Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 85.31 kDa 
• Atom Count: 5668 
• Residue Count: 732 
• Unique protein chains: 2

3RCE

Bacterial oligosaccharyltransferase PglB

• DOI: 10.2210/pdb3RCE/pdb

• Classification: Transferase/Peptide
• Organism(s): Campylobacter lari
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2011-03-31 Released: 2011-06-15 
• Deposition Author(s): Lizak, C., Gerber, S., Numao, S., Aebi, M., Locher, K.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.40 Å
• R-Value Free: 0.271 
• R-Value Work: 0.238 
• R-Value Observed: 0.241 

Literature

X-ray structure of a bacterial oligosaccharyltransferase.

Lizak, C., Gerber, S., Numao, S., Aebi, M., Locher, K.P.

(2011) Nature 474: 350-355

• PubMed: 21677752 
• DOI: 10.1038/nature10151
• Primary Citation of Related Structures:  
  3RCE


• PubMed Abstract: 
  

Asparagine-linked glycosylation is a post-translational modification of proteins containing the conserved sequence motif Asn-X-Ser/Thr. The attachment of oligosaccharides is implicated in diverse processes such as protein folding and quality control, organism development or host-pathogen interactions. The reaction is catalysed by oligosaccharyltransferase (OST), a membrane protein complex located in the endoplasmic reticulum. The central, catalytic enzyme of OST is the STT3 subunit, which has homologues in bacteria and archaea. Here we report the X-ray structure of a bacterial OST, the PglB protein of Campylobacter lari, in complex with an acceptor peptide. The structure defines the fold of STT3 proteins and provides insight into glycosylation sequon recognition and amide nitrogen activation, both of which are prerequisites for the formation of the N-glycosidic linkage. We also identified and validated catalytically important, acidic amino acid residues. Our results provide the molecular basis for understanding the mechanism of N-linked glycosylation.

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Organizational Affiliation: 

Institute of Microbiology, Department of Biology, ETH Zurich, CH-8093 Zurich, Switzerland.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Oligosaccharide transferase to N-glycosylate proteins	A	724	Campylobacter lari	Mutation(s): 1  Gene Names: pglB, Cla_1253 EC: 2.4.99.19
Membrane protein Mpstruc	Group:  TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group:  Oligosaccharyltransferases (OST)	Protein:  PglB OST in complex with acceptor peptide
Find proteins for B9KDD4 (Campylobacter lari (strain RM2100 / D67 / ATCC BAA-1060)) Explore B9KDD4  Go to UniProtKB:  B9KDD4

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Substrate Mimic Peptide	B	8	N/A	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	A	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PPN	B	L-PEPTIDE LINKING	C9 H10 N2 O4		PHE

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.40 Å
• R-Value Free: 0.271 
• R-Value Work: 0.238 
• R-Value Observed: 0.241 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.06	α = 90
b = 116.1	β = 90
c = 175.04	γ = 90

Software Package:

Software Name	Purpose
SHARP	phasing
PHENIX	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-03-31 
• Released Date: 2011-06-15 
Deposition Author(s): Lizak, C., Gerber, S., Numao, S., Aebi, M., Locher, K.P.

Revision History 

• Version 1.0: 2011-06-15
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2011-08-17
  Changes: Database references
• Version 1.3: 2013-05-22
  Changes: Refinement description
• Version 1.4: 2017-11-08
  Changes: Advisory, Refinement description