2WL8

X-ray crystal structure of Pex19p

• PDB DOI:  https://doi.org/10.2210/pdb2WL8/pdb

• Classification: PROTEIN TRANSPORT
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• Deposited: 2009-06-22 Released: 2010-06-23 
• Deposition Author(s): Schueller, N., Holton, S.J., Stanley, W.A., Song, Y.H., Konarev, P., Roessle, M., Erdmann, R., Schliebs, W., Wilmanns, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.239 
• R-Value Work: 0.199 
• R-Value Observed: 0.201 

Literature

The Peroxisomal Receptor Pex19P Forms a Helical Mpts Recognition Domain.

Schueller, N., Holton, S.J., Fodor, K., Milewski, M., Konarev, P., Stanley, W.A., Wolf, J., Erdmann, R., Schliebs, W., Song, Y.H., Wilmanns, M.

(2010) EMBO J 29: 2491

• PubMed: 20531392 
• DOI: https://doi.org/10.1038/emboj.2010.115
• Primary Citation of Related Structures:  
  2WL8


• PubMed Abstract: 
  

The protein Pex19p functions as a receptor and chaperone of peroxisomal membrane proteins (PMPs). The crystal structure of the folded C-terminal part of the receptor reveals a globular domain that displays a bundle of three long helices in an antiparallel arrangement. Complementary functional experiments, using a range of truncated Pex19p constructs, show that the structured alpha-helical domain binds PMP-targeting signal (mPTS) sequences with about 10 muM affinity. Removal of a conserved N-terminal helical segment from the mPTS recognition domain impairs the ability for mPTS binding, indicating that it forms part of the mPTS-binding site. Pex19p variants with mutations in the same sequence segment abolish correct cargo import. Our data indicate a divided N-terminal and C-terminal structural arrangement in Pex19p, which is reminiscent of a similar division in the Pex5p receptor, to allow separation of cargo-targeting signal recognition and additional functions.

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Organizational Affiliation: 

EMBL c/o DESY, Notkestrasse 85, Hamburg, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 57.47 kDa 
• Atom Count: 3,715 
• Modelled Residue Count: 432 
• Deposited Residue Count: 504 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PEROXISOMAL BIOGENESIS FACTOR 19	A, B, C, D	126	Homo sapiens	Mutation(s): 0  Gene Names: PEX19, HK33, PXF, OK/SW-cl.22 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P40855 (Homo sapiens) Explore P40855  Go to UniProtKB:  P40855
PHAROS:  P40855

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.239 
• R-Value Work: 0.199 
• R-Value Observed: 0.201 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.15	α = 90
b = 91.12	β = 90
c = 122.287	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
TRUNCATE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-06-23 
Deposition Author(s): Schueller, N., Holton, S.J., Stanley, W.A., Song, Y.H., Konarev, P., Roessle, M., Erdmann, R., Schliebs, W., Wilmanns, M.

Revision History  

• Version 1.0: 2010-06-23
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2011-09-21
  Changes: Database references
• Version 1.3: 2019-07-24
  Changes: Data collection