5VNJ

Crystal structure of Sec23a/Sec24a/Sec22 complexed with a C-terminal FF sorting motif (ERGIC-53)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.223 

wwPDB Validation   3D Report Full Report


This is version 1.1 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: https://doi.org/10.7554/eLife.26624
  • Primary Citation of Related Structures:  
    5VNE, 5VNF, 5VNG, 5VNH, 5VNI, 5VNJ, 5VNK, 5VNL, 5VNM, 5VNN, 5VNO

  • 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 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
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein transport protein Sec23A764Homo sapiensMutation(s): 0 
Gene Names: SEC23A
UniProt & NIH Common Fund Data Resources
Find proteins for Q15436 (Homo sapiens)
Explore Q15436 
Go to UniProtKB:  Q15436
PHAROS:  Q15436
GTEx:  ENSG00000100934 
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UniProt GroupQ15436
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Protein transport protein Sec24A748Homo sapiensMutation(s): 0 
Gene Names: SEC24A
UniProt & NIH Common Fund Data Resources
Find proteins for O95486 (Homo sapiens)
Explore O95486 
Go to UniProtKB:  O95486
PHAROS:  O95486
GTEx:  ENSG00000113615 
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UniProt GroupO95486
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Vesicle-trafficking protein SEC22b157Mus musculusMutation(s): 0 
Gene Names: Sec22bSec22l1
UniProt & NIH Common Fund Data Resources
Find proteins for O08547 (Mus musculus)
Explore O08547 
Go to UniProtKB:  O08547
IMPC:  MGI:1338759
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UniProt GroupO08547
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  • Reference Sequence

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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
C-terminal FF Ergic-535Homo sapiensMutation(s): 0 
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.223 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 147.955α = 90
b = 96.978β = 90.22
c = 129.549γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-07-05
    Type: Initial release
  • Version 1.1: 2023-10-04
    Changes: Data collection, Database references, Refinement description