5MSF | pdb_00005msf

MS2 PROTEIN CAPSID/RNA COMPLEX

• PDB DOI: https://doi.org/10.2210/pdb5MSF/pdb
• NAKB: 5MSF

• Classification: Virus/RNA
• Organism(s): Escherichia phage MS2
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1998-05-15 Released: 1998-11-11 
• Deposition Author(s): Rowsell, S., Stonehouse, N.J., Convery, M.A., Adams, C.J., Ellington, A.D., Hirao, I., Peabody, D.S., Stockley, P.G., Phillips, S.E.V.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.197 (Depositor), 0.188 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.185 (DCC) 

Starting Model: experimental

Literature

Crystal structures of a series of RNA aptamers complexed to the same protein target.

Rowsell, S., Stonehouse, N.J., Convery, M.A., Adams, C.J., Ellington, A.D., Hirao, I., Peabody, D.S., Stockley, P.G., Phillips, S.E.

(1998) Nat Struct Biol 5: 970-975

• PubMed: 9808042 
• DOI: https://doi.org/10.1038/2946
• Primary Citation Related Structures: 
  5MSF, 7MSF


• PubMed Abstract: 
  

  We have determined the crystal structures, at 2.8 A resolution, of two different RNA aptamers, each bound to MS2 coat protein. One of the aptamers contains a non-Watson-Crick base pair, while the other is missing one of the unpaired adenines that make sequence-specific contacts in the wild-type complex. Despite these differences, the RNA aptamers bind in the same location on the protein as the wild-type translational operator. Comparison of these new structures with other MS2-RNA complexes allows us to refine further the definition of the minimal recognition elements and suggests a possible application of the MS2 system for routine structure determination of small nucleic acid motifs.

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Organizational Affiliation: 
• School of Biochemistry and Molecular Biology, and North of England Structural Biology Centre, University of Leeds, UK.

Biological Assembly 1  

Global Symmetry: Icosahedral - I  (Explore in 3D)
Global Stoichiometry: Homo 180-mer - A180 

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

Macromolecule Content 

• Total Structure Weight: 52.87 kDa 
• Atom Count: 3,737 
• Modeled Residue Count: 421 
• Deposited Residue Count: 423 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
MS2 PROTEIN CAPSID	C [auth A], D [auth B], E [auth C]	129	Escherichia phage MS2	Mutation(s): 0  Gene Names: COAT PROTEIN
UniProt
Find proteins for P03612 (Escherichia phage MS2) Explore P03612  Go to UniProtKB:  P03612

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-R(*CP*CP*GP*GP*AP*GP*GP*AP*UP*CP*AP*CP*CP*AP*CP*GP*GP*G)-3'	A [auth R], B [auth S]	18	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.197 (Depositor), 0.188 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.185 (DCC) 

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 287.3	α = 90
b = 287.3	β = 90
c = 651.6	γ = 120

Software Package:

Software Name	Purpose
CCP4	model building
X-PLOR	refinement
MOSFLM	data reduction
CCP4	data scaling
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-11-11 
Deposition Author(s): Rowsell, S., Stonehouse, N.J., Convery, M.A., Adams, C.J., Ellington, A.D., Hirao, I., Peabody, D.S., Stockley, P.G., Phillips, S.E.V.

Revision History  

• Version 1.0: 1998-11-11
  Type: Initial release
  
• Version 1.1: 2008-05-22
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-02
  Changes: Database references, Derived calculations, Refinement description