PDBsum entry 5gai

Viral protein

PDB id: 5gai

Contents

Protein chains

(+ 6 more) 721 a.a.

(+ 6 more) 146 a.a.

662 a.a.

PDB id:

5gai

Name:

Viral protein

Title:

Probabilistic structural models of mature p22 bacteriophage portal, hub, and tailspike proteins

Structure:

Portal protein. Chain: a, b, c, d, e, f, g, h, i, j, w, x. Synonym: gene product 1, gp1, head-to-tail connector. Engineered: yes. Peptidoglycan hydrolase gp4. Chain: k, l, m, n, o, p, q, r, s, t, u, v. Synonym: gene product 4, gp4, internal virion protein gp4. Engineered: yes. Mutation: yes.

Source:

Enterobacteria phage p22. Organism_taxid: 10754. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_taxid: 562

Authors:

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

Key ref:

G.Pintilie et al. (2016). Resolution and Probabilistic Models of Components in CryoEM Maps of Mature P22 Bacteriophage. Biophys J, 110, 827-839. PubMed id: 26743049 DOI: 10.1016/j.bpj.2015.11.3522

Date:

01-Dec-15 Release date: 17-Feb-16

Protein chains

P26744  (PORTL_BPP22) -  Portal protein from Salmonella phage P22

Seq: 725 a.a.

Struc: 721 a.a.

Protein chains

P26746  (EXLYS_BPP22) -  Peptidoglycan hydrolase gp4 from Salmonella phage P22

Seq: 166 a.a.

Struc: 146 a.a.*

Protein chains

P12528  (FIBER_BPP22) -  Tail spike protein from Salmonella phage P22

Seq: 667 a.a.

Struc: 662 a.a.

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class 2: Chains Y, Z, 0: E.C.3.2.1.- - ?????
• Enzyme class 3: Chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X: E.C.?

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

DOI no: 10.1016/j.bpj.2015.11.3522

Biophys J 110:827-839 (2016)

PubMed id: 26743049

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

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

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. 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.