[English] 日本語
Yorodumi
- PDB-5f0k: Structure of VPS35 N terminal region -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5f0k
TitleStructure of VPS35 N terminal region
ComponentsVacuolar protein sorting-associated protein 35
KeywordsPROTEIN TRANSPORT / retromer / sorting nexin
Function / homology
Function and homology information


neurotransmitter receptor transport, endosome to plasma membrane / negative regulation of protein localization / regulation of dendritic spine maintenance / mitochondrion-derived vesicle / negative regulation of protein homooligomerization / tubular endosome / regulation of terminal button organization / positive regulation of Wnt protein secretion / WNT ligand biogenesis and trafficking / retromer, cargo-selective complex ...neurotransmitter receptor transport, endosome to plasma membrane / negative regulation of protein localization / regulation of dendritic spine maintenance / mitochondrion-derived vesicle / negative regulation of protein homooligomerization / tubular endosome / regulation of terminal button organization / positive regulation of Wnt protein secretion / WNT ligand biogenesis and trafficking / retromer, cargo-selective complex / mitochondrion to lysosome vesicle-mediated transport / 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 / protein localization to endosome / neurotransmitter receptor transport, endosome to postsynaptic membrane / retromer complex / vesicle-mediated transport in synapse / voluntary musculoskeletal movement / 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 / D1 dopamine receptor binding / regulation of presynapse assembly / intracellular protein transport / modulation of chemical synaptic transmission / protein destabilization / regulation of protein stability / negative regulation of inflammatory response / Wnt signaling pathway / positive regulation of protein catabolic process / positive regulation of canonical Wnt signaling pathway / late endosome / presynapse / early endosome / lysosome / neuron projection / endosome / endosome membrane / postsynaptic density / negative regulation of gene expression / lysosomal membrane / neuronal cell body / intracellular membrane-bounded organelle / positive regulation of gene expression / perinuclear region of cytoplasm / glutamatergic synapse / extracellular exosome / cytosol
Similarity search - Function
Vacuolar protein sorting-associated protein 35 / Vacuolar protein sorting-associated protein 35, C-terminal / Vacuolar protein sorting-associated protein 35 / Armadillo-type fold
Similarity search - Domain/homology
Vacuolar protein sorting-associated protein 35
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.074 Å
AuthorsLucas, M. / Gershlick, D. / Vidaurrazaga, A. / Rojas, A.L. / Bonifacino, J.S. / Hierro, A.
Funding support Spain, 3items
OrganizationGrant numberCountry
Carlos III Health InstituteBFU2014-59759-R 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: PDBE / Processing site: PDBE
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2016Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Vacuolar protein sorting-associated protein 35
B: Vacuolar protein sorting-associated protein 35
C: Vacuolar protein sorting-associated protein 35
D: Vacuolar protein sorting-associated protein 35
E: Vacuolar protein sorting-associated protein 35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)268,62232
Polymers266,4415
Non-polymers2,18027
Water32418
1
A: Vacuolar protein sorting-associated protein 35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7878
Polymers53,2881
Non-polymers4987
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Vacuolar protein sorting-associated protein 35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7857
Polymers53,2881
Non-polymers4966
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Vacuolar protein sorting-associated protein 35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,6995
Polymers53,2881
Non-polymers4104
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Vacuolar protein sorting-associated protein 35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,6596
Polymers53,2881
Non-polymers3705
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Vacuolar protein sorting-associated protein 35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,6936
Polymers53,2881
Non-polymers4045
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)200.700, 108.600, 167.900
Angle α, β, γ (deg.)90.000, 125.500, 90.000
Int Tables number5
Space group name H-MC121

-
Components

-
Protein , 1 types, 5 molecules ABCDE

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


Mass: 53288.270 Da / Num. of mol.: 5 / 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

-
Non-polymers , 5 types, 45 molecules

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


Mass: 62.068 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 56 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.6 / Details: 1.7 M AmSO4, 2% PEG 1000, 0.1 M Hepes pH 7.6

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97903 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 31, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97903 Å / Relative weight: 1
ReflectionNumber: 245225 / Rmerge(I) obs: 0.071 / Χ2: 2.95 / D res high: 2.79 Å / D res low: 50 Å / Num. obs: 137337 / % possible obs: 95.8
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obsIDRmerge(I) obs
12.4950144310.017
8.8312.49276710.014
7.218.83358210.018
6.257.21429610.036
5.596.25485410.044
5.15.59543310.039
4.725.1585210.037
4.424.72640610.04
4.164.42678310.044
3.954.16714710.065
3.773.95751010.095
3.613.77777110.141
3.463.61813110.207
3.343.46855210.211
3.233.34883010.313
3.123.23908210.43
3.033.12950810.591
2.943.03965610.881
2.872.941003111.184
2.792.87970311.465
ReflectionResolution: 2.95→50 Å / Num. obs: 62588 / % possible obs: 98.6 % / Redundancy: 2.3 % / Biso Wilson estimate: 53.87 Å2 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.05 / Rrim(I) all: 0.081 / Χ2: 1.042 / Net I/av σ(I): 14.61 / Net I/σ(I): 10.4 / Num. measured all: 141769
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.95-3.062.30.65662280.6970.520.8411.01298.7
3.06-3.182.20.46361910.8070.3690.5951.05898.6
3.18-3.322.20.29862450.9050.2380.3831.05998.8
3.32-3.52.30.19862540.9490.1580.2551.04298.6
3.5-3.722.20.1462410.9630.1130.1811.0398.8
3.72-42.30.09762560.9790.0780.1251.0598.9
4-4.412.30.06662580.9870.0530.0851.02598.6
4.41-5.042.30.05362790.9920.0430.0691.01598.6
5.04-6.352.30.04863180.9930.0390.0621.06298.9
6.35-502.30.02963180.9980.0240.0381.06797.4

-
Processing

Software
NameVersionClassification
PHENIXrefinement
HKL-2000data collection
SCALEPACKdata scaling
PDB_EXTRACT3.15data extraction
BUCCANEERmodel building
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 3.074→47.914 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 26.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2553 2724 4.99 %RANDOM
Rwork0.2058 51828 --
obs0.2084 54552 99.53 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 187.17 Å2 / Biso mean: 63.8509 Å2 / Biso min: 5.27 Å2
Refinement stepCycle: final / Resolution: 3.074→47.914 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17455 0 312 18 17785
Biso mean--66.15 27.35 -
Num. residues----2158
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00417824
X-RAY DIFFRACTIONf_angle_d0.62524011
X-RAY DIFFRACTIONf_chiral_restr0.0372805
X-RAY DIFFRACTIONf_plane_restr0.0033038
X-RAY DIFFRACTIONf_dihedral_angle_d14.27610985
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.074-3.12990.35391380.29212485262392
3.1299-3.19010.31671400.264226982838100
3.1901-3.25520.32751190.233527532872100
3.2552-3.3260.30581110.22527562867100
3.326-3.40330.30171690.215126822851100
3.4033-3.48840.29411600.205227362896100
3.4884-3.58270.28791600.217927082868100
3.5827-3.68810.29661310.239727532884100
3.6881-3.80710.30431250.21427412866100
3.8071-3.94310.22791660.189226862852100
3.9431-4.10090.24751520.181727532905100
4.1009-4.28740.21121380.173327122850100
4.2874-4.51330.23131390.166527602899100
4.5133-4.79580.2441410.169627362877100
4.7958-5.16570.21481510.174227662917100
5.1657-5.68480.22421400.201527492889100
5.6848-6.50570.24491320.24427542886100
6.5057-8.18980.27561540.23827892943100
8.1898-47.92010.20941580.194528112969100

+
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