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- PDB-8fud: Crystal structure of Vps29 in complex with Chaetomium thermophilu... -

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Basic information

Entry
Database: PDB / ID: 8fud
TitleCrystal structure of Vps29 in complex with Chaetomium thermophilum Vps5 (71 to 80)
Components
  • Putative vacuolar protein sorting-associated protein
  • Vacuolar protein sorting-associated protein 29
KeywordsPROTEIN TRANSPORT / Retromer / endosome / sorting nexin / membrane trafficking
Function / homology
Function and homology information


WNT ligand biogenesis and trafficking / retromer, cargo-selective complex / Golgi to vacuole transport / retromer complex / endocytic recycling / retrograde transport, endosome to Golgi / phosphatidylinositol binding / intracellular protein transport / endosome membrane / endosome ...WNT ligand biogenesis and trafficking / retromer, cargo-selective complex / Golgi to vacuole transport / retromer complex / endocytic recycling / retrograde transport, endosome to Golgi / phosphatidylinositol binding / intracellular protein transport / endosome membrane / endosome / identical protein binding / metal ion binding / cytosol
Similarity search - Function
Sorting nexin Vps5, BAR domain / Sorting nexin Vps5-like, C-terminal / Vps5 C terminal like / Vacuolar protein sorting-associated protein 29 / Phosphodiesterase MJ0936/Vps29 / Calcineurin-like phosphoesterase domain, lpxH-type / Calcineurin-like phosphoesterase superfamily domain / PhoX homologous domain, present in p47phox and p40phox. / PX domain profile. / PX domain ...Sorting nexin Vps5, BAR domain / Sorting nexin Vps5-like, C-terminal / Vps5 C terminal like / Vacuolar protein sorting-associated protein 29 / Phosphodiesterase MJ0936/Vps29 / Calcineurin-like phosphoesterase domain, lpxH-type / Calcineurin-like phosphoesterase superfamily domain / PhoX homologous domain, present in p47phox and p40phox. / PX domain profile. / PX domain / Phox homology / PX domain superfamily / AH/BAR domain superfamily / Metallo-dependent phosphatase-like
Similarity search - Domain/homology
PHOSPHATE ION / Putative vacuolar protein sorting-associated protein / Vacuolar protein sorting-associated protein 29
Similarity search - Component
Biological speciesMus musculus (house mouse)
Chaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsChen, K.-E. / Collins, B.
Funding support Australia, 2items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia) Australia
Australian Research Council (ARC) Australia
CitationJournal: Biorxiv / Year: 2024
Title: Molecular basis for the assembly of the Vps5-Vps17 SNX-BAR proteins with Retromer
Authors: Chen, K.E. / Tillu, V.A. / Gopaldass, N. / Chowdhury, S.R. / Leneva, N. / Kovtun, O. / Ruan, J. / Guo, Q. / Ariotti, N. / Mayer, A. / Collins, B.M.
History
DepositionJan 17, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 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 29
C: Putative vacuolar protein sorting-associated protein
D: Putative vacuolar protein sorting-associated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5028
Polymers44,1454
Non-polymers3574
Water4,576254
1
A: Vacuolar protein sorting-associated protein 29
C: Putative vacuolar protein sorting-associated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2594
Polymers22,0722
Non-polymers1872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1180 Å2
ΔGint-17 kcal/mol
Surface area8860 Å2
MethodPISA
2
B: Vacuolar protein sorting-associated protein 29
D: Putative vacuolar protein sorting-associated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2434
Polymers22,0722
Non-polymers1702
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1230 Å2
ΔGint-6 kcal/mol
Surface area9010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.051, 68.597, 211.139
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-330-

HOH

21A-370-

HOH

31A-407-

HOH

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ABCD

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


Mass: 21089.270 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Vps29 / Plasmid: pGEX4T2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9QZ88
#2: Protein/peptide Putative vacuolar protein sorting-associated protein


Mass: 983.031 Da / Num. of mol.: 2 / Fragment: residues 71-80 / Source method: obtained synthetically
Source: (synth.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
References: UniProt: G0SH11

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Non-polymers , 4 types, 258 molecules

#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#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-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 254 / 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: 2.22 Å3/Da / Density % sol: 44.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 40 mM KH2PO4, 16% PEG8000 and 5% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953644 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953644 Å / Relative weight: 1
ReflectionResolution: 1.68→42.46 Å / Num. obs: 44804 / % possible obs: 98.9 % / Redundancy: 7.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.017 / Rrim(I) all: 0.047 / Χ2: 0.51 / Net I/σ(I): 18.6 / Num. measured all: 332485
Reflection shellResolution: 1.68→1.71 Å / % possible obs: 91.4 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.301 / Num. measured all: 15268 / Num. unique obs: 2057 / CC1/2: 0.972 / Rpim(I) all: 0.116 / Rrim(I) all: 0.323 / Χ2: 0.26 / Net I/σ(I) obs: 4

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Processing

Software
NameVersionClassification
PHENIX1.19.2refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.68→41.62 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 20.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2025 2248 5.02 %
Rwork0.1769 --
obs0.1782 44766 98.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.68→41.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3050 0 21 254 3325
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093274
X-RAY DIFFRACTIONf_angle_d1.1344463
X-RAY DIFFRACTIONf_dihedral_angle_d6.57454
X-RAY DIFFRACTIONf_chiral_restr0.071504
X-RAY DIFFRACTIONf_plane_restr0.008572
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.68-1.710.29261300.23392427X-RAY DIFFRACTION92
1.71-1.750.22021370.20272644X-RAY DIFFRACTION98
1.75-1.80.24011390.18532616X-RAY DIFFRACTION98
1.8-1.850.21061390.17222590X-RAY DIFFRACTION99
1.85-1.90.22691260.17282684X-RAY DIFFRACTION99
1.9-1.960.18651320.17412624X-RAY DIFFRACTION99
1.96-2.030.20431380.18342614X-RAY DIFFRACTION99
2.03-2.110.23641480.18132659X-RAY DIFFRACTION99
2.11-2.210.21121460.17282659X-RAY DIFFRACTION99
2.21-2.330.19731330.17962672X-RAY DIFFRACTION99
2.33-2.470.22081350.18242685X-RAY DIFFRACTION99
2.47-2.660.23841380.18992684X-RAY DIFFRACTION99
2.66-2.930.21551450.19952699X-RAY DIFFRACTION99
2.93-3.360.1831460.17772715X-RAY DIFFRACTION99
3.36-4.230.18141460.15832726X-RAY DIFFRACTION100
4.23-41.620.18961700.16862820X-RAY DIFFRACTION99

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