PDBsum entry 2hqw

Metal binding protein

PDB id: 2hqw

Contents

Protein chains

138 a.a. *

22 a.a. *

Metals

_CA ×4

Waters ×66

* Residue conservation analysis

PDB id:

2hqw

Name:

Metal binding protein

Title:

Crystal structure of ca2+/calmodulin bound to nmda receptor nr1c1 peptide

Structure:

Calmodulin. Chain: a. Synonym: cam. Engineered: yes. Glutamate nmda receptor subunit zeta 1. Chain: b. Fragment: c-terminal tail, c1 region. Synonym: n-methyl-d-aspartate receptor subunit nr1, nr1c1 peptide. Engineered: yes

Source:

Rattus norvegicus. Norway rat. Organism_taxid: 10116. Gene: calm1, calm, cam, cam1. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Other_details: the peptide was chemically synthesized. The sequence of the peptide is naturally found in homo sapiens (human).

Resolution:

1.90Å R-factor: 0.207 R-free: 0.248

Authors:

Z.Akyol,L.Gakhar,B.R.Sorensen,J.H.Hell,M.A.Shea

Key ref:

Z.A.Ataman et al. (2007). The NMDA receptor NR1 C1 region bound to calmodulin: structural insights into functional differences between homologous domains. Structure, 15, 1603-1617. PubMed id: 18073110 DOI: 10.1016/j.str.2007.10.012

Date:

19-Jul-06 Release date: 13-Nov-07

Protein chain

P0DP29  (CALM1_RAT) -  Calmodulin-1 from Rattus norvegicus

Seq: 149 a.a.

Struc: 138 a.a.

Protein chain

P35439  (NMDZ1_RAT) -  Glutamate receptor ionotropic, NMDA 1 from Rattus norvegicus

Seq: 938 a.a.

Struc: 22 a.a.

DOI no: 10.1016/j.str.2007.10.012

Structure 15:1603-1617 (2007)

PubMed id: 18073110

The NMDA receptor NR1 C1 region bound to calmodulin: structural insights into functional differences between homologous domains.

Z.A.Ataman, L.Gakhar, B.R.Sorensen, J.W.Hell, M.A.Shea.

ABSTRACT

Calmodulin (CaM) regulates tetrameric N-methyl-D-aspartate receptors (NMDARs) by binding tightly to the C0 and C1 regions of its NR1 subunit. A crystal structure (2HQW; 1.96 A) of calcium-saturated CaM bound to NR1C1 (peptide spanning 875-898) showed that NR1 S890, whose phosphorylation regulates membrane localization, was solvent protected, whereas the endoplasmic reticulum retention motif was solvent exposed. NR1 F880 filled the CaM C-domain pocket, whereas T886 was closest to the N-domain pocket. This 1-7 pattern was most similar to that in the CaM-MARCKS complex. Comparison of CaM-ligand wrap-around conformations identified a core tetrad of CaM C-domain residues (FLMM(C)) that contacted all ligands consistently. An identical tetrad of N-domain residues (FLMM(N)) made variable sets of contacts with ligands. This CaM-NR1C1 structure provides a foundation for designing mutants to test the role of CaM in NR1 trafficking as well as insights into how the homologous CaM domains have different roles in molecular recognition.

Selected figure(s)

Figure 2.
Figure 2. Crystal Structure of the CaM-NR1C1p Complex
(A) NR1C1p sequence and structure superimposed on its electron density map contoured at 1.0σ.
(B and C) Alternate views of CaM-NR1C1p (2HQW) showing the CaM N-domain backbone (blue), the C domain (red), Ca^2+ ions and binding sites (yellow), and NR1C1p (gray). The figure was made with MacPymol.
(D and E) Alignment of 17 canonical CaM-target complexes by their Cα atoms of the (D) N-domain (residues 5–72; 68 atoms) and (E) C-domain (residues 84–146; 63 atoms) FLMM residues as described in Experimental Procedures.

Figure 4.
Figure 4. Distribution of CaM N- and C-Domain Contacts in the CaM-NR1C1p Complex
(A) N-domain residues ≤ 4.5 Å of NR1C1p shown as sticks; 17 contacts were made with NR1 residues 875–885 (gray), and 19 contacts were made with residues 885–896 (black).
(B) Sequence map of CaM residues ≤ 4.5 Å of NR1C1p. Residues in NR1C1p that make the highest number of contacts exclusively with the C domain (F880) and the N domain (T886) are boxed; the ER retention signal is underlined.
(C) C-domain residues ≤ 4.5 Å of NR1C1p shown as sticks; 27 contacts were made with residues 875–885, and 7 contacts were made with residues 885–896. Ca^2+ ions and binding sites (yellow in [A] and [C]) are designated I, II, III, and IV.
The figure was made with MacPymol.

The above figures are reprinted from an Open Access publication published by Cell Press: Structure (2007, 15, 1603-1617) copyright 2007.

Figures were selected by the author.