PDBsum entry 7nop

Viral protein

PDB id: 7nop

Contents

Protein chains

78 a.a.

217 a.a.

139 a.a.

PDB id:

7nop

Name:

Viral protein

Title:

Structure of the mature rsv ca lattice: group iv, hexamer-hexamer interface, class 5'beta

Structure:

Capsid protein p27, alternate cleaved 1. Chain: a, b, c, d, e, f, g, h, i, j. Engineered: yes

Source:

Rous sarcoma virus (strain praguE C). Rsv-prc. Organism_taxid: 11888. Strain: praguE C. Gene: gag. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008

Authors:

M.Obr,C.L.Ricana,N.Nikulin,J.-P.R.Feathers,M.Klanschnig,A.Thader, M.C.Johnson,V.M.Vogt,F.K.M.Schur,R.A.Dick

Key ref:

M.Obr et al. (2021). Structure of the mature Rous sarcoma virus lattice reveals a role for IP6 in the formation of the capsid hexamer. Nat Commun, 12, 3226. PubMed id: 34050170 DOI: 10.1107/S0907444909042073

Date:

25-Feb-21 Release date: 21-Apr-21

Protein chains

P03354  (POL_RSVP) -  Gag-Pol polyprotein from Rous sarcoma virus subgroup C (strain Prague)

Seq: 1603 a.a.

Struc: 78 a.a.

Protein chains

P03354  (POL_RSVP) -  Gag-Pol polyprotein from Rous sarcoma virus subgroup C (strain Prague)

Seq: 1603 a.a.

Struc: 217 a.a.

Protein chains

P03354  (POL_RSVP) -  Gag-Pol polyprotein from Rous sarcoma virus subgroup C (strain Prague)

Seq: 1603 a.a.

Struc: 139 a.a.

Enzyme reactions

• Enzyme class 2: Chains A, B, C, D, E, F, G, H, I, J: E.C.2.7.7.- - ?????
• Enzyme class 3: Chains A, B, C, D, E, F, G, H, I, J: E.C.2.7.7.49 - RNA-directed Dna polymerase.
• Reaction: DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate
• Enzyme class 4: Chains A, B, C, D, E, F, G, H, I, J: E.C.2.7.7.7 - DNA-directed Dna polymerase.
• Reaction: DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate
• Enzyme class 5: Chains A, B, C, D, E, F, G, H, I, J: E.C.3.1.-.-
• Enzyme class 6: Chains A, B, C, D, E, F, G, H, I, J: E.C.3.1.26.4 - ribonuclease H.
• Reaction: Endonucleolytic cleavage to 5'-phosphomonoester.
• Enzyme class 7: Chains A, B, C, D, E, F, G, H, I, J: E.C.3.4.23.- - ?????

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.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1107/S0907444909042073

Nat Commun 12:3226 (2021)

PubMed id: 34050170

Structure of the mature Rous sarcoma virus lattice reveals a role for IP6 in the formation of the capsid hexamer.

M.Obr, C.L.Ricana, N.Nikulin, J.R.Feathers, M.Klanschnig, A.Thader, M.C.Johnson, V.M.Vogt, F.K.M.Schur, R.A.Dick.

ABSTRACT

Inositol hexakisphosphate (IP6) is an assembly cofactor for HIV-1. We report here that IP6 is also used for assembly of Rous sarcoma virus (RSV), a retrovirus from a different genus. IP6 is ~100-fold more potent at promoting RSV mature capsid protein (CA) assembly than observed for HIV-1 and removal of IP6 in cells reduces infectivity by 100-fold. Here, visualized by cryo-electron tomography and subtomogram averaging, mature capsid-like particles show an IP6-like density in the CA hexamer, coordinated by rings of six lysines and six arginines. Phosphate and IP6 have opposing effects on CA in vitro assembly, inducing formation of T = 1 icosahedrons and tubes, respectively, implying that phosphate promotes pentamer and IP6 hexamer formation. Subtomogram averaging and classification optimized for analysis of pleomorphic retrovirus particles reveal that the heterogeneity of mature RSV CA polyhedrons results from an unexpected, intrinsic CA hexamer flexibility. In contrast, the CA pentamer forms rigid units organizing the local architecture. These different features of hexamers and pentamers determine the structural mechanism to form CA polyhedrons of variable shape in mature RSV particles.