PDBsum entry: 2bl6

Nucleocapsid protein

PDB id: 2bl6

Contents

Protein chain

37 a.a. *

Metals

_ZN ×2

* Residue conservation analysis

PDB id:

2bl6

Name:

Nucleocapsid protein

Title:

Solution structure of the zn complex of eiav ncp11(22-58) peptide, including two cchc zn-binding motifs.

Structure:

Nucleocapsid protein p11. Chain: a. Fragment: residues 381-417. Other_details: fragment 22-58 of ncp11 corresponds to 381- 417 of the whole eiav gag protein contains two zn ions in two cchc zn-binding domains

Source:

Synthetic: yes. Equine infectious anemia virus. Eiav. Organism_taxid: 11665. Variant: wyoming isolate

NMR struc:

30 models

Authors:

P.Amodeo,M.A.Castiglione-Morelli,A.Ostuni,A.Bavoso

Key ref:

P.Amodeo et al. (2006). Structural features in EIAV NCp11: a lentivirus nucleocapsid protein with a short linker. Biochemistry, 45, 5517-5526. PubMed id: 16634633 DOI: 10.1021/bi0524924

Date:

02-Mar-05 Release date: 10-Apr-06

Protein chain

P69732  (GAG_EIAVY) -  Gag polyprotein

Seq: 486 a.a.

Struc: 37 a.a.

 Gene Ontology (GO) functional annotation 

• Biochemical function: nucleic acid binding (2 terms)

DOI no: 10.1021/bi0524924

Biochemistry 45:5517-5526 (2006)

PubMed id: 16634633

Structural features in EIAV NCp11: a lentivirus nucleocapsid protein with a short linker.

P.Amodeo, M.A.Castiglione Morelli, A.Ostuni, G.Battistuzzi, A.Bavoso.

ABSTRACT

Lentiviral nucleocapsid proteins are a class of multifunctional proteins that play an essential role in RNA packaging and viral infectivity. They contain two CX(2)CX(4)HX(4)C zinc binding motifs connected by a basic linker of variable length. The 3D structure of a 37-aa peptide corresponding to sequence 22-58 from lentiviral EIAV nucleocapsid protein NCp11, complexed with zinc, has been determined by 2D (1)H NMR spectroscopy, simulated annealing, and molecular dynamics. The solution structure consists of two zinc binding domains held together by a five-residue basic linker Arg(38)-Ala-Pro-Lys-Val(42) that allows for spatial proximity between the two finger domains. Observed linker folding is stabilized by H bonded secondary structure elements, resulting in an Omega-shaped central region, asymmetrically centered on the linker. The conformational differences and similarities with other NC zinc binding knuckles have been systematically analyzed. The two CCHC motifs, both characterized by a peculiar Pro-Gly sequence preceding the His residue, although preserving Zn-binding geometry and chirality of other known NC proteins, exhibit local fold differences both between each other and in comparison with other previously characterized retroviral CCHC motifs.