PDBsum entry 3ffv

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protein Protein-protein interface(s) links
Protein binding PDB id
Protein chains
181 a.a. *
Waters ×510
* Residue conservation analysis
PDB id:
Name: Protein binding
Title: Crystal structure analysis of syd
Structure: Protein syd. Chain: a, b
Source: Escherichia coli. Organism_taxid: 83333. Strain: k12
2.00Å     R-factor:   0.182     R-free:   0.230
Authors: R.Maurus,G.D.Brayer
Key ref:
K.Dalal et al. (2009). Structure, binding, and activity of Syd, a SecY-interacting protein. J Biol Chem, 284, 7897-7902. PubMed id: 19139097 DOI: 10.1074/jbc.M808305200
04-Dec-08     Release date:   27-Jan-09    
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Protein chains
Pfam   ArchSchema ?
P0A8U0  (SYDP_ECOLI) -  Protein Syd
181 a.a.
181 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   5 terms 
  Biological process     regulation of protein complex assembly   1 term 
  Biochemical function     protein binding     1 term  


DOI no: 10.1074/jbc.M808305200 J Biol Chem 284:7897-7902 (2009)
PubMed id: 19139097  
Structure, binding, and activity of Syd, a SecY-interacting protein.
K.Dalal, N.Nguyen, M.Alami, J.Tan, T.F.Moraes, W.C.Lee, R.Maurus, S.S.Sligar, G.D.Brayer, F.Duong.
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.
  Selected figure(s)  
Figure 2.
Isolation of the Syd-SecYEG-Nanodisc complex and mass determination. A, SecYEG-Nanodisc (∼200 μg) incubated with a molar excess of Syd (∼100 μg) and then applied onto a Superdex 200 HR10/10 column equilibrated in TSG buffer. The fractions containing the complex Nd-SecYEG-Syd were pooled and concentrated to 1.2 mg/ml for subsequent multiangle light scattering analysis. B, multiangle light scattering of Syd, Nd-SecYEG, and Nd-SecYEG-Syd. In each case, about 100 μg of protein is loaded onto a Superdex 200 HR 10/30 column equilibrated in 10 mm HEPES, 50 mm NaCl, pH 7.4.
Figure 3.
Atomic structure and surface electrostatic of Syd and SecYEG. A, ribbon diagram representation of Syd (β-sheets, yellow; α-helices, magenta; loops, green) and space-filling representation showing the concave structure of the protein (180° rotation compared with right panel). Arrows denote the position of the “stalk” regions that consist of negatively charged protruding loops that delineate the concave region. B, electrostatic potential of the concave (left) and convex surface (right, 180° rotation). Blue and red represent electropositive and electronegative potential, respectively. The surface potential was set between -2.5 and +2.5 kT/e using the solvent-accessible area option of the software. C, electrostatic map of the archaeal SecY complex (Protein Data Bank code 1RH5) showing the position of the positively charged loops C4 and C5. The surface potential was generated using the parameters described in B. Positive charges are located near the predicted location of the phospholipids head group. Note that in E. coli, the loops C4 and C5 contain additional basic residues compared with Methanococcus jannaschii. In particular, three arginine residues are located at the tip of the loop C4 in the E. coli complex.
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2009, 284, 7897-7902) copyright 2009.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
  21282400 S.Banerjee, and C.M.Nimigean (2011).
Non-vesicular transfer of membrane proteins from nanoparticles to lipid bilayers.
  J Gen Physiol, 137, 217-223.  
19616329 F.Katzen, T.C.Peterson, and W.Kudlicki (2009).
Membrane protein expression: no cells required.
  Trends Biotechnol, 27, 455-460.  
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