-4.7914.40.073199.9
4.79-6.0314.30.076199.9
6.03-5013.40.071199.8

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
PDB_EXTRACT3data extraction
HKL-2000data collection
RefinementMethod to determine structure: SAD / Resolution: 2.8→50 Å
RfactorNum. reflection% reflection
Rfree0.268 1390 4.6 %
Rwork0.216 --
obs0.216 27869 92.1 %
Solvent computationBsol: 25.75 Å2
Displacement parametersBiso mean: 54.73 Å2
Baniso -1Baniso -2Baniso -3
1--23.696 Å20 Å20 Å2
2--12.032 Å20 Å2
3---11.664 Å2
Refinement stepCycle: LAST / Resolution: 2.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7579 0 12 49 7640
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.5071.5
X-RAY DIFFRACTIONc_mcangle_it2.6372
X-RAY DIFFRACTIONc_scbond_it2.212
X-RAY DIFFRACTIONc_scangle_it3.3762.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:PROTEIN_REP.PARAMCNS_TOPPAR:PROTEIN.TOP
X-RAY DIFFRACTION2CNS_TOPPAR:WATER_REP.PARAMCNS_TOPPAR:DNA-RNA.TOP
X-RAY DIFFRACTION3GOL.PARAMCNS_TOPPAR:WATER.TOP
X-RAY DIFFRACTION4CNS_TOPPAR:ION.TOP
X-RAY DIFFRACTION5GOL.TOP

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