5VNM

Crystal structure of Sec23a/Sec24a/Sec22 complexed with 4-phenylbutyric acid (15mM soaking)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.765 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.268 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

ER retention is imposed by COPII protein sorting and attenuated by 4-phenylbutyrate.

Ma, W.Goldberg, E.Goldberg, J.

(2017) Elife 6: --

  • DOI: 10.7554/eLife.26624
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Native cargo proteins exit the endoplasmic reticulum (ER) in COPII-coated vesicles, whereas resident and misfolded proteins are substantially excluded from vesicles by a retention mechanism that remains unresolved. We probed the ER retention process ...

    Native cargo proteins exit the endoplasmic reticulum (ER) in COPII-coated vesicles, whereas resident and misfolded proteins are substantially excluded from vesicles by a retention mechanism that remains unresolved. We probed the ER retention process using the proteostasis regulator 4-phenylbutyrate (4-PBA), which we show targets COPII protein to reduce the stringency of retention. 4-PBA competes with p24 proteins to bind COPII. When p24 protein uptake is blocked, COPII vesicles package resident proteins and an ER-trapped mutant LDL receptor. We further show that 4-PBA triggers the secretion of a KDEL-tagged luminal resident, implying that a compromised retention mechanism causes saturation of the KDEL retrieval system. The results indicate that stringent ER retention requires the COPII coat machinery to actively sort biosynthetic cargo from diffusible misfolded and resident ER proteins.


    Organizational Affiliation

    Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein transport protein Sec23A
A
764Homo sapiensMutation(s): 0 
Gene Names: SEC23A
Find proteins for Q15436 (Homo sapiens)
Go to Gene View: SEC23A
Go to UniProtKB:  Q15436
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Protein transport protein Sec24A
B
748Homo sapiensMutation(s): 0 
Gene Names: SEC24A
Find proteins for O95486 (Homo sapiens)
Go to Gene View: SEC24A
Go to UniProtKB:  O95486
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Vesicle-trafficking protein SEC22b
C
157Mus musculusMutation(s): 0 
Gene Names: Sec22b (Sec22l1)
Find proteins for O08547 (Mus musculus)
Go to UniProtKB:  O08547
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CLT
Query on CLT

Download SDF File 
Download CCD File 
B
4-PHENYL-BUTANOIC ACID
GAMMA-PHENYL-BUTYRIC ACID
C10 H12 O2
OBKXEAXTFZPCHS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.765 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.268 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 149.183α = 90.00
b = 96.800β = 90.22
c = 130.609γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
HKL-2000data scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2017-04-30 
  • Released Date: 2017-07-05 
  • Deposition Author(s): Ma, W., Goldberg, J.

Revision History 

  • Version 1.0: 2017-07-05
    Type: Initial release