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

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Basic information

Entry
Database: PDB / ID: 9sfw
TitleStructure of Pex8 in complex with peroxisomal receptor Pex5
Components
  • Peroxisomal biogenesis factor 8
  • Peroxisomal targeting signal receptor
KeywordsPROTEIN TRANSPORT / Peroxisomal translocation receptor / HEAT Repeat
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsEkal, L. / Mullapudi, E. / Chojnowski, G. / Wilmanns, M.
Funding support Germany, 1items
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, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 2, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 2, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peroxisomal biogenesis factor 8
B: Peroxisomal targeting signal receptor


Theoretical massNumber of molelcules
Total (without water)146,2242
Polymers146,2242
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Peroxisomal biogenesis factor 8 / Peroxin-8 / Peroxisomal protein PER3


Mass: 81081.195 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Pex8 construct missing 1-33aa was used for affinity purification and subsequent experimental analysis.
Source: (gene. exp.) Komagataella pastoris (fungus) / Gene: PEX8, PER3 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Lobstr / References: UniProt: Q01962
#2: Protein Peroxisomal targeting signal receptor / PTS1 receptor / PTS1R / Peroxin-5 / Peroxisomal protein PAS8


Mass: 65143.129 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
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.
Source: (gene. exp.) Komagataella pastoris (fungus) / Gene: PEX5, PAS8 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-CodonPlus-RIL / References: UniProt: P33292
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Pex8-Pex5 Complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.143 MDa / Experimental value: NO
Source (natural)Organism: Komagataella pastoris (fungus)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMHEPESHEPES1
2150 mMNaClNaCl1
30.5 mMTCEPTCEP1
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 279 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 750 nm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 64.5 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2EPUimage acquisition
4cryoSPARCCTF correction
7MOLREP11.9.02model fitting
9cryoSPARCinitial Euler assignment
10cryoSPARCfinal Euler assignment
12cryoSPARC3D reconstruction
13Servalcat0.4.32model refinement
14UCSF ChimeraX1.6.1model refinement
15ISOLDE1.6.0model refinement
16Coot0.9.8.5model refinement
CTF correctionType: NONE
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 85869 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT
Atomic model buildingDetails: version 3 / Source name: AlphaFold / Type: in silico model
RefinementResolution: 4.5→4.5 Å / Cor.coef. Fo:Fc: 0.926 / WRfactor Rwork: 0.389 / SU B: 34.783 / SU ML: 0.349 / Average fsc free: 0 / Average fsc overall: 0.9156 / Average fsc work: 0.9156
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rwork0.389 15242 -
all0.389 --
Rfree--0 %
obs--100 %
Solvent computationSolvent model: NONE
Displacement parametersBiso mean: 459.989 Å2
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0090.0127852
ELECTRON MICROSCOPYr_bond_other_d00.0167448
ELECTRON MICROSCOPYr_angle_refined_deg1.9321.81810645
ELECTRON MICROSCOPYr_angle_other_deg0.6581.75417135
ELECTRON MICROSCOPYr_dihedral_angle_1_deg4.5195957
ELECTRON MICROSCOPYr_dihedral_angle_2_deg6.993539
ELECTRON MICROSCOPYr_dihedral_angle_3_deg11.661101377
ELECTRON MICROSCOPYr_dihedral_angle_6_deg16.53210378
ELECTRON MICROSCOPYr_chiral_restr0.0820.21205
ELECTRON MICROSCOPYr_gen_planes_refined0.0070.029183
ELECTRON MICROSCOPYr_gen_planes_other0.0010.021825
ELECTRON MICROSCOPYr_nbd_refined0.2280.21742
ELECTRON MICROSCOPYr_symmetry_nbd_other0.1720.26288
ELECTRON MICROSCOPYr_nbtor_refined0.1760.23914
ELECTRON MICROSCOPYr_symmetry_nbtor_other0.070.23913
ELECTRON MICROSCOPYr_xyhbond_nbd_refined0.1110.2169
ELECTRON MICROSCOPYr_mcbond_it89.13947.5643840
ELECTRON MICROSCOPYr_mcbond_other89.13747.5683840
ELECTRON MICROSCOPYr_mcangle_it143.6385.0994793
ELECTRON MICROSCOPYr_mcangle_other143.62785.1034794
ELECTRON MICROSCOPYr_scbond_it98.79247.2614012
ELECTRON MICROSCOPYr_scbond_other98.78247.2624013
ELECTRON MICROSCOPYr_scangle_it160.12486.3765852
ELECTRON MICROSCOPYr_scangle_other160.1186.3815853
ELECTRON MICROSCOPYr_lrange_it198.505527.97932971
ELECTRON MICROSCOPYr_lrange_other198.503527.97732972
LS refinement shell

Refine-ID: ELECTRON MICROSCOPY / Num. reflection Rfree: _ / Total num. of bins used: 20 / % reflection obs: 100 %

Resolution (Å)Rfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc workWRfactor Rwork
5.6-5.7451.71411341.71411340.7491.714
5.745-5.9030.78610410.78610410.8380.786
5.903-6.0730.52110990.52110990.9050.521
6.073-6.260.3710210.3710210.9430.37
6.26-6.4650.24910290.24910290.9680.249
6.465-6.6920.1759780.1759780.980.175
6.692-6.9440.129300.129300.9860.12
6.944-7.2270.1129050.1129050.9870.112
7.227-7.5480.1428570.1428570.9860.142
7.548-7.9150.2028550.2028550.9760.202
7.915-8.3420.2517530.2517530.9620.251
8.342-8.8470.3057600.3057600.9490.305
8.847-9.4560.3547200.3547200.9290.354
9.456-10.2110.3956290.3956290.9230.395
10.211-11.1820.4086090.4086090.9050.408
11.182-12.4950.4085440.4085440.890.408
12.495-14.4140.4384810.4384810.8390.438
14.414-17.6220.4464110.4464110.7570.446
17.622-24.7860.423160.423160.7080.42
24.786-168.640.4221700.4221700.9610.422

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