3D5R

Crystal Structure of Efb-C (N138A) / C3d Complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.218 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Electrostatic contributions drive the interaction between Staphylococcus aureus protein Efb-C and its complement target C3d.

Haspel, N., Ricklin, D., Geisbrecht, B.V., Kavraki, L.E., Lambris, J.D.

(2008) Protein Sci 17: 1894-1906

  • DOI: 10.1110/ps.036624.108
  • Primary Citation of Related Structures:  
    3D5R, 3D5S

  • PubMed Abstract: 

    • The C3-inhibitory domain of Staphylococcus aureus extracellular fibrinogen-binding protein (Efb-C) defines a novel three-helix bundle motif that regulates complement activation. Previous crystallographic studies of Efb-C bound to its cognate subdomain of human C3 (C3d) identified Arg-131 and Asn-138 of Efb-C as key residues for its activity ...

    The C3-inhibitory domain of Staphylococcus aureus extracellular fibrinogen-binding protein (Efb-C) defines a novel three-helix bundle motif that regulates complement activation. Previous crystallographic studies of Efb-C bound to its cognate subdomain of human C3 (C3d) identified Arg-131 and Asn-138 of Efb-C as key residues for its activity. In order to characterize more completely the physical and chemical driving forces behind this important interaction, we employed in this study a combination of structural, biophysical, and computational methods to analyze the interaction of C3d with Efb-C and the single-point mutants R131A and N138A. Our results show that while these mutations do not drastically affect the structure of the Efb-C/C3d recognition complex, they have significant adverse effects on both the thermodynamic and kinetic profiles of the resulting complexes. We also characterized other key interactions along the Efb-C/C3d binding interface and found an intricate network of salt bridges and hydrogen bonds that anchor Efb-C to C3d, resulting in its potent complement inhibitory properties.

    Organizational Affiliation: 

    Department of Computer Science, Rice University, Houston, Texas 77005, USA.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Complement C3A,
C [auth B]		297Homo sapiensMutation(s): 1 
Gene Names: C3, CPAMD1
UniProt & NIH Common Fund Data Resources
Find proteins for P01024 (Homo sapiens)
Explore P01024 
Go to UniProtKB:  P01024
PHAROS:  P01024
Entity Groups  
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UniProt GroupP01024
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Fibrinogen-binding proteinB [auth C],
D		65Staphylococcus aureus subsp. aureus str. NewmanMutation(s): 1 
Gene Names: fib, efb, NWMN_1069
UniProt
Find proteins for A6QG59 (Staphylococcus aureus (strain Newman))
Explore A6QG59 
Go to UniProtKB:  A6QG59
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA6QG59
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.218 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.01α = 90
b = 91.01β = 90
c = 120.52γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement
PDB_EXTRACTdata extraction
SERGUIdata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2008-05-16 
  • Released Date: 2008-09-09 
    • Deposition Author(s): Geisbrecht, B.V.

Revision History  (Full details and data files)

  • Version 1.0: 2008-09-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description
  • Version 1.3: 2021-10-20
    Changes: Database references