Biological Assembly 1  

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Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 29674.10 
• Atom Count: 2100 
• Residue Count: 285 
• Unique protein chains: 1

1C5E

BACTERIOPHAGE LAMBDA HEAD PROTEIN D

• DOI: 10.2210/pdb1C5E/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Escherichia phage lambda


• Deposited: 1999-11-18 Released: 2000-03-08 
• Deposition Author(s): Yang, F., Forrer, P., Dauter, Z., Pluckthun, A., Wlodawer, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.1 Å
• R-Value Free: 0.133 

Literature

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.Mol.Biol. 7: 230-237

• PubMed: 10700283 
• DOI: 10.1038/73347


• 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.

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Organizational Affiliation: 

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

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
HEAD DECORATION PROTEIN	A, B, C	95	Escherichia phage lambda	Mutation(s): 0  Gene Names: D
Find proteins for P03712 (Escherichia phage lambda) Go to UniProtKB:  P03712

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
GOL	A, C	GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.1 Å
• R-Value Free: 0.133 
• Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 45.580	α = 90.00
b = 69.070	β = 104.32
c = 45.590	γ = 90.00

Software Package:

Software Name	Purpose
SHELXL-97	phasing
SCALEPACK	data scaling
SHELXL-97	refinement
SHELXL-97	model building
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1999-11-18 
• Released Date: 2000-03-08 
• Deposition Author(s): Yang, F., Forrer, P., Dauter, Z., Pluckthun, A., Wlodawer, A.

Revision History 

• Version 1.0: 2000-03-08
  Type: Initial release
• Version 1.1: 2008-04-26
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Non-polymer description, Version format compliance