PDBsum entry 1uow

Glycoprotein

PDB id: 1uow

Contents

Protein chain

157 a.a. *

Ligands

GOL

ACT

Metals

_CA ×2

Waters ×184

* Residue conservation analysis

PDB id:

1uow

Name:

Glycoprotein

Title:

Calcium binding domain c2b

Structure:

Synaptotagmin i. Chain: a. Fragment: c2b domain, residues 271-421. Synonym: syti, p65. Engineered: yes. Other_details: 2 calcium ions bound, this structure is at the same resolution as PDB entry 1tjx, but the latter contains deposited protons

Source:

Rattus norvegicus. Rat. Organism_taxid: 10116. Expressed in: escherichia coli. Expression_system_taxid: 469008.

Resolution:

1.04Å R-factor: 0.167 R-free: 0.184

Authors:

Y.Cheng,S.M.Sequeira,T.H.Sollner,D.J.Patel

Key ref:

Y.Cheng et al. (2004). Crystallographic identification of Ca2+ and Sr2+ coordination sites in synaptotagmin I C2B domain. Protein Sci, 13, 2665-2672. PubMed id: 15340165 DOI: 10.1110/ps.04832604

Date:

24-Sep-03 Release date: 16-Sep-04

Protein chain

P21707  (SYT1_RAT) -  Synaptotagmin-1 from Rattus norvegicus

Seq: 421 a.a.

Struc: 157 a.a.*

* PDB and UniProt seqs differ at 8 residue positions (black crosses)

DOI no: 10.1110/ps.04832604

Protein Sci 13:2665-2672 (2004)

PubMed id: 15340165

Crystallographic identification of Ca2+ and Sr2+ coordination sites in synaptotagmin I C2B domain.

Y.Cheng, S.M.Sequeira, L.Malinina, V.Tereshko, T.H.Söllner, D.J.Patel.

ABSTRACT

Synaptotagmin I has two tandem Ca(2+)-binding C(2) domains, which are essential for fast synchronous synaptic transmission in the central nervous system. We have solved four crystal structures of the C(2)B domain, one of them in the cation-free form at 1.50 A resolution, two in the Ca(2+)-bound form at 1.04 A (two bound Ca(2+) ions) and 1.65 A (three bound Ca(2+) ions) resolution and one in the Sr(2+)-bound form at 1.18 A (one bound Sr(2+) ion) resolution. The side chains of four highly conserved aspartic acids (D303, D309, D363, and D365) and two main chain oxygens (M302:O and Y364:O), together with water molecules, are in direct contact with two bound Ca(2+) ions (sites 1 and 2). At higher Ca(2+) concentrations, the side chain of N333 rotates and cooperates with D309 to generate a third Ca(2+) coordination site (site 3). Divalent cation binding sites 1 and 2 in the C(2)B domain were previously identified from NMR NOE patterns and titration studies, supplemented by site-directed mutation analysis. One difference between the crystal and NMR studies involves D371, which is not involved in coordination with any of the identified Ca(2+) sites in the crystal structures, while it is coordinated to Ca(2+) in site 2 in the NMR structure. In the presence of Sr(2+), which is also capable of triggering exocytosis, but with lower efficiency, only one cation binding site (site 1) was occupied in the crystallographic structure.

Selected figure(s)

Figure 1.
Figure 1. Structure of C[2]B-B. (A) Front and side view of ribbon diagrams of the structure of C[2]B-B with 2 Ca^2+ ions. -Strands are labeled from 1 to 8, while helices are labeled H1 and H2. Ca^2+ ions are labeled Ca1 and Ca2. (B) Front and back view of electrostatic potential surface of C[2]B-B. The acidic and basic residues are colored green and orange, respectively.

Figure 3.
Figure 3. Cation-binding sites in (A) superpositioned C[2]B-NMR structures and (B) C[2]B-B, (C) C[2]B-C, and (D) C[2]B-D crystal structures. The Ca^2+ and Sr2+ ions are colored orange. The oxygen atoms that coordinate the cations are colored red. Water molecules are represented as small red spheres. Dashed lines indicate pentagonal bipyramidyl coordination to Ca^2+ sites (B,C) and tetragonal bipyramidyl coordination to Sr2+ site (D) in the crystal structures.

The above figures are reprinted by permission from the Protein Society: Protein Sci (2004, 13, 2665-2672) copyright 2004.

Figures were selected by an automated process.