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 1.6 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
  • Primary Citation of Related Structures:  
    5GAI

  • 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 molecular components of a large assembly ...

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Portal proteinABCDEFGHABCDEFGHIJWX
721Salmonella virus P22Mutation(s): 0 
Gene Names: 1
Find proteins for P26744 (Salmonella phage P22)
Explore P26744 
Go to UniProtKB:  P26744
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Peptidoglycan hydrolase gp4KLMNOPQRKLMNOPQRSTUV
146Salmonella virus P22Mutation(s): 1 
Gene Names: 4
Find proteins for P26746 (Salmonella phage P22)
Explore P26746 
Go to UniProtKB:  P26746
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Tail fiber protein 0YZ662Salmonella virus P22Mutation(s): 0 
Gene Names: 9
EC: 3.2.1
Find proteins for P12528 (Salmonella phage P22)
Explore P12528 
Go to UniProtKB:  P12528
Protein Feature View
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  • Reference Sequence
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



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP41GM103832
National Institutes of Health/National Eye Institute (NIH/NEI)United StatesPN2EY016525
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM079429

Revision History  (Full details and data files)

  • Version 1.0: 2016-02-17
    Type: Initial release
  • Version 1.1: 2016-03-02
    Changes: Database references
  • Version 1.2: 2016-05-25
    Changes: Database references
  • Version 1.3: 2017-09-13
    Changes: Author supporting evidence, Data collection
  • Version 1.4: 2018-07-18
    Changes: Data collection
  • Version 1.5: 2019-12-11
    Changes: Author supporting evidence
  • Version 1.6: 2019-12-25
    Changes: Other