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- EMDB-16372: Structure of the peroxisomal Pex1/Pex6 ATPase complex bound to a ... -

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Basic information

Entry
Database: EMDB / ID: EMD-16372
TitleStructure of the peroxisomal Pex1/Pex6 ATPase complex bound to a substrate in single seam state
Map dataUnmasked and unmodified map generated with RELION.
Sample
  • Complex: Peroxisomal AAA ATPase complex Pex1/Pex6("single seam" state)
    • Complex: Peroxisomal AAA ATPase complex Pex1/Pex6("single seam" state)
      • Protein or peptide: Peroxisomal ATPase PEX1
      • Protein or peptide: Peroxisomal ATPase PEX6
    • Complex: Unknown peptide
      • Protein or peptide: unknown peptide
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
KeywordsAAA ATPase / peroxisomes / peroxisome biogenesis / peroxisome biogenesis disorders / Zellweger Syndrome / TRANSLOCASE
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) ...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: 4.1 Å
AuthorsRuettermann M / Koci M / Lill P / Geladas ED / Kaschani F / Klink BU / Erdmann R / Gatsogiannis C
Funding support Germany, 4 items
OrganizationGrant numberCountry
German Research Foundation (DFG)GA 2519/1-2 Germany
German Research Foundation (DFG)ER 178/7-2 Germany
German Research Foundation (DFG)INST 211/667-1 Germany
German Research Foundation (DFG)SFB 1430/1, A04 Germany
CitationJournal: Nat Commun / Year: 2023
Title: Structure of the peroxisomal Pex1/Pex6 ATPase complex bound to a substrate.
Authors: Maximilian Rüttermann / Michelle Koci / Pascal Lill / Ermis Dionysios Geladas / Farnusch Kaschani / Björn Udo Klink / Ralf Erdmann / Christos Gatsogiannis /
Abstract: The double-ring AAA+ ATPase Pex1/Pex6 is required for peroxisomal receptor recycling and is essential for peroxisome formation. Pex1/Pex6 mutations cause severe peroxisome associated developmental ...The double-ring AAA+ ATPase Pex1/Pex6 is required for peroxisomal receptor recycling and is essential for peroxisome formation. Pex1/Pex6 mutations cause severe peroxisome associated developmental disorders. Despite its pathophysiological importance, mechanistic details of the heterohexamer are not yet available. Here, we report cryoEM structures of Pex1/Pex6 from Saccharomyces cerevisiae, with an endogenous protein substrate trapped in the central pore of the catalytically active second ring (D2). Pairs of Pex1/Pex6(D2) subdomains engage the substrate via a staircase of pore-1 loops with distinct properties. The first ring (D1) is catalytically inactive but undergoes significant conformational changes resulting in alternate widening and narrowing of its pore. These events are fueled by ATP hydrolysis in the D2 ring and disengagement of a "twin-seam" Pex1/Pex6(D2) heterodimer from the staircase. Mechanical forces are propagated in a unique manner along Pex1/Pex6 interfaces that are not available in homo-oligomeric AAA-ATPases. Our structural analysis reveals the mechanisms of how Pex1 and Pex6 coordinate to achieve substrate translocation.
History
DepositionDec 19, 2022-
Header (metadata) releaseOct 4, 2023-
Map releaseOct 4, 2023-
UpdateOct 4, 2023-
Current statusOct 4, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16372.png

Downloads & links

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Map

FileDownload / File: emd_16372.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationUnmasked and unmodified map generated with RELION.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.68 Å/pix.
x 384 pix.
= 261.12 Å		0.68 Å/pix.
x 384 pix.
= 261.12 Å		0.68 Å/pix.
x 384 pix.
= 261.12 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.68 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.005
Minimum - Maximum-0.012870588 - 0.029848294
Average (Standard dev.)0.0001320825 (±0.0014757976)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 261.12 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Cryosparc NU-refined map

Fileemd_16372_additional_1.map
AnnotationCryosparc NU-refined map
Projections & Slices
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Histogram (log scale)

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Additional map: Density-modified map.

Fileemd_16372_additional_2.map
AnnotationDensity-modified map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Unmasked half map 1

Fileemd_16372_half_map_1.map
AnnotationUnmasked half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Unmasked half map 2

Fileemd_16372_half_map_2.map
AnnotationUnmasked half map 2
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : Peroxisomal AAA ATPase complex Pex1/Pex6("single seam" state)

EntireName: Peroxisomal AAA ATPase complex Pex1/Pex6("single seam" state)
Components
  • Complex: Peroxisomal AAA ATPase complex Pex1/Pex6("single seam" state)
    • Complex: Peroxisomal AAA ATPase complex Pex1/Pex6("single seam" state)
      • Protein or peptide: Peroxisomal ATPase PEX1
      • Protein or peptide: Peroxisomal ATPase PEX6
    • Complex: Unknown peptide
      • Protein or peptide: unknown peptide
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: Peroxisomal AAA ATPase complex Pex1/Pex6("single seam" state)

SupramoleculeName: Peroxisomal AAA ATPase complex Pex1/Pex6("single seam" state)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Molecular weightTheoretical: 774 KDa

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Supramolecule #2: Peroxisomal AAA ATPase complex Pex1/Pex6("single seam" state)

SupramoleculeName: Peroxisomal AAA ATPase complex Pex1/Pex6("single seam" state)
type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Supramolecule #3: Unknown peptide

SupramoleculeName: Unknown peptide / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: MH272-3f/alpha

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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: 92.758891 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: TILKNGAIQL LKKVILRSTV CKMDFPKDNL FVVYISDGAQ LPSQKGYASI VKCSLRQSKK SDSDNKSVGI PSKKIGVFIK CDSQIPENH IALSSHLWDA FFTHPMNGAK IKLEFLQMNQ ANIISGRNAT VNIKYFGKDV PTKSGDQYSK LLGGSLLTNN L ILPTEQII ...String:
TILKNGAIQL LKKVILRSTV CKMDFPKDNL FVVYISDGAQ LPSQKGYASI VKCSLRQSKK SDSDNKSVGI PSKKIGVFIK CDSQIPENH IALSSHLWDA FFTHPMNGAK IKLEFLQMNQ ANIISGRNAT VNIKYFGKDV PTKSGDQYSK LLGGSLLTNN L ILPTEQII IEIKKGESEQ QLCNLNEISN ESVQWKVTQM GKEEVKDIIE RHLPKHYHVK ETGEVSRTSK DEDDFITVNS IK KEMVNYL TSPIIATPAI ILDGKQGIGK TRLLKELINE VEKDHHIFVK YADCETLHET SNLDKTQKLI MEWCSFCYWY GPS LIVLDN VEALFGKPQA NDGDPSNNGQ WDNASKLLNF FINQVTKIFN KDNKRIRVLF SGKQKTQINP LLFDKHFVSE TWSL RAPDK HARAKLLEYF FSKNQIMKLN RDLQFSDLSL ETEGFSPLDL EIFTEKIFYD LQLERDCDNV VTRELFSKSL SAFTP SALR GVKLTKETNI KWGDIGALAN AKDVLLETLE WPTKYEPIFV NCPLRLRSGI LLYGYPGCGK TLLASAVAQQ CGLNFI SVK GPEILNKFIG ASEQNIRELF ERAQSVKPCI LFFDEFDSIA PKRGHDSTGV TDRVVNQLLT QMDGAEGLDG VYILAAT SR PDLIDSALLR PGRLDKSVIC NIPTESERLD ILQAIVNSKD KDTGQKKFAL EKNADLKLIA EKTAGFSGAD LQGLCYNA Y LKSVHRWLSA ADQSEVVPGN DNIEYFSINE HGRREENRLR LKTLLQQDVV HETKTSTSAA SELTAVVTIN DLLEACQET KPSISTSELV KLRGIYDRFQ KDR

UniProtKB: Peroxisomal ATPase PEX1

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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: 115.687094 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MKASLTFSLS GIYAPCSISR DIYLEYGDKK AECLYGTIRL PQYGPGCTPG KIVHCVLDDS LPFCSIVVPS KLFGFMPTQP TMDFCYFEP ILDNVVPVLD SVTFLINEQL YSKLMDLPQE MQQIQFLHYK YNINSMETVV HSRDILTSGL CQILNCSPFP Q GLVDFTET ...String:
MKASLTFSLS GIYAPCSISR DIYLEYGDKK AECLYGTIRL PQYGPGCTPG KIVHCVLDDS LPFCSIVVPS KLFGFMPTQP TMDFCYFEP ILDNVVPVLD SVTFLINEQL YSKLMDLPQE MQQIQFLHYK YNINSMETVV HSRDILTSGL CQILNCSPFP Q GLVDFTET QLILVNDTEQ KLSALKYANE DEEYALPKIG TNSALSIDLE SLPCTISRDL LRPAPHINDD NSIYAFTDAE TL LRLDVTS GSFITVSNMG CVRLVKLFVL LLPNGFKKRT IYAPPKIIAS FPDCSVVTIS KSNIGHTDIP IANQVFISRV GGW LQSQKC FQNIILTTLK KFFSESKRIL CQNDLIPIAF DSSMADLNIA EENDESDDED ELGQYYKNDS LVWFFVTSAE LDCF SKDNS HFIIDPNRTK LITTNITNRR PLPLSRSNLQ RYYGFAETFY YDLHIFPYVR QLVNILETSF NCSQRGITLN ASVLL HSTT NNVGKATMVR FASKYLGIHL LEIDCLSLTS NSRQLDSTSK IIGYIRAKCE NVLPYASPAV IFLAHLDSIL LDVNAN QDP EAIKLQKSIN FEMSKLLDDF TFKFPGTTFV GSVNNIDNVP SSFRSHMRFE ILVPVPSEAQ RLRIFQWYLS SHELNRD VQ QKVPVSYMDN ISFSSLSSYS AGLTPLDIKS IVETARMTAT ARFYQESKKC GWLPQSILIT QEDLSKATSK ARNEFSVS I GAPQIPNVTW DDIGGIDFVK GEILDTIDMP LKHPELFTSG MKKRSGILFY GPPGTGKTLM AKAIATNFSL NFFSVKGPE LLNMYIGESE ANVRRVFQKA REAKPCVIFF DQIDSVAPKR GNQGDSGGVM DRIVSQLLAE LDGMSTDADG VFVIGATNRP DLLDEALLR PGRFDKLLYL GIPDTDTKQL NILEALTRKF VLDNDVKLIE LAKLCPFNYT GADFYALCSD AMLNAMSRIA R MVEKKVSQ HNELTGENIS TRRWFDKIAT KEDTKVVVKM EDFLKAQEQL TPSVSRAELN HYEAVRANFE GA

UniProtKB: Peroxisomal ATPase PEX6

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Macromolecule #3: unknown peptide

MacromoleculeName: unknown peptide / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: MH272-3f/alpha
Molecular weightTheoretical: 783.958 Da
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)

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Macromolecule #4: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 10 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

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

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Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 10 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #6: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 6 / Number of copies: 2 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1.8 mg/mL
BufferpH: 7.4
GridModel: Quantifoil / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK II
Details: Grids were blotted for 3.5 sec and plunge-frozen after 1 sec drain time at 100% humidity.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 16763 / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1259079
Startup modelType of model: EMDB MAP
EMDB ID:

2585

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.4) / Number images used: 164610
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: SPHIRE (ver. 1.4)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.4)
Final 3D classificationSoftware - Name: RELION (ver. 3.1.4)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-8c0v:
Structure of the peroxisomal Pex1/Pex6 ATPase complex bound to a substrate in single seam state

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