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- PDB-5f0m: Structure of retromer VPS26-VPS35 subunits bound to SNX3 and DMT1... -

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Basic information

Entry
Database: PDB / ID: 5f0m
TitleStructure of retromer VPS26-VPS35 subunits bound to SNX3 and DMT1 (SeMet labeled)
Components
  • (Vacuolar protein sorting-associated protein ...) x 2
  • Natural resistance-associated macrophage protein 2
  • Sorting nexin-3
KeywordsPROTEIN TRANSPORT / retromer / sorting nexin
Function / homology
Function and homology information


negative regulation of early endosome to late endosome transport / vanadium ion transmembrane transporter activity / vanadium ion transport / paraferritin complex / Defective SLC11A2 causes hypochromic microcytic anemia, with iron overload 1 (AHMIO1) / lead ion transmembrane transporter activity / lead ion transport / nickel cation transmembrane transporter activity / transition metal ion transmembrane transporter activity / late endosome to Golgi transport ...negative regulation of early endosome to late endosome transport / vanadium ion transmembrane transporter activity / vanadium ion transport / paraferritin complex / Defective SLC11A2 causes hypochromic microcytic anemia, with iron overload 1 (AHMIO1) / lead ion transmembrane transporter activity / lead ion transport / nickel cation transmembrane transporter activity / transition metal ion transmembrane transporter activity / late endosome to Golgi transport / negative regulation of protein transport / protein to membrane docking / neurotransmitter receptor transport, endosome to plasma membrane / solute:proton symporter activity / membrane invagination / negative regulation of protein localization / regulation of dendritic spine maintenance / mitochondrion-derived vesicle / : / cadmium ion transmembrane transport / negative regulation of protein homooligomerization / tubular endosome / Metal ion SLC transporters / regulation of terminal button organization / positive regulation of Wnt protein secretion / nickel cation transport / manganese ion transport / WNT ligand biogenesis and trafficking / detection of oxygen / retromer, cargo-selective complex / mitochondrion to lysosome vesicle-mediated transport / intralumenal vesicle formation / cadmium ion transmembrane transporter activity / manganese ion transmembrane transporter activity / copper ion transmembrane transporter activity / negative regulation of lysosomal protein catabolic process / positive regulation of locomotion involved in locomotory behavior / iron import into cell / cobalt ion transport / cobalt ion transmembrane transporter activity / negative regulation of late endosome to lysosome transport / retromer complex binding / positive regulation of dopamine receptor signaling pathway / positive regulation of dopamine biosynthetic process / ferrous iron transmembrane transporter activity / phosphatidylinositol-5-phosphate binding / protein localization to endosome / neurotransmitter receptor transport, endosome to postsynaptic membrane / iron ion transmembrane transporter activity / retromer complex / vesicle-mediated transport in synapse / zinc ion transmembrane transporter activity / voluntary musculoskeletal movement / mitochondrial fragmentation involved in apoptotic process / iron ion transmembrane transport / transcytosis / copper ion transport / host-mediated suppression of symbiont invasion / basal part of cell / regulation of protein metabolic process / dopaminergic synapse / early phagosome / regulation of synapse maturation / phosphatidylinositol-3-phosphate binding / endocytic recycling / vacuole / phosphatidylinositol-4-phosphate binding / regulation of mitochondrion organization / regulation of Wnt signaling pathway / retrograde transport, endosome to Golgi / phosphatidylinositol-3,5-bisphosphate binding / response to iron ion / clathrin-coated vesicle / heme biosynthetic process / negative regulation of phagocytosis / positive regulation of protein localization to cell periphery / lysosome organization / positive regulation of mitochondrial fission / dendrite morphogenesis / erythrocyte development / cadmium ion binding / regulation of postsynapse assembly / regulation of macroautophagy / D1 dopamine receptor binding / regulation of presynapse assembly / response to bacterium / intracellular protein transport / brush border membrane / iron ion transport / trans-Golgi network / Iron uptake and transport / positive regulation of neuron projection development / recycling endosome / modulation of chemical synaptic transmission / protein destabilization / negative regulation of protein catabolic process / regulation of protein stability / multicellular organismal-level iron ion homeostasis / negative regulation of inflammatory response / Wnt signaling pathway
Similarity search - Function
Vertebrate SNX3, PX domain / : / Vacuolar protein sorting protein 26 related / Vacuolar protein sorting-associated protein 26 / Vacuolar protein sorting-associated protein 35 / Vacuolar protein sorting-associated protein 35, C-terminal / Vacuolar protein sorting-associated protein 35 / NRAMP family / Natural resistance-associated macrophage protein-like / Immunoglobulin-like - #640 ...Vertebrate SNX3, PX domain / : / Vacuolar protein sorting protein 26 related / Vacuolar protein sorting-associated protein 26 / Vacuolar protein sorting-associated protein 35 / Vacuolar protein sorting-associated protein 35, C-terminal / Vacuolar protein sorting-associated protein 35 / NRAMP family / Natural resistance-associated macrophage protein-like / Immunoglobulin-like - #640 / Phox-like domain / PX Domain / PhoX homologous domain, present in p47phox and p40phox. / PX domain profile. / PX domain / Phox homology / PX domain superfamily / Arrestin-like, C-terminal / Armadillo-type fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Sorting nexin-3 / Vacuolar protein sorting-associated protein 26A / Natural resistance-associated macrophage protein 2 / Vacuolar protein sorting-associated protein 35
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsLucas, M. / Gershlick, D. / Vidaurrazaga, A. / Rojas, A.L. / Bonifacino, J.S. / Hierro, A.
Funding support Spain, 3items
OrganizationGrant numberCountry
the Carlos III Health InstitutePI11/00121 Spain
Basque GovernmentPI2011-26 Spain
Spanish Ministry of Economy and CompetitivenessBFU2014-59759-R Spain
CitationJournal: Cell / Year: 2016
Title: Structural Mechanism for Cargo Recognition by the Retromer Complex.
Authors: Lucas, M. / Gershlick, D.C. / Vidaurrazaga, A. / Rojas, A.L. / Bonifacino, J.S. / Hierro, A.
History
DepositionNov 27, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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 35
B: Vacuolar protein sorting-associated protein 26A
C: Sorting nexin-3
D: Natural resistance-associated macrophage protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,39527
Polymers112,6144
Non-polymers1,78223
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11090 Å2
ΔGint-73 kcal/mol
Surface area45710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)369.480, 74.910, 57.390
Angle α, β, γ (deg.)90.000, 97.640, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Vacuolar protein sorting-associated protein ... , 2 types, 2 molecules AB

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


Mass: 53288.270 Da / Num. of mol.: 1 / Fragment: Residues 14-470
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VPS35, MEM3, TCCCTA00141 / Plasmid: pGST-Parallel2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q96QK1
#2: Protein Vacuolar protein sorting-associated protein 26A / Vesicle protein sorting 26A / hVPS26


Mass: 37913.312 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VPS26A, VPS26 / Plasmid: pET-Sumo3 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: O75436

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Protein / Protein/peptide , 2 types, 2 molecules CD

#3: Protein Sorting nexin-3 / Protein SDP3


Mass: 19193.814 Da / Num. of mol.: 1 / Fragment: Residues 14-470
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNX3 / Plasmid: pHis-MBP-Parallel2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O60493
#4: Protein/peptide Natural resistance-associated macrophage protein 2 / NRAMP 2 / Divalent cation transporter 1 / Divalent metal transporter 1 / DMT-1 / Solute carrier ...NRAMP 2 / Divalent cation transporter 1 / Divalent metal transporter 1 / DMT-1 / Solute carrier family 11 member 2


Mass: 2218.311 Da / Num. of mol.: 1 / Fragment: UNP residues 549-560
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC11A2, DCT1, DMT1, NRAMP2, OK/SW-cl.20 / Plasmid: pET-Sumo3 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: P49281

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Non-polymers , 3 types, 23 molecules

#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2

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Details

Has protein modificationY

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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: 3.5 Å3/Da / Density % sol: 64.82 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.8 M AmSO4, 0.1 M MES pH 6.0, 5% Glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.975 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 4, 2015
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975 Å / Relative weight: 1
ReflectionResolution: 3.1→56.89 Å / Num. obs: 55451 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 79.095 Å2 / Rmerge F obs: 0.996 / Rmerge(I) obs: 0.105 / Rrim(I) all: 0.124 / Χ2: 0.999 / Net I/σ(I): 8.57 / Num. measured all: 195953
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
3.1-3.280.7090.8831.331324899189111.04399.1
3.28-3.510.890.4642.529831846684450.54899.8
3.51-3.790.9610.2564.3827523783478310.303100
3.79-4.150.9840.1487.4125359723472230.17599.8
4.15-4.640.990.09911.123123652365090.11799.8
4.64-5.350.9930.0813.4520882575957580.095100
5.35-6.530.9890.08712.8217140488248720.10399.8
6.53-9.180.9970.0520.2513323378137710.05999.7
9.180.9980.03431.177448215021310.04199.1

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Processing

Software
NameVersionClassification
XSCALEdata scaling
REFMAC5.8.0135refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5F0L

5f0l


Resolution: 3.1→56.89 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.869 / WRfactor Rfree: 0.2377 / WRfactor Rwork: 0.1906 / FOM work R set: 0.8002 / SU B: 21.512 / SU ML: 0.354 / SU Rfree: 0.4388 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.439 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2537 1361 5 %RANDOM
Rwork0.2098 ---
obs0.212 25885 95.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 198.09 Å2 / Biso mean: 83.908 Å2 / Biso min: 35.18 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20 Å2-0.36 Å2
2---0.04 Å20 Å2
3---0.02 Å2
Refinement stepCycle: final / Resolution: 3.1→56.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7436 0 108 0 7544
Biso mean--88.93 --
Num. residues----912
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0197658
X-RAY DIFFRACTIONr_bond_other_d0.0010.027495
X-RAY DIFFRACTIONr_angle_refined_deg1.1611.98710313
X-RAY DIFFRACTIONr_angle_other_deg0.852317238
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0235908
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.88224.332374
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.752151400
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6731555
X-RAY DIFFRACTIONr_chiral_restr0.0640.21167
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0218446
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021717
X-RAY DIFFRACTIONr_mcbond_it3.1398.3823644
X-RAY DIFFRACTIONr_mcbond_other3.1398.3823643
X-RAY DIFFRACTIONr_mcangle_it5.35112.5654548
LS refinement shellResolution: 3.102→3.183 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.39 42 -
Rwork0.447 839 -
all-881 -
obs--41.77 %

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