Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Pseudo Symmetry: Cyclic - C2  (3D View)
Pseudo Stoichiometry: Homo 2-mer - A2 Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content

• Total Structure Weight: 173.75 kDa 
• Atom Count: 11927 
• Residue Count: 1490 
• Unique protein chains: 3

3EFO

Crystal Structure of the mammalian COPII-coat protein Sec23/24 bound to the transport signal sequence of syntaxin 5

• DOI: 10.2210/pdb3EFO/pdb

• Classification: PROTEIN TRANSPORT
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2008-09-09 Released: 2008-10-21 
• Deposition Author(s): Goldberg, J., Mancias, J.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.261 
• R-Value Work: 0.211 

Literature

Structural basis of cargo membrane protein discrimination by the human COPII coat machinery.

Mancias, J.D., Goldberg, J.

(2008) EMBO J 27: 2918-2928

• PubMed: 18843296 
• DOI: 10.1038/emboj.2008.208
• Primary Citation of Related Structures:  
  3EFO, 3EH1, 3EH2, 3EGD, 3EG9, 3EGX


• PubMed Abstract: 
  

Genomic analysis shows that the increased complexity of trafficking pathways in mammalian cells involves an expansion of the number of SNARE, Rab and COP proteins. Thus, the human genome encodes four forms of Sec24, the cargo selection subunit of the COPII vesicular coat, and this is proposed to increase the range of cargo accommodated by human COPII-coated vesicles. In this study, we combined X-ray crystallographic and biochemical analysis with functional assays of cargo packaging into COPII vesicles to establish molecular mechanisms for cargo discrimination by human Sec24 subunits. A conserved IxM packaging signal binds in a surface groove of Sec24c and Sec24d, but the groove is occluded in the Sec24a and Sec24b subunits. Conversely, LxxLE class transport signals and the DxE signal of VSV glycoprotein are selectively bound by Sec24a and Sec24b subunits. A comparative analysis of crystal structures of the four human Sec24 isoforms establishes the structural determinants for discrimination among these transport signals, and provides a framework to understand how an expansion of coat subunits extends the range of cargo proteins packaged into COPII-coated vesicles.

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Organizational Affiliation: 

Howard Hughes Medical Institute and the Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein transport protein Sec23A	A	765	Homo sapiens	Mutation(s): 0  Gene Names: SEC23A
Find proteins for Q15436 (Homo sapiens) Explore Q15436  Go to UniProtKB:  Q15436
NIH Common Fund Data Resources
PHAROS:  Q15436 GTEx:  ENSG00000100934

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
SEC24 related gene family, member D	B	770	Homo sapiens	Mutation(s): 0  Gene Names: SEC24D, KIAA0755
Find proteins for O94855 (Homo sapiens) Explore O94855  Go to UniProtKB:  O94855
NIH Common Fund Data Resources
PHAROS:  O94855 GTEx:  ENSG00000150961

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptide	C	7	N/A	Mutation(s): 0
Find proteins for Q13190 (Homo sapiens) Explore Q13190  Go to UniProtKB:  Q13190
NIH Common Fund Data Resources
PHAROS:  Q13190 GTEx:  ENSG00000162236

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	A, B	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.261 
• R-Value Work: 0.211 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.06	α = 90
b = 140.83	β = 90
c = 152.25	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
AMoRE	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-09-09 
• Released Date: 2008-10-21 
Deposition Author(s): Goldberg, J., Mancias, J.D.

Revision History 

• Version 1.0: 2008-10-21
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance