Experimental Data Snapshot

  • Resolution: 1.10 Å
  • R-Value Free: 0.133 
  • R-Value Observed: 0.099 

wwPDB Validation   3D Report Full Report

This is version 1.3 of the entry. See complete history


Novel fold and capsid-binding properties of the lambda-phage display platform protein gpD.

Yang, F.Forrer, P.Dauter, Z.Conway, J.F.Cheng, N.Cerritelli, M.E.Steven, A.C.Pluckthun, A.Wlodawer, A.

(2000) Nat Struct Biol 7: 230-237

  • DOI: https://doi.org/10.1038/73347
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The crystal structure of gpD, the capsid-stabilizing protein of bacteriophage lambda, was solved at 1.1 A resolution. Data were obtained from twinned crystals in space group P21 and refined with anisotropic temperature factors to an R-factor of 0.098 (Rfree = 0. 132). GpD (109 residues) has a novel fold with an unusually low content of regular secondary structure. Noncrystallographic trimers with substantial intersubunit interfaces were observed. The C-termini are well ordered and located on one side of the trimer, relatively far from its three-fold axis. The N-termini are disordered up to Ser 15, which is close to the three-fold axis and on the same side as the C-termini. A density map of the icosahedral viral capsid at 15 A resolution, obtained by cryo-electron microscopy and image reconstruction, reveals gpD trimers, seemingly indistinguishable from the ones seen in the crystals, at all three-fold sites. The map further reveals that the side of the trimer that binds to the capsid is the side on which both termini reside. Despite this orientation of the gpD trimer, fusion proteins connected by linker peptides to either terminus bind to the capsid, allowing protein and peptide display.

  • Organizational Affiliation

    Macromolecular Crystallography Laboratory, Program in Structural Biology, National Cancer Institute, Frederick Cancer Research and Development Center, Frederick, Maryland 21702, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C
95Lambdavirus lambdaMutation(s): 0 
Find proteins for P03712 (Escherichia phage lambda)
Explore P03712 
Go to UniProtKB:  P03712
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03712
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.10 Å
  • R-Value Free: 0.133 
  • R-Value Observed: 0.099 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.58α = 90
b = 69.07β = 104.32
c = 45.59γ = 90
Software Package:
Software NamePurpose
SHELXL-97model building
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-03-08
    Type: Initial release
  • Version 1.1: 2008-04-26
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2023-12-27
    Changes: Data collection, Database references, Derived calculations