5CBO | pdb_00005cbo

Fusion protein of mbp3-16 and B4 domain of protein A from staphylococcal aureus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 
    0.254 (Depositor), 0.197 (DCC) 
  • R-Value Work: 
    0.203 (Depositor), 0.157 (DCC) 
  • R-Value Observed: 
    0.207 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history

Literature

Connecting two proteins using a fusion alpha helix stabilized by a chemical cross linker.

Jeong, W.H.Lee, H.Song, D.H.Eom, J.H.Kim, S.C.Lee, H.S.Lee, H.Lee, J.O.

(2016) Nat Commun 7: 11031-11031

  • DOI: https://doi.org/10.1038/ncomms11031
  • Primary Citation Related Structures: 
    5CBN, 5CBO, 5COC, 5EWX

  • PubMed Abstract: 

    Building a sophisticated protein nano-assembly requires a method for linking protein components in a predictable and stable structure. Most of the cross linkers available have flexible spacers. Because of this, the linked hybrids have significant structural flexibility and the relative structure between their two components is largely unpredictable. Here we describe a method of connecting two proteins via a 'fusion α helix' formed by joining two pre-existing helices into a single extended helix. Because simple ligation of two helices does not guarantee the formation of a continuous helix, we used EY-CBS, a synthetic cross linker that has been shown to react selectively with cysteines in α-helices, to stabilize the connecting helix. Formation and stabilization of the fusion helix was confirmed by determining the crystal structures of the fusion proteins with and without bound EY-CBS. Our method should be widely applicable for linking protein building blocks to generate predictable structures.


  • Organizational Affiliation
    • Department of Chemistry, KAIST, Daejeon 34141, Korea.

Macromolecule Content 

  • Total Structure Weight: 229.12 kDa 
  • Atom Count: 16,150 
  • Modeled Residue Count: 2,112 
  • Deposited Residue Count: 2,112 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
mbp3-16,Immunoglobulin G-binding protein A
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
176synthetic constructStaphylococcus aureus
This entity is chimeric
Mutation(s): 5 
UniProt
Find proteins for P38507 (Staphylococcus aureus)
Explore P38507 
Go to UniProtKB:  P38507
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP38507
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.254 (Depositor), 0.197 (DCC) 
  • R-Value Work:  0.203 (Depositor), 0.157 (DCC) 
  • R-Value Observed: 0.207 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.497α = 90
b = 220.393β = 59.97
c = 85.524γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data collection
SCALEPACKdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-03-30
    Type: Initial release
  • Version 1.1: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description