5GAI

Probabilistic Structural Models of Mature P22 Bacteriophage Portal, Hub, and Tailspike proteins


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 10.5 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Resolution and Probabilistic Models of Components in CryoEM Maps of Mature P22 Bacteriophage.

Pintilie, G.Chen, D.H.Haase-Pettingell, C.A.King, J.A.Chiu, W.

(2016) Biophys.J. 110: 827-839

  • DOI: 10.1016/j.bpj.2015.11.3522

  • PubMed Abstract: 
  • CryoEM continues to produce density maps of larger and more complex assemblies with multiple protein components of mixed symmetries. Resolution is not always uniform throughout a cryoEM map, and it can be useful to estimate the resolution in specific ...

    CryoEM continues to produce density maps of larger and more complex assemblies with multiple protein components of mixed symmetries. Resolution is not always uniform throughout a cryoEM map, and it can be useful to estimate the resolution in specific molecular components of a large assembly. In this study, we present procedures to 1) estimate the resolution in subcomponents by gold-standard Fourier shell correlation (FSC); 2) validate modeling procedures, particularly at medium resolutions, which can include loop modeling and flexible fitting; and 3) build probabilistic models that combine high-accuracy priors (such as crystallographic structures) with medium-resolution cryoEM densities. As an example, we apply these methods to new cryoEM maps of the mature bacteriophage P22, reconstructed without imposing icosahedral symmetry. Resolution estimates based on gold-standard FSC show the highest resolution in the coat region (7.6 Å), whereas other components are at slightly lower resolutions: portal (9.2 Å), hub (8.5 Å), tailspike (10.9 Å), and needle (10.5 Å). These differences are indicative of inherent structural heterogeneity and/or reconstruction accuracy in different subcomponents of the map. Probabilistic models for these subcomponents provide new insights, to our knowledge, and structural information when taking into account uncertainty given the limitations of the observed density.


    Organizational Affiliation

    Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas. Electronic address: pintilie@bcm.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Portal protein
A, B, C, D, E, F, G, H, I, J, W, X
721Salmonella phage P22Mutation(s): 0 
Gene Names: 1
Find proteins for P26744 (Salmonella phage P22)
Go to UniProtKB:  P26744
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Peptidoglycan hydrolase gp4
K, L, M, N, O, P, Q, R, S, T, U, V
146Salmonella phage P22Mutation(s): 1 
Gene Names: 4
Find proteins for P26746 (Salmonella phage P22)
Go to UniProtKB:  P26746
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Tail fiber protein
Y, Z, 0
662Salmonella phage P22Mutation(s): 0 
Gene Names: 9
Find proteins for P12528 (Salmonella phage P22)
Go to UniProtKB:  P12528
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 10.5 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesP41GM103832
National Institutes of Health/National Eye InstituteUnited StatesPN2EY016525
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR01GM079429

Revision History 

  • Version 1.0: 2016-02-17
    Type: Initial release
  • Version 1.1: 2016-03-02
    Type: Database references
  • Version 1.2: 2016-05-25
    Type: Database references
  • Version 1.3: 2017-09-13
    Type: Author supporting evidence, Data collection
  • Version 1.4: 2018-07-18
    Type: Data collection