PDBsum entry 6crs

Virus

PDB id: 6crs

Contents

Protein chains

212 a.a.

244 a.a.

235 a.a.

PDB id:

6crs

Name:

Virus

Title:

Cryoem structure of human enterovirus d68 a-particle (ph 7.2 and 4 degrees celsius)

Structure:

Viral protein 1. Chain: a. Fragment: unp residues 565-861. Viral protein 3. Chain: b. Fragment: unp residues 318-564. Viral protein 2. Chain: c. Fragment: unp residues 70-317

Source:

Enterovirus d68. Organism_taxid: 42789. Strain: us/mo/14-18947. Cell_line: rhabdomyosarcoma. Cell_line: rhabdomyosarcoma

Authors:

Y.Liu,M.G.Rossmann

Key ref:

Y.Liu et al. (2018). Molecular basis for the acid-initiated uncoating of human enterovirus D68. Proc Natl Acad Sci U S A, 115, E12209. PubMed id: 30530701 DOI: 10.1073/pnas.1803347115

Date:

19-Mar-18 Release date: 19-Dec-18

Protein chain

A0A097BW12  (A0A097BW12_HED68) -  Genome polyprotein from Human enterovirus D68

Seq: 2188 a.a.

Struc: 212 a.a.

Protein chain

A0A097BW12  (A0A097BW12_HED68) -  Genome polyprotein from Human enterovirus D68

Seq: 2188 a.a.

Struc: 244 a.a.

Protein chain

A0A097BW12  (A0A097BW12_HED68) -  Genome polyprotein from Human enterovirus D68

Seq: 2188 a.a.

Struc: 235 a.a.

Enzyme reactions

• Enzyme class 2: Chains A, B, C: E.C.2.7.7.48 - RNA-directed Rna polymerase.
• Reaction: RNA(n) + a ribonucleoside 5'-triphosphate = RNA(n+1) + diphosphate
• Enzyme class 3: Chains A, B, C: E.C.3.4.22.28 - picornain 3C.
• Reaction: Selective cleavage of Gln-|-Gly bond in the poliovirus polyprotein. In other picornavirus reactions Glu may be substituted for Gln, and Ser or Thr for Gly.
• Enzyme class 4: Chains A, B, C: E.C.3.4.22.29 - picornain 2A.
• Reaction: Selective cleavage of Tyr-|-Gly bond in the picornavirus polyprotein. In other picornavirus reactions Glu may be substituted for Gln, and Ser or Thr for Gly.
• Enzyme class 5: Chains A, B, C: E.C.3.6.1.15 - nucleoside-triphosphate phosphatase.
• Reaction: a ribonucleoside 5'-triphosphate + H2O = a ribonucleoside 5'-diphosphate + phosphate + H⁺

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: 10.1073/pnas.1803347115

Proc Natl Acad Sci U S A 115:E12209 (2018)

PubMed id: 30530701

Molecular basis for the acid-initiated uncoating of human enterovirus D68.

Y.Liu, J.Sheng, A.L.W.van Vliet, G.Buda, F.J.M.van Kuppeveld, M.G.Rossmann.

ABSTRACT

Enterovirus D68 (EV-D68) belongs to a group of enteroviruses that contain a single positive-sense RNA genome surrounded by an icosahedral capsid. Like common cold viruses, EV-D68 mainly causes respiratory infections and is acid-labile. The molecular mechanism by which the acid-sensitive EV-D68 virions uncoat and deliver their genome into a host cell is unknown. Using cryoelectron microscopy (cryo-EM), we have determined the structures of the full native virion and an uncoating intermediate [the A (altered) particle] of EV-D68 at 2.2- and 2.7-Å resolution, respectively. These structures showed that acid treatment of EV-D68 leads to particle expansion, externalization of the viral protein VP1 N termini from the capsid interior, and formation of pores around the icosahedral twofold axes through which the viral RNA can exit. Moreover, because of the low stability of EV-D68, cryo-EM analyses of a mixed population of particles at neutral pH and following acid treatment demonstrated the involvement of multiple structural intermediates during virus uncoating. Among these, a previously undescribed state, the expanded 1 ("E1") particle, shows a majority of internal regions (e.g., the VP1 N termini) to be ordered as in the full native virion. Thus, the E1 particle acts as an intermediate in the transition from full native virions to A particles. Together, the present work delineates the pathway of EV-D68 uncoating and provides the molecular basis for the acid lability of EV-D68 and of the related common cold viruses.