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RCSB PDB
249,906
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1,068,577
Computed Structure Models (CSM)
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 2NOJ|pdb_00002noj

Crystal structure of Ehp / C3d complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 
    0.284 (Depositor), 0.290 (DCC) 
  • R-Value Work: 
    0.291 (Depositor), 0.290 (DCC) 
  • R-Value Observed: 
    0.290 (Depositor) 

Starting Model:experimental
View more details

wwPDB Validation  3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Characterization of Ehp, a Secreted Complement Inhibitory Protein from Staphylococcus aureus.

Hammel, M.Sfyroera, G.Pyrpassopoulos, S.Ricklin, D.Ramyar, K.X.Pop, M.Jin, Z.Lambris, J.D.Geisbrecht, B.V.

(2007) J Biological Chem 282: 30051-30061

  • PubMed17699522 Search on PubMed
  • DOI: https://doi.org/10.1074/jbc.M704247200
  • Primary Citation of Related Structures:  
    2NOJ

  • PubMed Abstract: 

    We report here the discovery and characterization of Ehp, a new secreted Staphylococcus aureus protein that potently inhibits the alternative complement activation pathway. Ehp was identified through a genomic scan as an uncharacterized secreted protein from S. aureus, and immunoblotting of conditioned S. aureus culture medium revealed that the Ehp protein was secreted at the highest levels during log-phase bacterial growth. The mature Ehp polypeptide is composed of 80 residues and is 44% identical to the complement inhibitory domain of S. aureus Efb (extracellular fibrinogen-binding protein). We observed preferential binding by Ehp to native and hydrolyzed C3 relative to fully active C3b and found that Ehp formed a subnanomolar affinity complex with these various forms of C3 by binding to its thioester-containing C3d domain. Site-directed mutagenesis demonstrated that Arg(75) and Asn(82) are important in forming the Ehp.C3d complex, but loss of these side chains did not completely disrupt Ehp/C3d binding. This suggested the presence of a second C3d-binding site in Ehp, which was mapped to the proximity of Ehp Asn(63). Further molecular level details of the Ehp/C3d interaction were revealed by solving the 2.7-A crystal structure of an Ehp.C3d complex in which the low affinity site had been mutationally inactivated. Ehp potently inhibited C3b deposition onto sensitized surfaces by the alternative complement activation pathway. This inhibition was directly related to Ehp/C3d binding and was more potent than that seen for Efb-C. An altered conformation in Ehp-bound C3 was detected by monoclonal antibody C3-9, which is specific for a neoantigen exposed in activated forms of C3. Our results suggest that increased inhibitory potency of Ehp relative to Efb-C is derived from the second C3-binding site in this new protein.


  • Organizational Affiliation
    • School of Biological Sciences, University of Missouri-Kansas City, Kansas City, Missouri 64110, USA.
Biological Assembly 1  

 Explore in 3DStructure |Sequence Annotations |Electron Density |Validation Report


Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 


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Biological assembly 1 assigned by authors.

Biological Assembly 2  

 Explore in 3DStructure |Sequence Annotations |Electron Density |Validation Report


Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 


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Biological assembly 2 assigned by authors.

Biological Assembly 3  

 Explore in 3DStructure |Sequence Annotations |Electron Density |Validation Report


Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 


Find Similar Assemblies

Biological assembly 3 assigned by authors.

Biological Assembly 4  

 Explore in 3DStructure |Sequence Annotations |Electron Density |Validation Report


Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 


Find Similar Assemblies

Biological assembly 4 assigned by authors.

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Macromolecule Content 

  • Total Structure Weight: 170.96 kDa 
  • Atom Count: 9,768 
  • Modeled Residue Count: 1,344 
  • Deposited Residue Count: 1,508 
  • Unique protein chains: 2

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Complement C3
A,C,E,G
297Homo sapiensMutation(s): 1 
Gene Names: C3
UniProt & NIH Common Fund Data Resources
Find proteins for P01024 (Homo sapiens)
Explore P01024 
Go to UniProtKB:  P01024
PHAROS:  P01024
GTEx:  ENSG00000125730 
Entity Groups 
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01024
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Efb homologous protein
B,D,F,H
80Staphylococcus aureus subsp. aureus Mu50Mutation(s): 1 
Gene Names: SAV1155
Entity Groups 
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.284 (Depositor), 0.290 (DCC) 
  • R-Value Work: 0.291 (Depositor), 0.290 (DCC) 
  • R-Value Observed: 0.290 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.894α = 90
b = 91.025β = 89.93
c = 122.595γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-08-14
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2020-01-22
    Changes: Database references, Derived calculations
  • Version 1.3: 2021-10-20
    Changes: Database references
  • Version 1.4: 2023-08-30
    Changes: Data collection, Refinement description
  • Version 1.5: 2024-11-13
    Changes: Structure summary
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RCSB PDB Core Operations are funded by theU.S. National Science Foundation (DBI-2321666), theUS Department of Energy (DE-SC0019749), and theNational Cancer Institute,National Institute of Allergy and Infectious Diseases, andNational Institute of General Medical Sciences of theNational Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.


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