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

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Basic information

Entry
Database: PDB / ID: 8ttc
TitleStructure of retromer VPS29-VPS35 (483-796) complexed with Fam21A repeat 20 (1289-1302)
Components
  • (Vacuolar protein sorting-associated protein ...) x 2
  • SER-ILE-PHE-ASP-ASP-ASP-MET-ASP-ASP-ILE-PHE-SER-SER-GLY
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 / regulation of terminal button organization / positive regulation of Wnt protein secretion / mitochondrion to lysosome vesicle-mediated transport ...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 / regulation of terminal button organization / positive regulation of Wnt protein secretion / mitochondrion to lysosome vesicle-mediated transport / vacuolar protein processing / retromer, cargo-selective complex / WASH complex / Golgi to vacuole transport / protein localization to organelle / positive regulation of locomotion involved in locomotory behavior / negative regulation of lysosomal protein catabolic process / phosphatidylinositol phosphate binding / negative regulation of late endosome to lysosome transport / retromer complex binding / regulation of Arp2/3 complex-mediated actin nucleation / vesicle-mediated transport in synapse / positive regulation of dopamine biosynthetic process / mitochondrial fragmentation involved in apoptotic process / positive regulation of dopamine receptor signaling pathway / neurotransmitter receptor transport, endosome to postsynaptic membrane / protein localization to endosome / retromer complex / voluntary musculoskeletal movement / dopaminergic synapse / transcytosis / regulation of synapse maturation / endocytic recycling / retrograde transport, endosome to Golgi / positive regulation of protein localization to cell periphery / endosomal transport / lysosome organization / positive regulation of mitochondrial fission / regulation of postsynapse assembly / D1 dopamine receptor binding / modulation of chemical synaptic transmission / protein destabilization / 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 / early endosome / lysosome / postsynapse / neuron projection / postsynaptic density / endosome / endosome membrane / negative regulation of gene expression / neuronal cell body / intracellular membrane-bounded organelle / synapse / positive regulation of gene expression / nucleolus / perinuclear region of cytoplasm / glutamatergic synapse / mitochondrion / metal ion binding / membrane / 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 / CITRIC ACID / 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: 3.01 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-ILE-PHE-ASP-ASP-ASP-MET-ASP-ASP-ILE-PHE-SER-SER-GLY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,72310
Polymers115,0815
Non-polymers6425
Water30617
1
A: Vacuolar protein sorting-associated protein 29
B: Vacuolar protein sorting-associated protein 35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,3416
Polymers56,7592
Non-polymers5824
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Vacuolar protein sorting-associated protein 29
D: Vacuolar protein sorting-associated protein 35
E: SER-ILE-PHE-ASP-ASP-ASP-MET-ASP-ASP-ILE-PHE-SER-SER-GLY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,3814
Polymers58,3223
Non-polymers591
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.763, 88.763, 328.291
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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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: 20521.668 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


Mass: 36237.102 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Vps35 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9EQH3

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Protein/peptide , 1 types, 1 molecules E

#3: Protein/peptide SER-ILE-PHE-ASP-ASP-ASP-MET-ASP-ASP-ILE-PHE-SER-SER-GLY / WASH complex subunit 2A


Mass: 1563.599 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q641Q2

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Non-polymers , 5 types, 22 molecules

#4: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-ACT / ACETATE ION


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


Mass: 18.015 Da / Num. of mol.: 17 / 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: 2.81 Å3/Da / Density % sol: 56.22 % / Description: Rod shape crystal
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 0.1 M Sodium Citrate pH 4.2, 0.2 M NaCl 16% PEG1000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95365 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jun 13, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95365 Å / Relative weight: 1
ReflectionResolution: 3.01→46.9 Å / Num. obs: 27047 / % possible obs: 99.6 % / Redundancy: 12.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.137 / Rpim(I) all: 0.04 / Rrim(I) all: 0.143 / Χ2: 0.54 / Net I/σ(I): 11.7 / Num. measured all: 348827
Reflection shellResolution: 3.01→3.2 Å / % possible obs: 97.9 % / Redundancy: 13.1 % / Rmerge(I) obs: 1.588 / Num. measured all: 54935 / Num. unique obs: 4201 / CC1/2: 0.812 / Rpim(I) all: 0.451 / Rrim(I) all: 1.652 / Χ2: 0.41 / 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: 3.01→46.58 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2705 1343 4.99 %
Rwork0.2376 --
obs0.2393 26912 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.01→46.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7736 0 43 17 7796
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0057939
X-RAY DIFFRACTIONf_angle_d1.08210709
X-RAY DIFFRACTIONf_dihedral_angle_d4.7311044
X-RAY DIFFRACTIONf_chiral_restr0.061183
X-RAY DIFFRACTIONf_plane_restr0.0071384
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.01-3.120.36841360.34122397X-RAY DIFFRACTION96
3.12-3.240.36121280.34612493X-RAY DIFFRACTION100
3.25-3.390.371360.29782536X-RAY DIFFRACTION100
3.39-3.570.37361040.26532531X-RAY DIFFRACTION100
3.57-3.790.27931290.25682519X-RAY DIFFRACTION100
3.8-4.090.28291330.23942539X-RAY DIFFRACTION100
4.09-4.50.26551490.21292560X-RAY DIFFRACTION100
4.5-5.150.23161290.20582579X-RAY DIFFRACTION100
5.15-6.480.24651440.24362614X-RAY DIFFRACTION100
6.49-46.580.24171550.21392801X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 1.5377 Å / Origin y: -27.7225 Å / Origin z: -43.1348 Å
111213212223313233
T0.454 Å20.066 Å20.0036 Å2-1.0536 Å20.0149 Å2--0.6335 Å2
L-0.3308 °20.219 °2-0.3207 °2-1.0034 °2-0.1173 °2--1.7213 °2
S0.0906 Å °0.0611 Å °-0.0125 Å °0.1034 Å °-0.2619 Å °-0.014 Å °-0.0581 Å °-0.0135 Å °0.1472 Å °
Refinement TLS groupSelection details: all

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