PDBsum entry 2hqw

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protein metals Protein-protein interface(s) links
Metal binding protein PDB id
Protein chains
138 a.a. *
22 a.a. *
_CA ×4
Waters ×66
* Residue conservation analysis
PDB id:
Name: Metal binding protein
Title: Crystal structure of ca2+/calmodulin bound to nmda receptor 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 p 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 of the peptide is naturally found in homo sapiens (human).
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
19-Jul-06     Release date:   13-Nov-07    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P62161  (CALM_RAT) -  Calmodulin
149 a.a.
138 a.a.
Protein chain
Pfam   ArchSchema ?
Q05586  (NMDZ1_HUMAN) -  Glutamate receptor ionotropic, NMDA 1
938 a.a.
22 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     plasma membrane   15 terms 
  Biological process     regulation of cytokinesis   20 terms 
  Biochemical function     enzyme regulator activity     19 terms  


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.
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.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21287611 S.E.O'Donnell, L.Yu, C.A.Fowler, and M.A.Shea (2011).
Recognition of β-calcineurin by the domains of calmodulin: Thermodynamic and structural evidence for distinct roles.
  Proteins, 79, 765-786.  
20953164 E.Y.Kim, C.H.Rumpf, F.Van Petegem, R.J.Arant, F.Findeisen, E.S.Cooley, E.Y.Isacoff, and D.L.Minor (2010).
Multiple C-terminal tail Ca(2+)/CaMs regulate Ca(V)1.2 function but do not mediate channel dimerization.
  EMBO J, 29, 3924-3938.
PDB code: 3oxq
20544963 M.D.Feldkamp, S.E.O'Donnell, L.Yu, and M.A.Shea (2010).
Allosteric effects of the antipsychotic drug trifluoperazine on the energetics of calcium binding by calmodulin.
  Proteins, 78, 2265-2282.  
20617039 T.Sasabe, and S.Ishiura (2010).
Alcoholism and alternative splicing of candidate genes.
  Int J Environ Res Public Health, 7, 1448-1466.  
19667066 H.Ishida, M.Rainaldi, and H.J.Vogel (2009).
Structural studies of soybean calmodulin isoform 4 bound to the calmodulin-binding domain of tobacco mitogen-activated protein kinase phosphatase-1 provide insights into a sequential target binding mode.
  J Biol Chem, 284, 28292-28305.
PDB code: 2kn2
19089983 T.I.Evans, and M.A.Shea (2009).
Energetics of calmodulin domain interactions with the calmodulin binding domain of CaMKII.
  Proteins, 76, 47-61.  
18940602 E.Y.Kim, C.H.Rumpf, Y.Fujiwara, E.S.Cooley, F.Van Petegem, and D.L.Minor (2008).
Structures of CaV2 Ca2+/CaM-IQ domain complexes reveal binding modes that underlie calcium-dependent inactivation and facilitation.
  Structure, 16, 1455-1467.
PDB codes: 3dve 3dvj 3dvk 3dvm
18583346 Q.Guo, J.E.Jureller, J.T.Warren, E.Solomaha, J.Florián, and W.J.Tang (2008).
Protein-protein docking and analysis reveal that two homologous bacterial adenylyl cyclase toxins interact with calmodulin differently.
  J Biol Chem, 283, 23836-23845.  
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