3FFV | pdb_00003ffv

Crystal Structure Analysis of Syd

• PDB DOI: https://doi.org/10.2210/pdb3FFV/pdb

• Classification: PROTEIN BINDING
• Organism(s): Escherichia coli K-12
• Mutation(s): No 


• Deposited: 2008-12-04 Released: 2009-01-27 
• Deposition Author(s): Maurus, R., Brayer, G.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.230 (Depositor), 0.181 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.189 (DCC) 
• R-Value Observed: 
  0.182 (Depositor) 

Literature

Structure, Binding, and Activity of Syd, a SecY-interacting Protein

Dalal, K., Nguyen, N., Alami, M., Tan, J., Moraes, T.F., Lee, W.C., Maurus, R., Sligar, S.S., Brayer, G.D., Duong, F.

(2009) J Biological Chem 284: 7897-7902

• PubMed: 19139097 
• DOI: https://doi.org/10.1074/jbc.M808305200
• Primary Citation Related Structures: 
  3FFV


• PubMed Abstract: 
  

  The Syd protein has been implicated in the Sec-dependent transport of polypeptides across the bacterial inner membrane. Using Nanodiscs, we here provide direct evidence that Syd binds the SecY complex, and we demonstrate that interaction involves the two electropositive and cytosolic loops of the SecY subunit. We solve the crystal structure of Syd and together with cysteine cross-link analysis, we show that a conserved concave and electronegative groove constitutes the SecY-binding site. At the membrane, Syd decreases the activity of the translocon containing loosely associated SecY-SecE subunits, whereas in detergent solution Syd disrupts the SecYEG heterotrimeric associations. These results support the role of Syd in proofreading the SecY complex biogenesis and point to the electrostatic nature of the Sec channel interaction with its cytosolic partners.

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Organizational Affiliation: 
• Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia V6T1Z3, Canada.

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: 41.46 kDa 
• Atom Count: 3,430 
• Modeled Residue Count: 362 
• Deposited Residue Count: 362 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein syd	A, B	181	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P0A8U0 (Escherichia coli (strain K12)) Explore P0A8U0  Go to UniProtKB:  P0A8U0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.230 (Depositor), 0.181 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.189 (DCC) 
• R-Value Observed: 0.182 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 167.6	α = 90
b = 167.6	β = 90
c = 41.6	γ = 120

Software Package:

Software Name	Purpose
MAR345dtb	data collection
SOLVE	phasing
CNS	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-01-27 
Deposition Author(s): Maurus, R., Brayer, G.D.

Revision History  

• Version 1.0: 2009-01-27
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-11-27
  Changes: Data collection, Database references, Structure summary