Biological Assembly 1  

 3D View: Structure

Global Symmetry: Helical - H  (3D View)
Global Stoichiometry: Homo 35-mer - A35 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 183.51 kDa 
• Atom Count: 12950 
• Modelled Residue Count: 1750 
• Deposited Residue Count: 1750 
• Unique protein chains: 1

2MJZ

Capsid model of M13 bacteriophage virus from Magic-angle spinning NMR and Rosetta modeling

• DOI: 10.2210/pdb2MJZ/pdb
• BMRB: 19747

• Classification: VIRAL PROTEIN
• Organism(s): Escherichia virus M13
• Mutation(s): No 


• Deposited: 2014-01-22 Released: 2015-01-07 
• Deposition Author(s): Morag, O., Sgourakis, N.G., Baker, D., Goldbourt, A.

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Experimental Data Snapshot

• Method: SOLID-STATE NMR
• Conformers Calculated: 5000 
• Conformers Submitted: 3 
• Selection Criteria: target function 

Literature

The NMR-Rosetta capsid model of M13 bacteriophage reveals a quadrupled hydrophobic packing epitope.

Morag, O., Sgourakis, N.G., Baker, D., Goldbourt, A.

(2015) Proc Natl Acad Sci U S A 112: 971-976

• PubMed: 25587134 
• DOI: 10.1073/pnas.1415393112
• Primary Citation of Related Structures:  
  2MJZ


• PubMed Abstract: 
  

Filamentous phage are elongated semiflexible ssDNA viruses that infect bacteria. The M13 phage, belonging to the family inoviridae, has a length of ∼1 μm and a diameter of ∼7 nm. Here we present a structural model for the capsid of intact M13 bacteriophage using Rosetta model building guided by structure restraints obtained from magic-angle spinning solid-state NMR experimental data. The C5 subunit symmetry observed in fiber diffraction studies was enforced during model building. The structure consists of stacked pentamers with largely alpha helical subunits containing an N-terminal type II β-turn; there is a rise of 16.6-16.7 Å and a tilt of 36.1-36.6° between consecutive pentamers. The packing of the subunits is stabilized by a repeating hydrophobic stacking pocket; each subunit participates in four pockets by contributing different hydrophobic residues, which are spread along the subunit sequence. Our study provides, to our knowledge, the first magic-angle spinning NMR structure of an intact filamentous virus capsid and further demonstrates the strength of this technique as a method of choice to study noncrystalline, high-molecular-weight molecular assemblies.

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Organizational Affiliation: 

School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Ramat Aviv 69978, Tel Aviv, Israel; and [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein G8P	A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z, AA [auth a], BA [auth b], CA [auth c], DA [auth d], EA [auth e], FA [auth f], GA [auth g], HA [auth h], IA [auth i]	50	Escherichia virus M13	Mutation(s): 0  Gene Names: VIII
Find proteins for P69541 (Enterobacteria phage M13) Explore P69541  Go to UniProtKB:  P69541

Experimental Data & Validation

Experimental Data

• Method: SOLID-STATE NMR
• Conformers Calculated: 5000 
• Conformers Submitted: 3 
• Selection Criteria: target function 
• OLDERADO: 2MJZ Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-01-22 
• Released Date: 2015-01-07 
Deposition Author(s): Morag, O., Sgourakis, N.G., Baker, D., Goldbourt, A.

Revision History  

• Version 1.0: 2015-01-07
  Type: Initial release
  
• Version 1.1: 2015-01-14
  Changes: Database references, Structure summary
• Version 1.2: 2015-01-21
  Changes: Other
• Version 1.3: 2015-02-04
  Changes: Database references
• Version 1.4: 2015-02-11
  Changes: Database references