4L9O | pdb_00004l9o

Crystal Structure of the Sec13-Sec16 blade-inserted complex from Pichia pastoris

• PDB DOI: https://doi.org/10.2210/pdb4L9O/pdb

• Classification: PROTEIN TRANSPORT
• Organism(s): Komagataella pastoris, Komagataella phaffii GS115
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-06-18 Released: 2013-10-02 
• Deposition Author(s): McMahon, C., Jeffrey, P.D., Hughson, F.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.205 (Depositor), 0.206 (DCC) 
• R-Value Work: 
  0.173 (Depositor), 0.176 (DCC) 
• R-Value Observed: 
  0.174 (Depositor) 

Starting Model: experimental

Literature

Sec16 influences transitional ER sites by regulating rather than organizing COPII.

Bharucha, N., Liu, Y., Papanikou, E., McMahon, C., Esaki, M., Jeffrey, P.D., Hughson, F.M., Glick, B.S.

(2013) Mol Biol Cell 24: 3406-3419

• PubMed: 24006484 
• DOI: https://doi.org/10.1091/mbc.E13-04-0185
• Primary Citation Related Structures: 
  4L9O


• PubMed Abstract: 
  

  During the budding of coat protein complex II (COPII) vesicles from transitional endoplasmic reticulum (tER) sites, Sec16 has been proposed to play two distinct roles: negatively regulating COPII turnover and organizing COPII assembly at tER sites. We tested these ideas using the yeast Pichia pastoris. Redistribution of Sec16 to the cytosol accelerates tER dynamics, supporting a negative regulatory role for Sec16. To evaluate a possible COPII organization role, we dissected the functional regions of Sec16. The central conserved domain, which had been implicated in coordinating COPII assembly, is actually dispensable for normal tER structure. An upstream conserved region (UCR) localizes Sec16 to tER sites. The UCR binds COPII components, and removal of COPII from tER sites also removes Sec16, indicating that COPII recruits Sec16 rather than the other way around. We propose that Sec16 does not in fact organize COPII. Instead, regulation of COPII turnover can account for the influence of Sec16 on tER sites.

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Organizational Affiliation: 
• Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637 Department of Molecular Biology, Princeton University, Princeton, NJ 08544.

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)

Macromolecule Content 

• Total Structure Weight: 77.47 kDa 
• Atom Count: 5,356 
• Modeled Residue Count: 641 
• Deposited Residue Count: 698 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sec16,Protein transport protein SEC13	A, B	349	Komagataella pastoris, Komagataella phaffii GS115 This entity is chimeric	Mutation(s): 0  Gene Names: SEC16, SEC13, PAS_chr1-3_0057
UniProt
Find proteins for P53024 (Komagataella phaffii (strain GS115 / ATCC 20864)) Explore P53024  Go to UniProtKB:  P53024
Find proteins for Q45TY0 (Komagataella pastoris) Explore Q45TY0  Go to UniProtKB:  Q45TY0
UniProt Groups	P53024Q45TY0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	G [auth A], H [auth A], I [auth A], J [auth A], K [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA	C [auth A], D [auth A], L [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	E [auth A], F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.205 (Depositor), 0.206 (DCC) 
• R-Value Work:  0.173 (Depositor), 0.176 (DCC) 
• R-Value Observed: 0.174 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.509	α = 90
b = 49.32	β = 111.7
c = 90.904	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
CBASS	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-10-02 
Deposition Author(s): McMahon, C., Jeffrey, P.D., Hughson, F.M.

Revision History  

• Version 1.0: 2013-10-02
  Type: Initial release
  
• Version 1.1: 2014-02-05
  Changes: Database references
• Version 1.2: 2017-06-21
  Changes: Database references, Source and taxonomy, Structure summary
• Version 1.3: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description