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- PDB-8rks: Structure of VPS29-VPS35 bound to the LFa motif R21 of Fam21. -

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Basic information

Entry
Database: PDB / ID: 8rks
TitleStructure of VPS29-VPS35 bound to the LFa motif R21 of Fam21.
Components
  • Vacuolar protein sorting-associated protein 29Vacuole
  • Vacuolar protein sorting-associated protein 35Vacuole
  • WASH complex subunit 2A
KeywordsTRANSPORT PROTEIN / Retromer / FAM21 / Membrane trafficking
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 / 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 / regulation of postsynapse assembly / mitochondrion-derived vesicle / negative regulation of protein localization / 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 / WASH complex / vesicle-mediated transport in synapse / WNT ligand biogenesis and trafficking / phosphatidylinositol phosphate binding / retromer complex binding / negative regulation of late endosome to lysosome transport / regulation of Arp2/3 complex-mediated actin nucleation / negative regulation of lysosomal protein catabolic process / positive regulation of dopamine receptor signaling pathway / positive regulation of dopamine biosynthetic process / mitochondrial fragmentation involved in apoptotic process / dopaminergic synapse / retromer complex / neurotransmitter receptor transport, endosome to postsynaptic membrane / protein localization to endosome / regulation of synapse maturation / voluntary musculoskeletal movement / regulation of protein metabolic process / transcytosis / endocytic recycling / positive regulation of protein localization to cell periphery / retrograde transport, endosome to Golgi / regulation of mitochondrion organization / endosomal transport / positive regulation of mitochondrial fission / lysosome organization / regulation of presynapse assembly / D1 dopamine receptor binding / regulation of macroautophagy / intracellular protein transport / protein destabilization / regulation of protein stability / modulation of chemical synaptic transmission / Wnt signaling pathway / negative regulation of inflammatory response / positive regulation of protein catabolic process / positive regulation of canonical Wnt signaling pathway / late endosome / protein transport / presynapse / early endosome membrane / 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 / nucleolus / perinuclear region of cytoplasm / extracellular exosome / metal ion binding / plasma membrane / cytosol
Similarity search - Function
FAM21/CAPZIP domain / WASH complex subunit CAP-Z interacting, central region / 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 phosphatase-like / Armadillo-type fold
Similarity search - Domain/homology
WASH complex subunit 2A / Vacuolar protein sorting-associated protein 35 / Vacuolar protein sorting-associated protein 29
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsRomano-Moreno, M. / Astorga-Simon, E.N. / Rojas, A.L. / Hierro, A.
Funding support Spain, 2items
OrganizationGrant numberCountry
Ministerio de Ciencia e Innovacion (MCIN)PID2020-119132GB-I00 Spain
Ministry of Economy and Competitiveness (MINECO)BFU2017-88766-R Spain
CitationJournal: Protein Sci. / Year: 2024
Title: Retromer-mediated recruitment of the WASH complex involves discrete interactions between VPS35, VPS29, and FAM21.
Authors: Romano-Moreno, M. / Astorga-Simon, E.N. / Rojas, A.L. / Hierro, A.
History
DepositionDec 30, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 24, 2024Provider: repository / Type: Initial release

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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 35
C: Vacuolar protein sorting-associated protein 29
D: Vacuolar protein sorting-associated protein 35
E: Vacuolar protein sorting-associated protein 29
F: Vacuolar protein sorting-associated protein 35
G: Vacuolar protein sorting-associated protein 29
H: Vacuolar protein sorting-associated protein 35
K: WASH complex subunit 2A
I: WASH complex subunit 2A
J: WASH complex subunit 2A
L: WASH complex subunit 2A


Theoretical massNumber of molelcules
Total (without water)228,62912
Polymers228,62912
Non-polymers00
Water0
1
A: Vacuolar protein sorting-associated protein 29
B: Vacuolar protein sorting-associated protein 35
K: WASH complex subunit 2A


Theoretical massNumber of molelcules
Total (without water)57,1573
Polymers57,1573
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3940 Å2
ΔGint-22 kcal/mol
Surface area21050 Å2
MethodPISA
2
C: Vacuolar protein sorting-associated protein 29
D: Vacuolar protein sorting-associated protein 35
L: WASH complex subunit 2A


Theoretical massNumber of molelcules
Total (without water)57,1573
Polymers57,1573
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4300 Å2
ΔGint-23 kcal/mol
Surface area20930 Å2
MethodPISA
3
E: Vacuolar protein sorting-associated protein 29
F: Vacuolar protein sorting-associated protein 35
I: WASH complex subunit 2A


Theoretical massNumber of molelcules
Total (without water)57,1573
Polymers57,1573
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4160 Å2
ΔGint-21 kcal/mol
Surface area21000 Å2
MethodPISA
4
G: Vacuolar protein sorting-associated protein 29
H: Vacuolar protein sorting-associated protein 35
J: WASH complex subunit 2A


Theoretical massNumber of molelcules
Total (without water)57,1573
Polymers57,1573
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4240 Å2
ΔGint-22 kcal/mol
Surface area20780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.267, 139.095, 146.147
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 20531.705 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VPS29, DC15, DC7, MDS007 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UBQ0
#2: Protein
Vacuolar protein sorting-associated protein 35 / Vacuole / hVPS35 / Maternal-embryonic 3 / Vesicle protein sorting 35


Mass: 35834.652 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VPS35, MEM3, TCCCTA00141 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96QK1
#3: Protein/peptide
WASH complex subunit 2A


Mass: 790.818 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: FAM21 Peptide / Source: (gene. exp.) Homo sapiens (human) / Gene: WASHC2A, FAM21A, FAM21B / Production host: synthetic construct (others) / References: UniProt: Q641Q2

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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: 2.64 Å3/Da / Density % sol: 53.41 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1 M NaCl, 20% PEG3350 0.1 M Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97907 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97907 Å / Relative weight: 1
ReflectionResolution: 2.972→146.15 Å / Num. obs: 31911 / % possible obs: 65.4 % / Redundancy: 7 % / Rmerge(I) obs: 0.166 / Rpim(I) all: 0.067 / Rrim(I) all: 0.18 / Net I/σ(I): 7.4
Reflection shellResolution: 2.972→3.315 Å / % possible obs: 11.7 % / Redundancy: 7 % / Rmerge(I) obs: 1.576 / Num. measured all: 11011 / Num. unique obs: 1584 / Rpim(I) all: 0.639 / Rrim(I) all: 1.703 / Net I/σ(I) obs: 1.3

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Processing

Software
NameVersionClassification
PHENIX1.19.1refinement
Aimlessdata scaling
autoPROCdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→146.15 Å / Cross valid method: THROUGHOUT / σ(F): 90.94 / Phase error: 30.54 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2877 1647 5.2 %
Rwork0.2508 --
obs0.2555 31647 73.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.1→146.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15571 0 0 0 15571
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00215895
X-RAY DIFFRACTIONf_angle_d0.52321472
X-RAY DIFFRACTIONf_dihedral_angle_d4.7072070
X-RAY DIFFRACTIONf_chiral_restr0.0412381
X-RAY DIFFRACTIONf_plane_restr0.0042784
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.20.4091260.3464457X-RAY DIFFRACTION12
3.2-3.320.4522400.3588810X-RAY DIFFRACTION21
3.32-3.450.3476680.31421255X-RAY DIFFRACTION32
3.45-3.60.28041170.28762146X-RAY DIFFRACTION55
3.6-3.790.35231680.27273179X-RAY DIFFRACTION82
3.8-4.030.3042290.26293648X-RAY DIFFRACTION93
4.03-4.340.27981550.2543711X-RAY DIFFRACTION95
4.34-4.780.27431990.23253691X-RAY DIFFRACTION94
4.78-5.470.30782060.23813679X-RAY DIFFRACTION94
5.47-6.890.28642010.24913704X-RAY DIFFRACTION94
6.9-146.150.26321890.25243769X-RAY DIFFRACTION94

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