[English] 日本語
Yorodumi
- PDB-5f0m: Structure of retromer VPS26-VPS35 subunits bound to SNX3 and DMT1... -

+
Open data


ID or keywords:

Loading...

-
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 / inorganic cation transmembrane transporter activity / regulation of dendritic spine maintenance / mitochondrion-derived vesicle / cadmium ion transmembrane transport / Metal ion SLC transporters / negative regulation of protein homooligomerization / tubular endosome / regulation of terminal button organization / positive regulation of Wnt protein secretion / manganese ion transport / nickel cation transport / mitochondrion to lysosome vesicle-mediated transport / detection of oxygen / WNT ligand biogenesis and trafficking / retromer, cargo-selective complex / intralumenal vesicle formation / cadmium ion transmembrane transporter activity / manganese ion transmembrane transporter activity / positive regulation of locomotion involved in locomotory behavior / iron import into cell / negative regulation of lysosomal protein catabolic process / copper ion transmembrane transporter activity / cobalt ion transport / cobalt ion transmembrane transporter activity / negative regulation of late endosome to lysosome transport / retromer complex binding / vesicle-mediated transport in synapse / positive regulation of dopamine biosynthetic process / mitochondrial fragmentation involved in apoptotic process / positive regulation of dopamine receptor signaling pathway / ferrous iron transmembrane transporter activity / phosphatidylinositol-5-phosphate binding / neurotransmitter receptor transport, endosome to postsynaptic membrane / protein localization to endosome / iron ion transmembrane transporter activity / retromer complex / zinc ion transmembrane transporter activity / voluntary musculoskeletal movement / iron ion transmembrane transport / copper ion transport / host-mediated suppression of symbiont invasion / basal part of cell / dopaminergic synapse / regulation of protein metabolic process / transcytosis / regulation of synapse maturation / endocytic recycling / early phagosome / phosphatidylinositol-3-phosphate binding / vacuole / regulation of Wnt signaling pathway / retrograde transport, endosome to Golgi / phosphatidylinositol-4-phosphate binding / phosphatidylinositol-3,5-bisphosphate binding / regulation of mitochondrion organization / response to iron ion / positive regulation of protein localization to cell periphery / clathrin-coated vesicle / heme biosynthetic process / dendrite morphogenesis / lysosome organization / negative regulation of phagocytosis / positive regulation of mitochondrial fission / cadmium ion binding / regulation of postsynapse assembly / regulation of presynapse assembly / regulation of macroautophagy / D1 dopamine receptor binding / erythrocyte development / intracellular protein transport / response to bacterium / trans-Golgi network / modulation of chemical synaptic transmission / Iron uptake and transport / brush border membrane / protein destabilization / regulation of protein stability / negative regulation of protein catabolic process / recycling endosome / positive regulation of neuron projection development / multicellular organismal-level iron ion homeostasis / negative regulation of inflammatory response / Wnt signaling pathway / recycling endosome membrane
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
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

-
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

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more