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- PDB-8tta: Structure of retromer VPS29-VPS35 (483-796) complexed with Fam21A... -

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Basic information

Entry
Database: PDB / ID: 8tta
TitleStructure of retromer VPS29-VPS35 (483-796) complexed with Fam21A repeat 21 (1328-1341)
Components
  • (Vacuolar protein sorting-associated protein ...) x 2
  • SER-ASN-ILE-PHE-ASP-ASP-PRO-LEU-ASN-ALA-PHE-GLY-GLY-GLN
KeywordsPROTEIN TRANSPORT / Vps29 / Vps35 / Fam21 / Retromer / WASH complex / Endosome / endocytosis
Function / homology
Function and homology information


WNT ligand biogenesis and trafficking / neurotransmitter receptor transport, endosome to plasma membrane / negative regulation of protein localization / regulation of dendritic spine maintenance / mitochondrion-derived vesicle / negative regulation of protein homooligomerization / tubular endosome / positive regulation of Wnt protein secretion / mitochondrion to lysosome vesicle-mediated transport / regulation of terminal button organization ...WNT ligand biogenesis and trafficking / neurotransmitter receptor transport, endosome to plasma membrane / negative regulation of protein localization / regulation of dendritic spine maintenance / mitochondrion-derived vesicle / negative regulation of protein homooligomerization / tubular endosome / positive regulation of Wnt protein secretion / mitochondrion to lysosome vesicle-mediated transport / regulation of terminal button organization / retromer, cargo-selective complex / WASH complex / vacuolar protein processing / regulation of postsynapse assembly / protein localization to organelle / positive regulation of locomotion involved in locomotory behavior / phosphatidylinositol phosphate binding / retromer complex binding / negative regulation of lysosomal protein catabolic process / negative regulation of late endosome to lysosome transport / positive regulation of dopamine biosynthetic process / positive regulation of dopamine receptor signaling pathway / regulation of Arp2/3 complex-mediated actin nucleation / vesicle-mediated transport in synapse / Golgi to vacuole transport / retromer complex / mitochondrial fragmentation involved in apoptotic process / protein localization to endosome / neurotransmitter receptor transport, endosome to postsynaptic membrane / voluntary musculoskeletal movement / dopaminergic synapse / regulation of synapse maturation / transcytosis / endocytic recycling / retrograde transport, endosome to Golgi / positive regulation of protein localization to cell periphery / endosomal transport / positive regulation of mitochondrial fission / lysosome organization / D1 dopamine receptor binding / intracellular protein transport / protein destabilization / modulation of chemical synaptic transmission / 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 / postsynapse / lysosome / postsynaptic density / early endosome / endosome membrane / endosome / neuron projection / negative regulation of gene expression / intracellular membrane-bounded organelle / neuronal cell body / glutamatergic synapse / synapse / positive regulation of gene expression / nucleolus / perinuclear region of cytoplasm / mitochondrion / membrane / metal ion binding / plasma membrane / cytosol / cytoplasm
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
ACETATE ION / DI(HYDROXYETHYL)ETHER / WASH complex subunit 2A / Vacuolar protein sorting-associated protein 35 / Vacuolar protein sorting-associated protein 29
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.46 Å
AuthorsChen, K.-E. / Guo, Q. / Collins, B.M.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP1156493 Australia
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2024
Title: Structural basis for coupling of the WASH subunit FAM21 with the endosomal SNX27-Retromer complex.
Authors: Guo, Q. / Chen, K.E. / Gimenez-Andres, M. / Jellett, A.P. / Gao, Y. / Simonetti, B. / Liu, M. / Danson, C.M. / Heesom, K.J. / Cullen, P.J. / Collins, B.M.
History
DepositionAug 13, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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: SER-ASN-ILE-PHE-ASP-ASP-PRO-LEU-ASN-ALA-PHE-GLY-GLY-GLN
F: SER-ASN-ILE-PHE-ASP-ASP-PRO-LEU-ASN-ALA-PHE-GLY-GLY-GLN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,88411
Polymers118,4296
Non-polymers4555
Water18010
1
A: Vacuolar protein sorting-associated protein 29
B: Vacuolar protein sorting-associated protein 35
E: SER-ASN-ILE-PHE-ASP-ASP-PRO-LEU-ASN-ALA-PHE-GLY-GLY-GLN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,3995
Polymers59,2143
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Vacuolar protein sorting-associated protein 29
D: Vacuolar protein sorting-associated protein 35
F: SER-ASN-ILE-PHE-ASP-ASP-PRO-LEU-ASN-ALA-PHE-GLY-GLY-GLN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,4866
Polymers59,2143
Non-polymers2713
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)123.730, 165.577, 68.000
Angle α, β, γ (deg.)90.00, 117.51, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Vacuolar protein sorting-associated protein ... , 2 types, 4 molecules ACBD

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


Mass: 21626.832 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Vps29 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q9QZ88
#2: Protein Vacuolar protein sorting-associated protein 35 / Maternal-embryonic 3 / Vesicle protein sorting 35


Mass: 36092.973 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Vps35, Mem3 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q9EQH3

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Protein/peptide , 1 types, 2 molecules EF

#3: Protein/peptide SER-ASN-ILE-PHE-ASP-ASP-PRO-LEU-ASN-ALA-PHE-GLY-GLY-GLN / WASH complex subunit 2A


Mass: 1494.562 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q641Q2

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Non-polymers , 4 types, 15 molecules

#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.73 Å3/Da / Density % sol: 54.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5
Details: 0.1 M MES pH 6.5, 0.1 M Magnesium Acetate, 10% PEG10,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 7, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 3.46→49.31 Å / Num. obs: 15793 / % possible obs: 99.3 % / Redundancy: 7 % / CC1/2: 0.993 / Rmerge(I) obs: 0.342 / Rpim(I) all: 0.139 / Rrim(I) all: 0.37 / Χ2: 0.51 / Net I/σ(I): 4.5 / Num. measured all: 110783
Reflection shellResolution: 3.46→3.79 Å / % possible obs: 97.6 % / Redundancy: 7.1 % / Rmerge(I) obs: 1.233 / Num. measured all: 26173 / Num. unique obs: 3693 / CC1/2: 0.762 / Rpim(I) all: 0.494 / Rrim(I) all: 1.33 / Χ2: 0.46 / Net I/σ(I) obs: 1.3

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.46→48.75 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2525 787 5.01 %
Rwork0.2214 --
obs0.223 15694 99.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.46→48.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7908 0 30 10 7948
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0058097
X-RAY DIFFRACTIONf_angle_d1.07510918
X-RAY DIFFRACTIONf_dihedral_angle_d5.2381065
X-RAY DIFFRACTIONf_chiral_restr0.0591200
X-RAY DIFFRACTIONf_plane_restr0.0081416
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.46-3.680.32721380.28732403X-RAY DIFFRACTION96
3.68-3.960.24421180.24422514X-RAY DIFFRACTION100
3.96-4.360.30511230.222478X-RAY DIFFRACTION100
4.36-4.990.23871350.2052490X-RAY DIFFRACTION100
4.99-6.290.26831230.22062522X-RAY DIFFRACTION100
6.29-48.750.20721500.19682500X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -38.8286 Å / Origin y: -38.4088 Å / Origin z: 15.5122 Å
111213212223313233
T0.2132 Å20.1156 Å2-0.0018 Å2-0.2329 Å2-0.1516 Å2--0.1727 Å2
L0.1806 °20.0576 °2-0.2131 °2-0.1124 °20.0083 °2--0.2061 °2
S0.0671 Å °0.2754 Å °-0.0467 Å °0.1322 Å °-0.0891 Å °-0.0672 Å °-0.012 Å °-0.3131 Å °-0.001 Å °
Refinement TLS groupSelection details: all

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