PDBsum entry 1efn

Complex (sh3 domain/viral enhancer)

PDB id: 1efn

Contents

Protein chains

57 a.a. *

104 a.a. *

Ligands

PBM ×2

Waters ×99

* Residue conservation analysis

PDB id:

1efn

Name:

Complex (sh3 domain/viral enhancer)

Title:

HIV-1 nef protein in complex with r96i mutant fyn sh3 domain

Structure:

Fyn tyrosine kinase. Chain: a, c. Fragment: sh3 domain, residues 85-141. Synonym: src-homology 3 domain. Engineered: yes. Mutation: yes. HIV-1 nef protein. Chain: b, d. Fragment: conserved core domain of nef, residues 71-203.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: HIV-1 nef. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Human immunodeficiency virus 1. Organism_taxid: 11676. Strain: nl4-3.

Biol. unit:

Tetramer (from PQS)

Resolution:

2.50Å R-factor: 0.215 R-free: 0.282

Authors:

C.-H.Lee,J.Kuriyan

Key ref:

C.H.Lee et al. (1996). Crystal structure of the conserved core of HIV-1 Nef complexed with a Src family SH3 domain. Cell, 85, 931-942. PubMed id: 8681387 DOI: 10.1016/S0092-8674(00)81276-3

Date:

29-Jun-96 Release date: 11-Jan-97

Protein chains

P06241  (FYN_HUMAN) -  Tyrosine-protein kinase Fyn from Homo sapiens

Seq: 537 a.a.

Struc: 57 a.a.*

Protein chains

P03406  (NEF_HV1BR) -  Protein Nef from Human immunodeficiency virus type 1 group M subtype B (isolate BRU/LAI)

Seq: 206 a.a.

Struc: 104 a.a.*

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

Enzyme reactions

• Enzyme class: Chains A, C: E.C.2.7.10.2 - non-specific protein-tyrosine kinase.
• Reaction: L-tyrosyl-[protein] + ATP = O-phospho-L-tyrosyl-[protein] + ADP + H⁺

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

Added reference

DOI no: 10.1016/S0092-8674(00)81276-3

Cell 85:931-942 (1996)

PubMed id: 8681387

Crystal structure of the conserved core of HIV-1 Nef complexed with a Src family SH3 domain.

C.H.Lee, K.Saksela, U.A.Mirza, B.T.Chait, J.Kuriyan.

ABSTRACT

The crystal structure of the conserved core of HIV-1 Nef has been determined in complex with the SH3 domain of a mutant Fyn tyrosine kinase (a single amino acid substitution, Arg-96 to isoleucine), to which Nef binds tightly. The conserved PxxP sequence motif of Nef, known to be important for optimal viral replication, is part of a polyproline type II helix that engages the SH3 domain in a manner resembling closely the interaction of isolated peptides with SH3 domains. The Nef-SH3 structure also reveals how high affinity and specificity in the SH3 interaction is achieved by the presentation of the PxxP motif within the context of the folded structure of Nef.

Selected figure(s)

Figure 2.
Figure 2. Structure of Nef–SH3 Complex(A and B) Stereo diagrams of the polypeptide backbones of Nef[core] and Fyn(R96I) SH3. The N-terminal helical layer of Nef[core] (residues 71–120), which forms the SH3 interaction surface, is colored yellow. The rest of Nef[core] (residues 121–203) is colored green. The disordered loop (residues 149–178) between βC and βD is indicated as a dotted line. The Fyn(R96I) SH3 domain is in blue. Also shown are the side chains of the conserved tryptophan of SH3 (residue 119, in red), the specificity-conferring isoleucine of SH3 (residue 96, in red), and the two prolines that define the PxxP motif of Nef (residues 72 and 75, in yellow). The views in (A) and (B) are approximately orthogonal. The figure was prepared using MOLSCRIPT ([23]) and Raster3D ( [1]).(C) The molecular surface of Nef[core], with Fyn(R96I) SH3. The local electrostatic potential of Nef[core] was calculated in the absence of the SH3 domain using GRASP ([27]). The molecular surface is colored according to the local electrostatic potential, with colors ranging from dark blue (most positive region) to deep red (most negative) through white (neutral). The SH3 domain is shown as a blue tube. The side chains of Trp-119 and Ile-96 of SH3 are shown in yellow. Trp-113 and Phe-90 of Nef separate the binding pocket for Ile-96 of SH3 from the hydrophobic crevice that is available for potential interaction with other molecules. Arg-106 of Nef, located at the lower left edge of the crevice, is implicated in the association of Nef with a Ser kinase activity ( [33]).

Figure 5.
Figure 5. Tertiary Interactions between Nef[core] and Fyn(R96I) SH3 Domain(A) Molecular surface of Nef, showing the binding site for the isoleucine side chain of the SH3 domain.(B) Comparison of the interactions in the two complexes in the crystal. The polypeptide backbones of Nef and the SH3 domain are shown as green and blue tubes, respectively. Side chains of Nef are shown in pink and in yellow (displayed under their respective molecular surfaces). SH3 side chains are shown in red. Hydrogen bonding interactions are shown as dashed lines. Hydrogen bonds to backbone positions are indicated by the placement of white circles along the backbone ribbon. For clarity, the side chain of Ile-96 is not shown, and instead the Cα position of this residue is indicated with a red circle. The structure on the left is the complex that is the focus of the major part of the discussion in the text. The structure on the right is that of the second independent complex in the crystal. Note the slight change in the relative orientation of the Nef and SH3 components of the complex (see text). The side chain of Asp-86 forms a hydrogen bond with Thr-97 in the RT loop of the second complex. For clarity, this interaction is not shown.

The above figures are reprinted by permission from Cell Press: Cell (1996, 85, 931-942) copyright 1996.

Figures were selected by an automated process.