3FFV

Crystal Structure Analysis of Syd

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.182 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


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 Biol Chem 284: 7897-7902

  • DOI: 10.1074/jbc.M808305200
  • Primary Citation of 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 ...

    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.

    Organizational Affiliation: 

    Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia V6T1Z3, Canada.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Protein sydA, B181Escherichia coli K-12Mutation(s): 0 
Gene Names: syd, ydr, b2793, JW2764
UniProt
Find proteins for P0A8U0 (Escherichia coli (strain K12))
Explore P0A8U0 
Go to UniProtKB:  P0A8U0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A8U0
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.182 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 167.6α = 90
b = 167.6β = 90
c = 41.6γ = 120
Software Package:
Software NamePurpose
MAR345dtbdata collection
SOLVEphasing
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-01-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance