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- EMDB-54867: Structure of Pex8 in complex with peroxisomal receptor Pex5 -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-54867
TitleStructure of Pex8 in complex with peroxisomal receptor Pex5
Map data
Sample
  • Complex: Pex8-Pex5 Complex
    • Protein or peptide: Peroxisomal biogenesis factor 8
    • Protein or peptide: Peroxisomal targeting signal receptor
KeywordsPeroxisomal translocation receptor / HEAT Repeat / PROTEIN TRANSPORT
Function / homology
Function and homology information


peroxisome matrix targeting signal-1 binding / protein import into peroxisome matrix, docking / peroxisomal membrane / peroxisomal matrix / cytosol
Similarity search - Function
: / : / Peroxin 8 protein-like, N-terminal domain / PEX8 C-terminal domain / PEX8 helical domain / PEX8 central TPR-like domain / PEX5/PEX5L / Tetratricopeptide repeat / Tetratricopeptide repeat / Tetratricopeptide repeat ...: / : / Peroxin 8 protein-like, N-terminal domain / PEX8 C-terminal domain / PEX8 helical domain / PEX8 central TPR-like domain / PEX5/PEX5L / Tetratricopeptide repeat / Tetratricopeptide repeat / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
Peroxisomal targeting signal receptor / Peroxisomal biogenesis factor 8
Similarity search - Component
Biological speciesKomagataella pastoris (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsEkal L / Mullapudi E / Chojnowski G / Wilmanns M
Funding support Germany, 1 items
OrganizationGrant numberCountry
German Research Foundation (DFG)WI 1058/9-2 Germany
CitationJournal: To Be Published
Title: Cryo-EM structure of Pichia pastoris Pex8-Pex5 receptor complex
Authors: Ekal L / Mullapudi E / Chojnowski G / WIlmanns M
History
DepositionAug 21, 2025-
Header (metadata) releaseSep 2, 2026-
Map releaseSep 2, 2026-
UpdateSep 2, 2026-
Current statusSep 2, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54867.png

Downloads & links

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Map

FileDownload / File: emd_54867.map.gz / Format: CCP4 / Size: 54.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.36 Å/pix.
x 242 pix.
= 329.12 Å		1.36 Å/pix.
x 242 pix.
= 329.12 Å		1.36 Å/pix.
x 242 pix.
= 329.12 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.36 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.41741168 - 1.2518618
Average (Standard dev.)-0.0005422754 (±0.0225411)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions242242242
Spacing242242242
CellA=B=C: 329.12 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_54867_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_54867_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Pex8-Pex5 Complex

EntireName: Pex8-Pex5 Complex
Components
  • Complex: Pex8-Pex5 Complex
    • Protein or peptide: Peroxisomal biogenesis factor 8
    • Protein or peptide: Peroxisomal targeting signal receptor

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Supramolecule #1: Pex8-Pex5 Complex

SupramoleculeName: Pex8-Pex5 Complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Komagataella pastoris (fungus)
Molecular weightTheoretical: 143 KDa

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Macromolecule #1: Peroxisomal biogenesis factor 8

MacromoleculeName: Peroxisomal biogenesis factor 8 / type: protein_or_peptide / ID: 1
Details: Pex8 construct missing 1-33aa was used for affinity purification and subsequent experimental analysis.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Komagataella pastoris (fungus)
Molecular weightTheoretical: 81.081195 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MYRLGSQGRS IQSQLQNGDS SSGRPLQLQG TGMREAQRIP QQLDYLLAEI ISPNEDTNVI GYLAYYYPKL KNEQNVALLT DFFLRCPTY FSHSNVVSLR NNYPVMEAFN YIMTTKFKVS QPTVPFYRFY AAVLASLLNC EKTDPSHHWK LIPILTGVLL S IKGRDDVE ...String:
MYRLGSQGRS IQSQLQNGDS SSGRPLQLQG TGMREAQRIP QQLDYLLAEI ISPNEDTNVI GYLAYYYPKL KNEQNVALLT DFFLRCPTY FSHSNVVSLR NNYPVMEAFN YIMTTKFKVS QPTVPFYRFY AAVLASLLNC EKTDPSHHWK LIPILTGVLL S IKGRDDVE LYPDHSRSIK GSDTAVAQLL QRCLLRFYQS GDARSYDLNA LVIISMSCAL DYVEDDTIKK ILYCFNYTRA II DLIYYSP YGLNDSDIPL LSDSSVNSQS FDQLLNNNPA LKHLNRLSFL FERTVKLNDG SIQSNLNDID ISLNKMQSFS EKL SKKISV LDDDSSKGVG QLLRQCLYAS IIIHQAILTT FFQLDNADYT KYFLPSFSRK ILSILFNLFF IVDRIGTGGF QPYN FVYLT CLQGIIQYDM KTAESLVKTF TTGINYSSLK DSEVARAKLL FTLNLMEQIV NICSDDLRLE LIVPLVEDLV NNKNA CVDI HNHVFKSIFE SAHSVILKFF TVVDSSVKNV DYETNVTLVS EKIIPYLTLV IDQFPEFLSI NQLDIAIETI SRTVFP DSP IYSYDKNISS MFLNVLFNKC LTVDNDELVE LPAIEAVVAP KNDEENNTSD AQDGGPKELQ SLNDLKSRRS ALISALI SV FPLIPVKDYT KWLSIAFYDL IVATPERTER AFLQERLWDC VVGTNKYDPQ KGNLGIMWWY ENVNAQSTAK L

UniProtKB: Peroxisomal biogenesis factor 8

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Macromolecule #2: Peroxisomal targeting signal receptor

MacromoleculeName: Peroxisomal targeting signal receptor / type: protein_or_peptide / ID: 2
Details: The mismatch highlighted in the alignment is due to a small peptide in the structure, spanning residues 54-66, which is aligning incorrectly at the region starting with residue 243 in the sample sequence.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Komagataella pastoris (fungus)
Molecular weightTheoretical: 65.143129 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MSLIGGGSDC AAGSNPLAQF TKHTQHDTSL QQSMRNGEFQ QGNQRMMRNE STMSPMERQQ MDQFMQQQNN PAFNFQPMQH ELNVMQQNM NAPQQVANNS WNQEFRMKDP MVANAPSAQV QTPVQSTNWA QDFQQAGPEV QHHAQQHQHP ILSVPGVRAG I YGGGRLMG ...String:
MSLIGGGSDC AAGSNPLAQF TKHTQHDTSL QQSMRNGEFQ QGNQRMMRNE STMSPMERQQ MDQFMQQQNN PAFNFQPMQH ELNVMQQNM NAPQQVANNS WNQEFRMKDP MVANAPSAQV QTPVQSTNWA QDFQQAGPEV QHHAQQHQHP ILSVPGVRAG I YGGGRLMG GSMMNRAAQM QQQNPAQAQT SEQSQTQWED QFKDIESMLN SKTQEPKTKQ QEQNTFEQVW DDIQVSYADV EL TNDQFQA QWEKDFAQYA EGRLNYGEYK YEEKNQFRND PDAYEIGMRL MESGAKLSEA GLAFEAAVQQ DPKHVDAWLK LGE VQTQNE KESDGIAALE KCLELDPTNL AALMTLAISY INDGYDNAAY ATLERWIETK YPDIASRARS SNPDLDGGDR IEQN KRVTE LFMKAAQLSP DVASMDADVQ TGLGVLFYSM EEFDKTIDCF KAAIEVEPDK ALNWNRLGAA LANYNKPEEA VEAYS RALQ LNPNFVRARY NLGVSFINMG RYKEAVEHLL TGISLHEVEG VDASEMSSNQ GLQNNALVET LKRAFLGMNR RDLVDK VYP GMGLAQFRKM FDF

UniProtKB: Peroxisomal targeting signal receptor

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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

Concentration1.0 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
50.0 mMHEPESHEPES
150.0 mMNaClNaCl
0.5 mMTCEPTCEP
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 90 sec.
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 279 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 64.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.75 µm / Nominal magnification: 130000
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

CTF correctionSoftware - Name: cryoSPARC / Type: NONE
Startup modelType of model: INSILICO MODEL
In silico model: Pex8-Pex5 complex structure prediction with AlphaFold 3
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 85869
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model / Details: version 3
RefinementProtocol: RIGID BODY FIT
Output model

PDB-9sfw:
Structure of Pex8 in complex with peroxisomal receptor Pex5

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