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- PDB-5osh: Structure of retromer VPS29-VPS35C subunits complexed with RidL N... -

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Basic information

Entry
Database: PDB / ID: 5osh
TitleStructure of retromer VPS29-VPS35C subunits complexed with RidL N-terminal domain (1-236)
Components
  • Interaptin
  • Vacuolar protein sorting-associated protein 29Vacuole
  • Vacuolar protein sorting-associated protein 35Vacuole
KeywordsTRANSPORT PROTEIN / Retromer / Legionella pneumophila
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 / vesicle-mediated transport in synapse / WNT ligand biogenesis and trafficking / negative regulation of late endosome to lysosome transport / 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 / protein localization to endosome / neurotransmitter receptor transport, endosome to postsynaptic membrane / 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 / lysosome organization / positive regulation of mitochondrial fission / 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 / presynapse / 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 / perinuclear region of cytoplasm / extracellular exosome / metal ion binding / cytosol
Similarity search - Function
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
: / Vacuolar protein sorting-associated protein 35 / Vacuolar protein sorting-associated protein 29
Similarity search - Component
Biological speciesHomo sapiens (human)
Legionella pneumophila subsp. pneumophila ATCC 43290 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 4.3 Å
AuthorsRomano-Moreno, M. / Rojas, A.L. / Lucas, M. / Isupov, M.N. / Hierro, A.
Funding support Spain, 3items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessBFU2014-59759-R Spain
Spanish Ministry of Economy and CompetitivenessSEV-2016-0644 Spain
iNEXTH2020 653706
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Molecular mechanism for the subversion of the retromer coat by the Legionella effector RidL.
Authors: Romano-Moreno, M. / Rojas, A.L. / Williamson, C.D. / Gershlick, D.C. / Lucas, M. / Isupov, M.N. / Bonifacino, J.S. / Machner, M.P. / Hierro, A.
History
DepositionAug 17, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 13, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jan 3, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 2, 2019Group: Data collection / Structure summary / Category: struct / Item: _struct.title
Revision 1.4May 8, 2024Group: Author supporting evidence / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization

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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: Interaptin
D: Vacuolar protein sorting-associated protein 29
E: Vacuolar protein sorting-associated protein 35
F: Interaptin
G: Vacuolar protein sorting-associated protein 29
H: Vacuolar protein sorting-associated protein 35
I: Interaptin
J: Vacuolar protein sorting-associated protein 29
K: Vacuolar protein sorting-associated protein 35
L: Interaptin


Theoretical massNumber of molelcules
Total (without water)322,49912
Polymers322,49912
Non-polymers00
Water0
1
A: Vacuolar protein sorting-associated protein 29
B: Vacuolar protein sorting-associated protein 35
C: Interaptin


Theoretical massNumber of molelcules
Total (without water)80,6253
Polymers80,6253
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Vacuolar protein sorting-associated protein 29
E: Vacuolar protein sorting-associated protein 35
F: Interaptin


Theoretical massNumber of molelcules
Total (without water)80,6253
Polymers80,6253
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
G: Vacuolar protein sorting-associated protein 29
H: Vacuolar protein sorting-associated protein 35
I: Interaptin


Theoretical massNumber of molelcules
Total (without water)80,6253
Polymers80,6253
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
J: Vacuolar protein sorting-associated protein 29
K: Vacuolar protein sorting-associated protein 35
L: Interaptin


Theoretical massNumber of molelcules
Total (without water)80,6253
Polymers80,6253
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.201, 173.243, 445.775
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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: 34459.242 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
Interaptin


Mass: 25633.861 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila ATCC 43290 (bacteria)
Gene: lp12_2303 / Production host: Escherichia coli (E. coli) / References: UniProt: G8UZ99

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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: 5.4 Å3/Da / Density % sol: 77.22 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1 M sodium chloride 0.1 M Tris pH 8.0 4-8% PEG6000.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 3→222.89 Å / Num. obs: 93761 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 6.954 % / Biso Wilson estimate: 104.762 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.094 / Rrim(I) all: 0.101 / Χ2: 1.012 / Net I/σ(I): 12.6 / Num. measured all: 651993
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
3-3.196.5462.3150.74148490.3412.51797.8
3.19-3.417.2371.0791.72142020.7661.16299.2
3.41-3.687.0910.5173.6132300.9290.55899.2
3.68-4.036.7480.2377.32121980.9820.25799.2
4.03-4.57.2230.1214.06110680.9950.12999.3
4.5-5.196.8240.07520.3297390.9980.08199.3
5.19-6.337.2610.06324.683380.9980.06799.8
6.33-8.886.8190.03537.8564660.9990.03899.5
8.88-222.896.7720.0356.1136710.9990.03298.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XSCALEdata scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 4.3→222.89 Å / Cor.coef. Fo:Fc: 0.872 / Cor.coef. Fo:Fc free: 0.84 / SU B: 69.519 / SU ML: 0.799 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.945
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3109 2460 5.1 %RANDOM
Rwork0.2537 ---
obs0.2566 46155 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 578.19 Å2 / Biso mean: 260.86 Å2 / Biso min: 92.06 Å2
Baniso -1Baniso -2Baniso -3
1--3.09 Å20 Å20 Å2
2---0.79 Å20 Å2
3---3.88 Å2
Refinement stepCycle: final / Resolution: 4.3→222.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22276 0 0 0 22276
Num. residues----2767
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01922724
X-RAY DIFFRACTIONr_bond_other_d0.0020.0221201
X-RAY DIFFRACTIONr_angle_refined_deg1.3741.96130645
X-RAY DIFFRACTIONr_angle_other_deg0.98349394
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2352754
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.34124.9331125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.834154191
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.22915116
X-RAY DIFFRACTIONr_chiral_restr0.0730.23376
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0225030
X-RAY DIFFRACTIONr_gen_planes_other0.0020.024466
LS refinement shellResolution: 4.3→4.412 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.4 179 -
Rwork0.393 3320 -
all-3499 -
obs--100 %

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