6XMI

Structure of Fab4 bound to P22 TerL(1-33)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.51 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.168 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Recognition of an alpha-helical hairpin in P22 large terminase by a synthetic antibody fragment.

Lokareddy, R.K.Ko, Y.H.Hong, N.Doll, S.G.Paduch, M.Niederweis, M.Kossiakoff, A.A.Cingolani, G.

(2020) Acta Crystallogr D Struct Biol 76: 876-888

  • DOI: https://doi.org/10.1107/S2059798320009912
  • Primary Citation of Related Structures:  
    6VI1, 6VI2, 6XMI

  • PubMed Abstract: 

    The genome-packaging motor of tailed bacteriophages and herpesviruses is a multisubunit protein complex formed by several copies of a large (TerL) and a small (TerS) terminase subunit. The motor assembles transiently at the portal protein vertex of an empty precursor capsid to power the energy-dependent packaging of viral DNA. Both the ATPase and nuclease activities associated with genome packaging reside in TerL. Structural studies of TerL from bacteriophage P22 have been hindered by the conformational flexibility of this enzyme and its susceptibility to proteolysis. Here, an unbiased, synthetic phage-display Fab library was screened and a panel of high-affinity Fabs against P22 TerL were identified. This led to the discovery of a recombinant antibody fragment, Fab4, that binds a 33-amino-acid α-helical hairpin at the N-terminus of TerL with an equilibrium dissociation constant K d of 71.5 nM. A 1.51 Å resolution crystal structure of Fab4 bound to the TerL epitope (TLE) together with a 1.15 Å resolution crystal structure of the unliganded Fab4, which is the highest resolution ever achieved for a Fab, elucidate the principles governing the recognition of this novel helical epitope. TLE adopts two different conformations in the asymmetric unit and buries as much as 1250 Å 2 of solvent-accessible surface in Fab4. TLE recognition is primarily mediated by conformational changes in the third complementarity-determining region of the Fab4 heavy chain (CDR H3) that take place upon epitope binding. It is demonstrated that TLE can be introduced genetically at the N-terminus of a target protein, where it retains high-affinity binding to Fab4.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locust Street, JAH-4E, Philadelphia, PA 19107, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fab Light chainA,
C [auth D]
215Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Fab Heavy chainB,
D [auth E]
243Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Terminase, large subunitE [auth F],
F [auth C]
33Lederbergvirus P22Mutation(s): 0 
EC: 3.1.21 (PDB Primary Data), 3.6.4 (PDB Primary Data)
UniProt
Find proteins for P26745 (Salmonella phage P22)
Explore P26745 
Go to UniProtKB:  P26745
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UniProt GroupP26745
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.51 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.168 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.18α = 90
b = 86.395β = 97.72
c = 86.151γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM100888
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesOD017987
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesCA56036

Revision History  (Full details and data files)

  • Version 1.0: 2020-08-19
    Type: Initial release
  • Version 1.1: 2020-09-09
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Database references, Refinement description