PDBsum entry 6y9v

Viral protein

PDB id: 6y9v

Contents

Protein chains

146 a.a.

(+ 2 more) 220 a.a.

164 a.a.

74 a.a.

PDB id:

6y9v

Name:

Viral protein

Title:

Structure of the native full-length HIV-1 capsid protein in complex with cyclophilin a from helical assembly (-8,13)

Structure:

Gag-pol polyprotein. Chain: a, b, c, d, g, h, n, y, d, e, j, k. Synonym: pr160gag-pol. Ec: 3.4.23.16,2.7.7.49,2.7.7.7,3.1.26.13,3.1.13.2,2.7.7.-,3.1.-.-. Engineered: yes. Peptidyl-prolyl cis-trans isomerase a. Chain: j. Synonym: ppiase a,cyclophilin a,cyclosporin a-binding protein, rotamase a.

Source:

Human immunodeficiency virus 1. Organism_taxid: 11676. Gene: gag-pol. Expressed in: escherichia coli. Expression_system_taxid: 562. Homo sapiens. Human. Organism_taxid: 9606. Gene: ppia, cypa.

Authors:

T.Ni,S.Gerard,G.Zhao,J.Ning,P.Zhang

Key ref:

T.Ni et al. (2020). Intrinsic curvature of the HIV-1 CA hexamer underlies capsid topology and interaction with cyclophilin A. Nat Struct Mol Biol, 27, 855-862. PubMed id: 32747784 DOI: 10.1038/s41594-020-0467-8

Date:

10-Mar-20 Release date: 19-Aug-20

Protein chains

P04591  (GAG_HV1H2) -  Gag polyprotein from Human immunodeficiency virus type 1 group M subtype B (isolate HXB2)

Seq: 500 a.a.

Struc: 146 a.a.

Protein chains

P04591  (GAG_HV1H2) -  Gag polyprotein from Human immunodeficiency virus type 1 group M subtype B (isolate HXB2)

Seq: 500 a.a.

Struc: 220 a.a.

Protein chain

P62937  (PPIA_HUMAN) -  Peptidyl-prolyl cis-trans isomerase A from Homo sapiens

Seq: 165 a.a.

Struc: 164 a.a.

Protein chains

P04591  (GAG_HV1H2) -  Gag polyprotein from Human immunodeficiency virus type 1 group M subtype B (isolate HXB2)

Seq: 500 a.a.

Struc: 74 a.a.

Enzyme reactions

• Enzyme class 1: Chains A, B, C, D, G, H, N, Y, d, e, j, k: E.C.2.7.7.- - ?????
• Enzyme class 2: Chains A, B, C, D, G, H, N, Y, d, e, j, k: E.C.2.7.7.49 - RNA-directed Dna polymerase.
• Reaction: DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate
• Enzyme class 3: Chains A, B, C, D, G, H, N, Y, d, e, j, k: E.C.2.7.7.7 - DNA-directed Dna polymerase.
• Reaction: DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate
• Enzyme class 4: Chains A, B, C, D, G, H, N, Y, d, e, j, k: E.C.3.1.-.-
• Enzyme class 5: Chains A, B, C, D, G, H, N, Y, d, e, j, k: E.C.3.1.13.2 - exoribonuclease H.
• Reaction: Exonucleolytic cleavage to 5'-phosphomonoester oligonucleotides in both 5'- to 3'- and 3'- to 5'-directions.
• Enzyme class 6: Chains A, B, C, D, G, H, N, Y, d, e, j, k: E.C.3.1.26.13 - retroviral ribonuclease H.
• Enzyme class 7: Chains A, B, C, D, G, H, N, Y, d, e, j, k: E.C.3.4.23.16 - HIV-1 retropepsin.
• Reaction: Specific for a P1 residue that is hydrophobic, and P1' variable, but often Pro.
• Enzyme class 8: Chain J: E.C.5.2.1.8 - peptidylprolyl isomerase.
• Reaction: [protein]-peptidylproline (omega=180) = [protein]-peptidylproline (omega=0)

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: 10.1038/s41594-020-0467-8

Nat Struct Mol Biol 27:855-862 (2020)

PubMed id: 32747784

Intrinsic curvature of the HIV-1 CA hexamer underlies capsid topology and interaction with cyclophilin A.

T.Ni, S.Gerard, G.Zhao, K.Dent, J.Ning, J.Zhou, J.Shi, J.Anderson-Daniels, W.Li, S.Jang, A.N.Engelman, C.Aiken, P.Zhang.

ABSTRACT

The mature retrovirus capsid consists of a variably curved lattice of capsid protein (CA) hexamers and pentamers. High-resolution structures of the curved assembly, or in complex with host factors, have not been available. By devising cryo-EM methodologies for exceedingly flexible and pleomorphic assemblies, we have determined cryo-EM structures of apo-CA hexamers and in complex with cyclophilin A (CypA) at near-atomic resolutions. The CA hexamers are intrinsically curved, flexible and asymmetric, revealing the capsomere and not the previously touted dimer or trimer interfaces as the key contributor to capsid curvature. CypA recognizes specific geometries of the curved lattice, simultaneously interacting with three CA protomers from adjacent hexamers via two noncanonical interfaces, thus stabilizing the capsid. By determining multiple structures from various helical symmetries, we further revealed the essential plasticity of the CA molecule, which allows formation of continuously curved conical capsids and the mechanism of capsid pattern sensing by CypA.