PDBsum entry 3rpb

Endocytosis/exocytosis

PDB id: 3rpb

Contents

Protein chain

140 a.a. *

* Residue conservation analysis

PDB id:

3rpb

Name:

Endocytosis/exocytosis

Title:

The c2b-domain of rabphilin: structural variations in a janus-faced domain

Structure:

Rabphilin 3-a. Chain: a. Fragment: c2b domain. Engineered: yes

Source:

Rattus norvegicus. Norway rat. Organism_taxid: 10116. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Expression_system_variant: de3

NMR struc:

20 models

Authors:

J.Ubach,J.Garcia,M.P.Nittler,T.C.Sudhof,J.Rizo

Key ref:

J.Ubach et al. (1999). Structure of the Janus-faced C2B domain of rabphilin. Nat Cell Biol, 1, 106-112. PubMed id: 10559882 DOI: 10.1038/10076

Date:

19-Apr-99 Release date: 23-Dec-99

Protein chain

P47709  (RP3A_RAT) -  Rabphilin-3A from Rattus norvegicus

Seq: 684 a.a.

Struc: 140 a.a.

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1038/10076

Nat Cell Biol 1:106-112 (1999)

PubMed id: 10559882

Structure of the Janus-faced C2B domain of rabphilin.

J.Ubach, J.García, M.P.Nittler, T.C.Südhof, J.Rizo.

ABSTRACT

C2 domains are widespread protein modules that often occur as tandem repeats in many membrane-trafficking proteins such as synaptotagmin and rabphilin. The first and second C2 domains (C2A and C2B, respectively) have a high degree of homology but also specific differences. The structure of the C2A domain of synaptotagmin I has been extensively studied but little is known about the C2B domains. We have used NMR spectroscopy to determine the solution structure of the C2B domain of rabphilin. The overall structure of the C2B domain is very similar to that of other C2 domains, with a rigid beta-sandwich core and loops at the top (where Ca2+ binds) and the bottom. Surprisingly, a relatively long alpha-helix is inserted at the bottom of the domain and is conserved in all C2B domains. Our results, together with the Ca(2+)-independent interactions observed for C2B domains, indicate that these domains have a Janus-faced nature, with a Ca(2+)-binding top surface and a Ca(2+)-independent bottom surface.

Selected figure(s)

Figure 3.
Figure 3. Solution structure of the C[2]B domain. a, Backbone superposition of the 20 simulated annealing structures of the C[2]B domain (residues 541 -677). N and C indicate the amino and carboxy termini, respectively. The numbers indicate the positions of several residues to help identify the orientation of the molecule. b, Superposition of the 20 structures showing only the heavy atoms of side chains in a slice of 12 Å within the centre of the domain. c, Ribbon diagram of the C[2]B domain in the same orientation as a and b. The -strands have been labelled 1 -8 and the positions of the two helices and the Ca^2+-binding region (loops 1 -3) have also been indicated. d, Ribbon diagram of the C[2]B domain in an orientation approximately perpendicular to that of c, which shows how helix 2 runs parallel between the two -sheets. The ribbon diagrams were prepared with the program Molscript49.

Figure 6.
Figure 6. Taxonomy of C[2] domains. a, Topologies of the different subclasses of C[2] domains that have been identified and that we refer to as topologies IA (SytI C[ 2]A domain and PKC- C[2] domain), IB (rabphilin C[ 2]B domain), IIA (PLC- 1 and cPLA[2] C[2] domains) and IIB (PKC- ) (see text). For simplicity, very short -helices within loops of several C[2] domains have not been included in the classification. b, Superpositions of the backbone of the rabphilin C[2]B domain (red) with the backbone of C[2] domains from the other three subclasses (black). The superpositions with SytI C[2]A domain (PDB code 1RSY) and the cPLA[2] C[2] domain (PDB code 1RLW) are shown in the same orientation as Fig. 3a -c . The superposition with the PKC- C[2] domain (PDB code 1BDY) is shown with helix 2 in front, as in Fig. 3d. The positions of secondary structure elements discussed in the text (strand 8 and helix 2) are indicated.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Cell Biol (1999, 1, 106-112) copyright 1999.

Figures were selected by the author.