9SFW | pdb_00009sfw

Structure of Pex8 in complex with peroxisomal receptor Pex5

PDB DOI: https://doi.org/10.2210/pdb9SFW/pdb
EM Map EMD-54867: EMDB EMDataResource

Classification: PROTEIN TRANSPORT
Organism(s): Komagataella pastoris
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-08-21 Released: 2026-09-02
Deposition Author(s): Ekal, L., Mullapudi, E., Chojnowski, G., Wilmanns, M.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 4.50 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Validation slider image for 9SFW

This is version 1.0 of the entry. See complete history.

Literature

Cryo-EM structure of Pichia pastoris Pex8-Pex5 receptor complex

Ekal, L., Mullapudi, E., Chojnowski, G., WIlmanns, M.

To be published.

Macromolecule Content

Total Structure Weight: 146.22 kDa
Atom Count: 7,698
Modeled Residue Count: 961
Deposited Residue Count: 1,289
Unique protein chains: 2

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peroxisomal biogenesis factor 8	A	713	Komagataella pastoris	Mutation(s): 0 Gene Names: PEX8, PER3
UniProt
Find proteins for Q01962 (Komagataella pastoris) Explore Q01962 Go to UniProtKB: Q01962
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q01962
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Peroxisomal targeting signal receptor	B	576	Komagataella pastoris	Mutation(s): 0 Gene Names: PEX5, PAS8
UniProt
Find proteins for P33292 (Komagataella pastoris) Explore P33292 Go to UniProtKB: P33292
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P33292
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 4.50 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC
MODEL REFINEMENT	Servalcat	0.4.32
MODEL REFINEMENT	UCSF ChimeraX	1.6.1
MODEL REFINEMENT	ISOLDE	1.6.0
MODEL REFINEMENT	Coot	0.9.8.5

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-09-02

Deposition Author(s):

Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	WI 1058/9-2

Revision History (Full details and data files)

Version 1.0: 2026-09-02
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.