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- PDB-8ttd: Structure of VPS29 complexed with Fam21A repeat 21 (1328-1341) -

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Basic information

Entry
Database: PDB / ID: 8ttd
TitleStructure of VPS29 complexed with Fam21A repeat 21 (1328-1341)
Components
  • SER-ASN-ILE-PHE-ASP-ASP-PRO-LEU-ASN-ALA-PHE-GLY-GLY-GLN
  • Vacuolar protein sorting-associated protein 29
KeywordsPROTEIN TRANSPORT / Vps29 / Fam21 / Retromer / WASH complex / Endosome / endocytosis
Function / homology
Function and homology information


WNT ligand biogenesis and trafficking / retromer, cargo-selective complex / Golgi to vacuole transport / WASH complex / phosphatidylinositol phosphate binding / retromer complex binding / regulation of Arp2/3 complex-mediated actin nucleation / protein localization to endosome / retromer complex / endocytic recycling ...WNT ligand biogenesis and trafficking / retromer, cargo-selective complex / Golgi to vacuole transport / WASH complex / phosphatidylinositol phosphate binding / retromer complex binding / regulation of Arp2/3 complex-mediated actin nucleation / protein localization to endosome / retromer complex / endocytic recycling / retrograde transport, endosome to Golgi / endosomal transport / protein transport / early endosome membrane / early endosome / endosome membrane / intracellular membrane-bounded organelle / nucleolus / 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 29 / Phosphodiesterase MJ0936/Vps29 / Calcineurin-like phosphoesterase domain, lpxH-type / Calcineurin-like phosphoesterase superfamily domain / Metallo-dependent phosphatase-like
Similarity search - Domain/homology
FORMIC ACID / WASH complex subunit 2A / Vacuolar protein sorting-associated protein 29
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.011 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

Downloads & links

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Assembly

Deposited unit
A: Vacuolar protein sorting-associated protein 29
B: SER-ASN-ILE-PHE-ASP-ASP-PRO-LEU-ASN-ALA-PHE-GLY-GLY-GLN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6303
Polymers22,5842
Non-polymers461
Water46826
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area640 Å2
ΔGint-6 kcal/mol
Surface area8800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.342, 43.342, 165.139
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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


Mass: 21089.270 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Vps29 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9QZ88
#2: 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.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q641Q2
#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O
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: 1.98 Å3/Da / Density % sol: 37.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2 M Magnesium Formate, 20% PEG3350

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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: Feb 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95365 Å / Relative weight: 1
ReflectionResolution: 2.01→41.28 Å / Num. obs: 12765 / % possible obs: 99.9 % / Redundancy: 18.8 % / CC1/2: 1 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.013 / Rrim(I) all: 0.053 / Χ2: 0.5 / Net I/σ(I): 25.4 / Num. measured all: 239643
Reflection shellResolution: 2.01→2.06 Å / % possible obs: 99 % / Redundancy: 19.2 % / Rmerge(I) obs: 0.475 / Num. measured all: 17499 / Num. unique obs: 911 / CC1/2: 0.972 / Rpim(I) all: 0.11 / Rrim(I) all: 0.488 / Χ2: 0.37 / Net I/σ(I) obs: 4.5

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.011→36.602 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 25.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2411 692 5.45 %
Rwork0.1842 --
obs0.1873 12700 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.011→36.602 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1492 0 3 26 1521
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071547
X-RAY DIFFRACTIONf_angle_d1.0532101
X-RAY DIFFRACTIONf_dihedral_angle_d15.726920
X-RAY DIFFRACTIONf_chiral_restr0.066239
X-RAY DIFFRACTIONf_plane_restr0.006268
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0113-2.16650.27921330.19672365X-RAY DIFFRACTION100
2.1665-2.38450.24231070.20622351X-RAY DIFFRACTION100
2.3845-2.72950.30131680.22392340X-RAY DIFFRACTION100
2.7295-3.43850.30671590.2222377X-RAY DIFFRACTION100
3.4385-36.6020.18371250.15692575X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -17.9833 Å / Origin y: -3.7482 Å / Origin z: -13.9535 Å
111213212223313233
T0.3495 Å20.1531 Å20.026 Å2-0.3122 Å2-0.0182 Å2--0.2876 Å2
L3.3029 °2-0.3953 °20.3125 °2-4.5921 °20.9787 °2--6.3965 °2
S-0.1187 Å °-0.2009 Å °0.0291 Å °0.3565 Å °-0.0919 Å °0.1828 Å °0.16 Å °-0.0356 Å °0.1536 Å °
Refinement TLS groupSelection details: all

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