[English] 日本語
Yorodumi
- EMDB-41788: S. cerevisiae Pex1/Pex6 with 1 mM ATP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-41788
TitleS. cerevisiae Pex1/Pex6 with 1 mM ATP
Map data
Sample
  • Complex: Pex1/Pex6 AAA-ATPase
    • Protein or peptide: Peroxisomal ATPase PEX1
    • Protein or peptide: Peroxisomal ATPase PEX6
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
KeywordsPeroxisome AAA-ATPase unfoldase / MOTOR PROTEIN
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 / cryo EM / Resolution: 3.89 Å
AuthorsGardner BM / Richardson CD / Martin A / Lander GC / Chowdhury S
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)K99GM121880 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R01NS095892 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: J Biol Chem / Year: 2024
Title: The N1 domain of the peroxisomal AAA-ATPase Pex6 is required for Pex15 binding and proper assembly with Pex1.
Authors: Bashir A Ali / Ryan M Judy / Saikat Chowdhury / Nicole K Jacobsen / Dominic T Castanzo / Kaili L Carr / Chris D Richardson / Gabriel C Lander / Andreas Martin / Brooke M Gardner /
Abstract: The heterohexameric ATPases associated with diverse cellular activities (AAA)-ATPase Pex1/Pex6 is essential for the formation and maintenance of peroxisomes. Pex1/Pex6, similar to other AAA-ATPases, ...The heterohexameric ATPases associated with diverse cellular activities (AAA)-ATPase Pex1/Pex6 is essential for the formation and maintenance of peroxisomes. Pex1/Pex6, similar to other AAA-ATPases, uses the energy from ATP hydrolysis to mechanically thread substrate proteins through its central pore, thereby unfolding them. In related AAA-ATPase motors, substrates are recruited through binding to the motor's N-terminal domains or N terminally bound cofactors. Here, we use structural and biochemical techniques to characterize the function of the N1 domain in Pex6 from budding yeast, Saccharomyces cerevisiae. We found that although Pex1/ΔN1-Pex6 is an active ATPase in vitro, it does not support Pex1/Pex6 function at the peroxisome in vivo. An X-ray crystal structure of the isolated Pex6 N1 domain shows that the Pex6 N1 domain shares the same fold as the N-terminal domains of PEX1, CDC48, and NSF, despite poor sequence conservation. Integrating this structure with a cryo-EM reconstruction of Pex1/Pex6, AlphaFold2 predictions, and biochemical assays shows that Pex6 N1 mediates binding to both the peroxisomal membrane tether Pex15 and an extended loop from the D2 ATPase domain of Pex1 that influences Pex1/Pex6 heterohexamer stability. Given the direct interactions with both Pex15 and the D2 ATPase domains, the Pex6 N1 domain is poised to coordinate binding of cofactors and substrates with Pex1/Pex6 ATPase activity.
History
DepositionAug 29, 2023-
Header (metadata) releaseDec 13, 2023-
Map releaseDec 13, 2023-
UpdateJan 10, 2024-
Current statusJan 10, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_41788.png

Downloads & links

-
Map

FileDownload / File: emd_41788.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.15 Å
Density
Contour LevelBy AUTHOR: 0.107
Minimum - Maximum-0.19697793 - 0.4874597
Average (Standard dev.)-0.0009041298 (±0.021826863)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 322.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_41788_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_41788_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Pex1/Pex6 AAA-ATPase

EntireName: Pex1/Pex6 AAA-ATPase
Components
  • Complex: Pex1/Pex6 AAA-ATPase
    • Protein or peptide: Peroxisomal ATPase PEX1
    • Protein or peptide: Peroxisomal ATPase PEX6
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

-
Supramolecule #1: Pex1/Pex6 AAA-ATPase

SupramoleculeName: Pex1/Pex6 AAA-ATPase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 637 KDa

-
Macromolecule #1: Peroxisomal ATPase PEX1

MacromoleculeName: Peroxisomal ATPase PEX1 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 118.653977 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTTTKRLKFE NLRIQFSNAI VGNFLRLPHS IINVLESTNY AIQEFGIAVH SHNSDIPIVH LGWDGHDSGS SENVVLINPV LATVYDLNQ KSPLVDLYIQ RYDHTHLATE VYVTPETSDD WEIIDANAMR FQNGEILHQT RIVTPGETLI CYLEGIVTKF K IDRVEPSM ...String:
MTTTKRLKFE NLRIQFSNAI VGNFLRLPHS IINVLESTNY AIQEFGIAVH SHNSDIPIVH LGWDGHDSGS SENVVLINPV LATVYDLNQ KSPLVDLYIQ RYDHTHLATE VYVTPETSDD WEIIDANAMR FQNGEILHQT RIVTPGETLI CYLEGIVTKF K IDRVEPSM KSARITDGSL VVVAPKVNKT RLVKAEYGHS NKTILKNGAI QLLKKVILRS TVCKMDFPKD NLFVVYISDG AQ LPSQKGY ASIVKCSLRQ SKKSDSDNKS VGIPSKKIGV FIKCDSQIPE NHIALSSHLW DAFFTHPMNG AKIKLEFLQM NQA NIISGR NATVNIKYFG KDVPTKSGDQ YSKLLGGSLL TNNLILPTEQ IIIEIKKGES EQQLCNLNEI SNESVQWKVT QMGK EEVKD IIERHLPKHY HVKETGEVSR TSKDEDDFIT VNSIKKEMVN YLTSPIIATP AIILDGKQGI GKTRLLKELI NEVEK DHHI FVKYADCETL HETSNLDKTQ KLIMEWCSFC YWYGPSLIVL DNVEALFGKP QANDGDPSNN GQWDNASKLL NFFINQ VTK IFNKDNKRIR VLFSGKQKTQ INPLLFDKHF VSETWSLRAP DKHARAKLLE YFFSKNQIMK LNRDLQFSDL SLETEGF SP LDLEIFTEKI FYDLQLERDC DNVVTRELFS KSLSAFTPSA LRGVKLTKET NIKWGDIGAL ANAKDVLLET LEWPTKYE P IFVNCPLRLR SGILLYGYPG CGKTLLASAV AQQCGLNFIS VKGPEILNKF IGASEQNIRE LFERAQSVKP CILFFDEFD SIAPKRGHDS TGVTDRVVNQ LLTQMDGAEG LDGVYILAAT SRPDLIDSAL LRPGRLDKSV ICNIPTESER LDILQAIVNS KDKDTGQKK FALEKNADLK LIAEKTAGFS GADLQGLCYN AYLKSVHRWL SAADQSEVVP GNDNIEYFSI NEHGRREENR L RLKTLLQQ DVVHETKTST SAASELTAVV TINDLLEACQ ETKPSISTSE LVKLRGIYDR FQKDRNGEMP NGENSIDIGS RL SLMGSSD YKDDDDK

UniProtKB: Peroxisomal ATPase PEX1

-
Macromolecule #2: Peroxisomal ATPase PEX6

MacromoleculeName: Peroxisomal ATPase PEX6 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 117.306758 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSSHHHHHH SQDPMKASLT FSLSGIYAPC SISRDIYLEY GDKKAECLYG TIRLPQYGPG CTPGKIVHCV LDDSLPFCSI VVPSKLFGF MPTQPTMDFC YFEPILDNVV PVLDSVTFLI NEQLYSKLMD LPQEMQQIQF LHYKYNINSM ETVVHSRDIL T SGLCQILN ...String:
MGSSHHHHHH SQDPMKASLT FSLSGIYAPC SISRDIYLEY GDKKAECLYG TIRLPQYGPG CTPGKIVHCV LDDSLPFCSI VVPSKLFGF MPTQPTMDFC YFEPILDNVV PVLDSVTFLI NEQLYSKLMD LPQEMQQIQF LHYKYNINSM ETVVHSRDIL T SGLCQILN CSPFPQGLVD FTETQLILVN DTEQKLSALK YANEDEEYAL PKIGTNSALS IDLESLPCTI SRDLLRPAPH IN DDNSIYA FTDAETLLRL DVTSGSFITV SNMGCVRLVK LFVLLLPNGF KKRTIYAPPK IIASFPDCSV VTISKSNIGH TDI PIANQV FISRVGGWLQ SQKCFQNIIL TTLKKFFSES KRILCQNDLI PIAFDSSMAD LNIAEENDES DDEDELGQYY KNDS LVWFF VTSAELDCFS KDNSHFIIDP NRTKLITTNI TNRRPLPLSR SNLQRYYGFA ETFYYDLHIF PYVRQLVNIL ETSFN CSQR GITLNASVLL HSTTNNVGKA TMVRFASKYL GIHLLEIDCL SLTSNSRQLD STSKIIGYIR AKCENVLPYA SPAVIF LAH LDSILLDVNA NQDPEAIKLQ KSINFEMSKL LDDFTFKFPG TTFVGSVNNI DNVPSSFRSH MRFEILVPVP SEAQRLR IF QWYLSSHELN RDVQQKVPVS YMDNISFSSL SSYSAGLTPL DIKSIVETAR MTATARFYQE SKKCGWLPQS ILITQEDL S KATSKARNEF SVSIGAPQIP NVTWDDIGGI DFVKGEILDT IDMPLKHPEL FTSGMKKRSG ILFYGPPGTG KTLMAKAIA TNFSLNFFSV KGPELLNMYI GESEANVRRV FQKAREAKPC VIFFDEIDSV APKRGNQGDS GGVMDRIVSQ LLAELDGMST DADGVFVIG ATNRPDLLDE ALLRPGRFDK LLYLGIPDTD TKQLNILEAL TRKFVLDNDV KLIELAKLCP FNYTGADFYA L CSDAMLNA MSRIARMVEK KVSQHNELTG ENISTRRWFD KIATKEDTKV VVKMEDFLKA QEQLTPSVSR AELNHYEAVR AN FEGA

UniProtKB: Peroxisomal ATPase PEX6

-
Macromolecule #3: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 10 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM / Adenosine triphosphate

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration3.5 mg/mL
BufferpH: 7.6
Component:
ConcentrationNameFormula
1.0 mMATPAdenosine triphosphate
60.0 mMHEPES
50.0 mMsodium chlorideNaClSodium chloride
50.0 mMpotassium chlorideKCl
10.0 mMmagnesium chlorideMgCl2
5.0 %glycerol
0.5 mMEDTAEthylenediaminetetraacetic acid
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TALOS ARCTICA
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated magnification: 43478 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 43478
TemperatureMin: 83.0 K / Max: 83.0 K
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average exposure time: 12.0 sec. / Average electron dose: 54.0 e/Å2
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

-
Image processing

Particle selectionNumber selected: 2355327
Details: Lowpass (20A) template picking of 200nm diameter particles using cryoSPARC 3.3.2.
Startup modelType of model: EMDB MAP
EMDB ID:

6359


Details: 30A lowpass filtered
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.2)
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.89 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 106005

-
Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
Output model

PDB-8u0v:
S. cerevisiae Pex1/Pex6 with 1 mM ATP

+
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