5VNN

Crystal structure of Sec23a/Sec24a/Sec22 complexed with 4-phenylbutyric acid (50mM soaking)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.211 

wwPDB Validation   3D Report Full Report



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:  
    5VNF, 5VNE, 5VNH, 5VNG, 5VNJ, 5VNI, 5VNL, 5VNK, 5VNN, 5VNM

  • 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

    Howard Hughes Medical Institute, New York, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Protein transport protein Sec23AA764Homo sapiensMutation(s): 0 
Gene Names: SEC23A
Find proteins for Q15436 (Homo sapiens)
Explore Q15436 
Go to UniProtKB:  Q15436
NIH Common Fund Data Resources
PHAROS  Q15436
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Protein transport protein Sec24AB748Homo sapiensMutation(s): 0 
Gene Names: SEC24A
Find proteins for O95486 (Homo sapiens)
Explore O95486 
Go to UniProtKB:  O95486
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PHAROS  O95486
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Vesicle-trafficking protein SEC22bC157Mus musculusMutation(s): 0 
Gene Names: Sec22bSec22l1
Find proteins for O08547 (Mus musculus)
Explore O08547 
Go to UniProtKB:  O08547
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Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CLT
Query on CLT

Download CCD File 
B
4-PHENYL-BUTANOIC ACID
C10 H12 O2
OBKXEAXTFZPCHS-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.211 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 148.016α = 90
b = 97.715β = 89.59
c = 128.967γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2017-05-01 
  • Released Date: 2017-07-05 
  • Deposition Author(s): Ma, W., Goldberg, J.

Revision History 

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