[English] 日本語
Yorodumi
- EMDB-2583: S. cerevisiae Pex1/6 wild type complex bound to gammaS ATP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-2583
TitleS. cerevisiae Pex1/6 wild type complex bound to gammaS ATP
Map datanegative stain reconstruction of wild type Pex1/6 complex bound to gammaS ATP
Sample
  • Sample: S. cerevisiae Pex1/Pex6 wild type complex
  • Protein or peptide: peroxisomal biogenesis factor 1 (Pex1)
  • Protein or peptide: peroxisomal biogenesis factor 6 (Pex6)
KeywordsType-II AAA+ protein complex / heterohexamer / peroxisomal biogenesis
Function / homology
Function and homology information


protein import into peroxisome matrix, receptor recycling / protein import into peroxisome matrix / protein transporter activity / peroxisomal membrane / ATPase complex / protein unfolding / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / peroxisome / ATP hydrolysis activity / ATP binding / cytosol
Similarity search - Function
Peroxisome biogenesis factor 1, N-terminal, psi beta-barrel fold / : / Peroxisome biogenesis factor 1, N-terminal / CDC48 domain 2-like superfamily / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core ...Peroxisome biogenesis factor 1, N-terminal, psi beta-barrel fold / : / Peroxisome biogenesis factor 1, N-terminal / CDC48 domain 2-like superfamily / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Peroxisomal ATPase PEX1 / Peroxisomal ATPase PEX6
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / negative staining / Resolution: 21.0 Å
AuthorsCiniawsky S / Grimm I / Saffian D / Girzalsky W / Erdmann R / Wendler P
CitationJournal: Nat Commun / Year: 2015
Title: Molecular snapshots of the Pex1/6 AAA+ complex in action.
Authors: Susanne Ciniawsky / Immanuel Grimm / Delia Saffian / Wolfgang Girzalsky / Ralf Erdmann / Petra Wendler /
Abstract: The peroxisomal proteins Pex1 and Pex6 form a heterohexameric type II AAA+ ATPase complex, which fuels essential protein transport across peroxisomal membranes. Mutations in either ATPase in humans ...The peroxisomal proteins Pex1 and Pex6 form a heterohexameric type II AAA+ ATPase complex, which fuels essential protein transport across peroxisomal membranes. Mutations in either ATPase in humans can lead to severe peroxisomal disorders and early death. We present an extensive structural and biochemical analysis of the yeast Pex1/6 complex. The heterohexamer forms a trimer of Pex1/6 dimers with a triangular geometry that is atypical for AAA+ complexes. While the C-terminal nucleotide-binding domains (D2) of Pex6 constitute the main ATPase activity of the complex, both D2 harbour essential substrate-binding motifs. ATP hydrolysis results in a pumping motion of the complex, suggesting that Pex1/6 function involves substrate translocation through its central channel. Mutation of the Walker B motif in one D2 domain leads to ATP hydrolysis in the neighbouring domain, giving structural insights into inter-domain communication of these unique heterohexameric AAA+ assemblies.
History
DepositionFeb 19, 2014-
Header (metadata) releaseMar 19, 2014-
Map releaseJul 1, 2015-
UpdateJul 1, 2015-
Current statusJul 1, 2015Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.5
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD_2583.tif

Downloads & links

-
Map

FileDownload / File: emd_2583.map.gz / Format: CCP4 / Size: 15.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationnegative stain reconstruction of wild type Pex1/6 complex bound to gammaS ATP
Voxel sizeX=Y=Z: 2.9 Å
Density
Contour LevelBy AUTHOR: 0.5 / Movie #1: 0.5
Minimum - Maximum-5.24901199 - 9.90154457
Average (Standard dev.)0.01875458 (±0.34628552)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 464.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.92.92.9
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z464.000464.000464.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS160160160
D min/max/mean-5.2499.9020.019

-
Supplemental data

-
Sample components

-
Entire : S. cerevisiae Pex1/Pex6 wild type complex

EntireName: S. cerevisiae Pex1/Pex6 wild type complex
Components
  • Sample: S. cerevisiae Pex1/Pex6 wild type complex
  • Protein or peptide: peroxisomal biogenesis factor 1 (Pex1)
  • Protein or peptide: peroxisomal biogenesis factor 6 (Pex6)

-
Supramolecule #1000: S. cerevisiae Pex1/Pex6 wild type complex

SupramoleculeName: S. cerevisiae Pex1/Pex6 wild type complex / type: sample / ID: 1000
Details: heterohexamer purified and assembled in the presence of nucleotide
Oligomeric state: heterohexamer / Number unique components: 2
Molecular weightExperimental: 700 KDa / Theoretical: 700 KDa / Method: gel filtration

-
Macromolecule #1: peroxisomal biogenesis factor 1 (Pex1)

MacromoleculeName: peroxisomal biogenesis factor 1 (Pex1) / type: protein_or_peptide / ID: 1 / Name.synonym: Pas1 / Number of copies: 3 / Oligomeric state: heterohexamer / Recombinant expression: Yes
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast / Organelle: peroxisome / Location in cell: cytosol
Molecular weightExperimental: 117 KDa / Theoretical: 117 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria) / Recombinant strain: Tuner / Recombinant plasmid: pGEX-4T-2
SequenceUniProtKB: Peroxisomal ATPase PEX1

-
Macromolecule #2: peroxisomal biogenesis factor 6 (Pex6)

MacromoleculeName: peroxisomal biogenesis factor 6 (Pex6) / type: protein_or_peptide / ID: 2 / Name.synonym: Pas8 / Number of copies: 3 / Oligomeric state: heterohexamer / Recombinant expression: Yes
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast / Organelle: peroxisome / Location in cell: cytosol
Molecular weightExperimental: 116 KDa / Theoretical: 116 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria) / Recombinant strain: Tuner / Recombinant plasmid: pETDuet-1
SequenceUniProtKB: Peroxisomal ATPase PEX6

-
Experimental details

-
Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.05 mg/mL
BufferpH: 7.5
Details: 20mM Tris-HCl, 20mM NaCl, 10mM MgCl2, 2.5 mM gammaS ATP
StainingType: NEGATIVE
Details: Grid with adsorbed protein was stained with 2% uranyl acetate for 15 seconds and blotted to near dryness.
GridDetails: 400 Cu mesh continuous carbon grid
VitrificationCryogen name: NONE / Instrument: OTHER

-
Electron microscopy

MicroscopeFEI TECNAI SPIRIT
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.2 mm / Nominal defocus max: 1.0 µm / Nominal defocus min: 0.35 µm / Nominal magnification: 103448
Sample stageSpecimen holder model: SIDE ENTRY, EUCENTRIC
DateSep 26, 2011
Image recordingCategory: CCD / Film or detector model: FEI EAGLE (4k x 4k) / Digitization - Sampling interval: 30 µm / Number real images: 94 / Average electron dose: 18 e/Å2
Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company

-
Image processing

CTF correctionDetails: phase flipping of micrographs
Final two d classificationNumber classes: 500
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 21.0 Å / Resolution method: OTHER / Software - Name: MRC, IMAGIC, SPIDER / Number images used: 3895

+
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