2M5S | pdb_00002m5s

High-resolution NMR structure and cryo-EM imaging support multiple functional roles for the accessory I-domain of phage P22 coat protein

• PDB DOI: https://doi.org/10.2210/pdb2M5S/pdb
• BMRB: 18566

• Classification: VIRAL PROTEIN
• Organism(s): Lederbergvirus P22
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-03-05 Released: 2014-03-05 
• Deposition Author(s): Rizzo, A.A., Suhanovsky, M.M., Baker, M.L., Fraser, L.C.R., Jones, L.M., Rempel, D.L., Gross, M.L., Chiu, W., Alexandrescu, A.T., Teschke, C.M.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 300 
• Conformers Submitted: 30 
• Selection Criteria: structures with the lowest energy 

Literature

Multiple Functional Roles of the Accessory I-Domain of Bacteriophage P22 Coat Protein Revealed by NMR Structure and CryoEM Modeling.

Rizzo, A.A., Suhanovsky, M.M., Baker, M.L., Fraser, L.C., Jones, L.M., Rempel, D.L., Gross, M.L., Chiu, W., Alexandrescu, A.T., Teschke, C.M.

(2014) Structure 22: 830-841

• PubMed: 24836025 
• DOI: https://doi.org/10.1016/j.str.2014.04.003
• Primary Citation Related Structures: 
  2M5S


• PubMed Abstract: 
  

  Some capsid proteins built on the ubiquitous HK97-fold have accessory domains imparting specific functions. Bacteriophage P22 coat protein has a unique insertion domain (I-domain). Two prior I-domain models from subnanometer cryoelectron microscopy (cryoEM) reconstructions differed substantially. Therefore, the I-domain's nuclear magnetic resonance structure was determined and also used to improve cryoEM models of coat protein. The I-domain has an antiparallel six-stranded β-barrel fold, not previously observed in HK97-fold accessory domains. The D-loop, which is dynamic in the isolated I-domain and intact monomeric coat protein, forms stabilizing salt bridges between adjacent capsomers in procapsids. The S-loop is important for capsid size determination, likely through intrasubunit interactions. Ten of 18 coat protein temperature-sensitive-folding substitutions are in the I-domain, indicating its importance in folding and stability. Several are found on a positively charged face of the β-barrel that anchors the I-domain to a negatively charged surface of the coat protein HK97-core.

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Organizational Affiliation: 
• Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA.
Verna and Marrs McLean Department of Biochemistry and Molecular Biology, National Center for Macromolecular Imaging, Baylor College of Medicine, Houston, TX 77030, USA.
Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA.
Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA. Electronic address: [e-mail].
Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA; Department of Chemistry, University of Connecticut, Storrs, CT 06269, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 13.87 kDa 
• Atom Count: 915 
• Modeled Residue Count: 124 
• Deposited Residue Count: 130 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Coat protein	A	130	Lederbergvirus P22	Mutation(s): 0  Gene Names: 5, gp5 coat protein
UniProt
Find proteins for P26747 (Salmonella phage P22) Explore P26747  Go to UniProtKB:  P26747

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 300 
• Conformers Submitted: 30 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-03-05 
Deposition Author(s): Rizzo, A.A., Suhanovsky, M.M., Baker, M.L., Fraser, L.C.R., Jones, L.M., Rempel, D.L., Gross, M.L., Chiu, W., Alexandrescu, A.T., Teschke, C.M.

Revision History  

• Version 1.0: 2014-03-05
  Type: Initial release
  
• Version 1.1: 2014-06-18
  Changes: Database references
• Version 1.2: 2014-07-02
  Changes: Database references
• Version 1.3: 2024-05-01
  Changes: Data collection, Database references