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- PDB-5osi: Structure of retromer VPS29-VPS35C subunits complexed with RidL h... -

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Basic information

Entry
Database: PDB / ID: 5osi
TitleStructure of retromer VPS29-VPS35C subunits complexed with RidL harpin loop (163-176)
Components
  • (Vacuolar protein sorting-associated protein ...) x 2
  • Interaptin
KeywordsTRANSPORT PROTEIN / Retromer / Legionella pneumophila
Function / homology
Function and homology information


neurotransmitter receptor transport, endosome to plasma membrane / negative regulation of protein localization / mitochondrion-derived vesicle / regulation of dendritic spine maintenance / negative regulation of protein homooligomerization / tubular endosome / regulation of terminal button organization / positive regulation of Wnt protein secretion / retromer, cargo-selective complex / mitochondrion to lysosome vesicle-mediated transport ...neurotransmitter receptor transport, endosome to plasma membrane / negative regulation of protein localization / mitochondrion-derived vesicle / regulation of dendritic spine maintenance / negative regulation of protein homooligomerization / tubular endosome / regulation of terminal button organization / positive regulation of Wnt protein secretion / retromer, cargo-selective complex / mitochondrion to lysosome vesicle-mediated transport / WNT ligand biogenesis and trafficking / negative regulation of lysosomal protein catabolic process / positive regulation of locomotion involved in locomotory behavior / negative regulation of late endosome to lysosome transport / positive regulation of dopamine receptor signaling pathway / positive regulation of dopamine biosynthetic process / neurotransmitter receptor transport, endosome to postsynaptic membrane / protein localization to endosome / vesicle-mediated transport in synapse / voluntary musculoskeletal movement / retromer complex / mitochondrial fragmentation involved in apoptotic process / transcytosis / regulation of protein metabolic process / dopaminergic synapse / regulation of synapse maturation / endocytic recycling / regulation of mitochondrion organization / retrograde transport, endosome to Golgi / positive regulation of protein localization to cell periphery / lysosome organization / positive regulation of mitochondrial fission / regulation of postsynapse assembly / regulation of macroautophagy / regulation of presynapse assembly / D1 dopamine receptor binding / intracellular protein transport / protein destabilization / modulation of chemical synaptic transmission / regulation of protein stability / negative regulation of inflammatory response / Wnt signaling pathway / positive regulation of protein catabolic process / late endosome / positive regulation of canonical Wnt signaling pathway / presynapse / early endosome / lysosome / endosome / neuron projection / endosome membrane / postsynaptic density / negative regulation of gene expression / lysosomal membrane / intracellular membrane-bounded organelle / neuronal cell body / positive regulation of gene expression / perinuclear region of cytoplasm / glutamatergic synapse / extracellular exosome / metal ion binding / cytosol
Similarity search - Function
Vacuolar protein sorting-associated protein 35, helical subcomplex Vps35-C / 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 phosphatases / Purple Acid Phosphatase; chain A, domain 2 ...Vacuolar protein sorting-associated protein 35, helical subcomplex Vps35-C / 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 phosphatases / Purple Acid Phosphatase; chain A, domain 2 / Metallo-dependent phosphatase-like / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / 4-Layer Sandwich / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / Interaptin / 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 / MOLECULAR REPLACEMENT / Resolution: 2.52 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 9, 2019Group: Data collection / Structure summary / Category: struct / Item: _struct.title
Revision 1.4Jan 17, 2024Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / pdbx_initial_refinement_model
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)231,04926
Polymers230,27411
Non-polymers77515
Water4,071226
1
A: Vacuolar protein sorting-associated protein 29
B: Vacuolar protein sorting-associated protein 35
C: Interaptin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,0935
Polymers57,9693
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Vacuolar protein sorting-associated protein 29
E: Vacuolar protein sorting-associated protein 35
F: Interaptin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,1166
Polymers57,9693
Non-polymers1473
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
G: Vacuolar protein sorting-associated protein 29
H: Vacuolar protein sorting-associated protein 35
I: Interaptin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,1166
Polymers57,9693
Non-polymers1473
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
J: Vacuolar protein sorting-associated protein 29
K: Vacuolar protein sorting-associated protein 35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,7239
Polymers56,3662
Non-polymers3567
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.554, 138.993, 126.637
Angle α, β, γ (deg.)90.000, 92.780, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Vacuolar protein sorting-associated protein ... , 2 types, 8 molecules ADGJBEHK

#1: Protein
Vacuolar protein sorting-associated protein 29 / 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 / hVPS35 / Maternal-embryonic 3 / Vesicle protein sorting 35


Mass: 35834.652 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

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Protein/peptide , 1 types, 3 molecules CFI

#3: Protein/peptide Interaptin


Mass: 1602.824 Da / Num. of mol.: 3 / Fragment: UNP residues 163-176
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, UniProt: Q5ZT54*PLUS

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Non-polymers , 3 types, 241 molecules

#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / Source method: isolated from a natural source / Formula: H2O

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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: 2.24 Å3/Da / Density % sol: 44.97 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1 M NaCl, 20% PEG3350 0.1 M Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97907 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97907 Å / Relative weight: 1
ReflectionResolution: 2.52→126.49 Å / Num. obs: 68126 / % possible obs: 99.8 % / Redundancy: 6.2 % / Biso Wilson estimate: 39.897 Å2 / Rpim(I) all: 0.062 / Rrim(I) all: 0.155 / Net I/σ(I): 8.5 / Num. measured all: 425544
Reflection shell

Diffraction-ID: 1 / Redundancy: 6.1 %

Resolution (Å)Mean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) all% possible all
2.52-2.561.933990.4551.13499.7
6.84-126.6520.335060.0230.057100

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Processing

Software
NameVersionClassification
xia2data scaling
REFMAC5.8.0158refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2R17

2r17


Resolution: 2.52→126.49 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.888 / SU B: 13.251 / SU ML: 0.279 / SU R Cruickshank DPI: 2.3903 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 2.39 / ESU R Free: 0.341
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2668 3452 5.1 %RANDOM
Rwork0.2048 ---
obs0.2079 64447 99.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 121.99 Å2 / Biso mean: 52.082 Å2 / Biso min: 15.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.94 Å20 Å20.26 Å2
2---0.8 Å20 Å2
3----0.16 Å2
Refinement stepCycle: final / Resolution: 2.52→126.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15612 0 48 226 15886
Biso mean--61.45 40.14 -
Num. residues----1940
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01916014
X-RAY DIFFRACTIONr_bond_other_d0.0010.0214994
X-RAY DIFFRACTIONr_angle_refined_deg1.2441.9621618
X-RAY DIFFRACTIONr_angle_other_deg0.91334870
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.73451937
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.39324.621779
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.64152890
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7021581
X-RAY DIFFRACTIONr_chiral_restr0.0690.22398
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02117613
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023184
LS refinement shellResolution: 2.52→2.585 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 253 -
Rwork0.309 4721 -
all-4974 -
obs--98.89 %

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