Primary Citation PubMed: 3145979
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Assessing local structural perturbations in proteins.
(2005) BMC Bioinformatics 6
PubMed: 16159393 | PubMedCentral: PMC1239910 | DOI: 10.1186/1471-2105-6-226
A) The closed state of calmodulin (left, PDB code: 1MXE), the open state (right, PDB code: 3CLN) and a standard whole molecule superposition (middle).
Publication Year: 2005
FlexOracle: predicting flexible hinges by identification of stable domains.
(2007) BMC Bioinformatics 8
PubMed: 17587456 | PubMedCentral: PMC1933439 | DOI: 10.1186/1471-2105-8-215
Morph ID: f958972-2168 PDB ID: 3cln.
Publication Year: 2007
Long-range intra-protein communication can be transmitted by correlated side-chain fluctuations alone.
(2011) PLoS Comput Biol 7
PubMed: 21980271 | PubMedCentral: PMC3182858 | DOI: 10.1371/journal.pcbi.1002168
The extended structure of calmodulin (3cln  ), as shown in Fig. 2(a) , provides an exemplary test case for examining how side-chain fluctuations are correlated within the folded protein.
For calmodulin, a crystal structure at 2.2 Å was used (3cln  ).
The crystal structure (a) and contact map (b) of calcium-bound calmodulin (3cln  ).
Publication Year: 2011
A novel trans conformation of ligand-free calmodulin.
(2013) PLoS One 8
PubMed: 23382982 | PubMedCentral: PMC3558517 | DOI: 10.1371/journal.pone.0054834
B: Side-by-side comparison of the novel trans (current structure, blue) and extended trans (pdb code 3CLN, dark salmon) conformations of CaM.
Publication Year: 2013
Local functional descriptors for surface comparison based binding prediction.
(2012) BMC Bioinformatics 13
PubMed: 23176080 | PubMedCentral: PMC3585919 | DOI: 10.1186/1471-2105-13-314
Table 2 Results from tests of the atomic predictor on finding the binding location of calcium ions PDB Code 1ANX 1AYP 1CGV 1CLM 1OMD 3CLN 1SAC 2SCP 3ICB 3PAL 5CPV ROC Area 0.92 0.57 1.00 0.94 0.95 0.9... 0.96 0.97 0.96 0.98 0.97 Shown are the 11 proteins used as test cases by Altman et.
Publication Year: 2012
A general and robust ray-casting-based algorithm for triangulating surfaces at the nanoscale.
PubMed: 23577073 | PubMedCentral: PMC3618509 | DOI: 10.1371/journal.pone.0059744
To assess the numerical accuracy of both the computed area and volume on the main component, we took the calmodulin protein (PDB code 3CLN) as a reference system.
(2013) PLoS Comput Biol 9
PubMed: 23843752 | PubMedCentral: PMC3699289 | DOI: 10.1371/journal.pcbi.1003106
g007 Figure 7 Cartoon representation of the protein calmodulin in its two conformations: “closed” on the left (derived from PDB id: 1CFD) and “open” on the right (deriv... d from PDB id: 3CLN).
Three-dimensional electron crystallography of protein microcrystals.
(2013) Elife 2
PubMed: 24252878 | PubMedCentral: PMC3831942 | DOI: 10.7554/eLife.01345
Models for molecular replacement validation DOI: http://dx.doi.org/10.7554/eLife.01345.016 Protein PDB ID Molecular weight (kDa) Symmetry Unit cell dimensions MR solution Hen Egg White Lysozyme * 4AXT... 14.3 P4 3 2 1 2 a = b = 78.24 Å Yes c = 37.47 Å α = β = γ = 90° T4 Lysozyme † 2LZM 18.7 P3 2 12 a = b = 61.20 Å No c = 96.80 Å α = β = 90° γ = 120° Calmodulin ‡ 3CLN 16.7 P1 a = 29.71 Å, No b = 53.79 Å, c = 24.99 Å α = 94.13°, β = 97.57°, γ = 89.46° Dodecin § 4B2J 8.5 F4 1 32 a = b = c = 142.90 Å No α = β = γ = 90° αA Crystallin # 3L1E 11.9 P4 1 2 1 2 a = b = 56.22 Å, No c = 68.66 Å α = β = γ = 90° * Cipriani et al. (2012) .
Designing molecular dynamics simulations to shift populations of the conformational states of calmodulin.
PubMed: 24339763 | PubMedCentral: PMC3854495 | DOI: 10.1371/journal.pcbi.1003366
These systems are assumed to be at physiological pH. a Unless otherwise indicated, residues are assigned charge states according to pH IS-p : physiological ionic strength, IS-l : low ionic strength, E... 31+: residue E31 is protonated, E 31 A : residue E31 is mutated to A, pH – l : low pH. b Abbreviations: E: Extended, C: Compact; The details of each simulation are as follows; the label for each type of simulation is indicated in parentheses and will be used throughout the text: ( ) Initial coordinates are taken from the extended 3CLN pdb coded structure and all residues are assigned their standard protonation states to study the conformational dynamics of extended form in solution.
There are many examples for the extended form in the protein data bank (PDB) and we utilize that with PDB code 3CLN whereby the coordinates of the first four and the last residue are not reported  .
During the MD simulation, the initial (X-ray derived) structure 3CLN is only transient and the conformations sampled in regions I and II do not overlap with any of those from the NMR ensemble.
We display in figure 2 , the locations of experimental structures on the reduced conformational space for 3CLN, 1PRW (the extended and compact crystal structures, respectively) and 2K0E (160 NMR solution structures).
( ) Starting from 3CLN and all residues having the same protonation states as in ( ), the system is neutralized by 15 Na + ions.
Also marked are the wild CaM extended (3CLN), compact (1PRW) crystal structures (black empty circles) and the 160 structures from the 2K0E NMR ensemble (black dots).
Extended conformers similar to 3CLN in general have low occupancies although some other extended conformers have occupancies as high as 35%.
We have previously reported the RMSD comparison for the overall structure as well as the N- and C-lobes of various x-ray structures, including 3CLN, 1PRW and five ligand bound forms  .
PubMed ID is not available.
Published in 2014
6 The structures of Ca 2+ -bound CaM [Protein Data Bank (PDB) entry 3cln] 7 and the Fas death domain (PDB entry 1ddf) with the binding region for CaM colored blue 6 , 8 are shown in Figure S1 of the S... pporting Information .
Publication Year: 2014
Insights into mechanism kinematics for protein motion simulation.
(2014) BMC Bioinformatics 15
PubMed: 24923224 | PubMedCentral: PMC4080786 | DOI: 10.1186/1471-2105-15-184
Finally, the last protein is the Calmodulin protein, pdb entry 3cln (see Figure 10 ) with 2201 atoms and 284 degrees of freedom.
Table 5 3cln Protein results Type of simulation rmsd ( Å ) Energy (%) RP (% of atoms inside preferred zones) Step duration Simulation duration Type 1 6.34 2.7 90 301 s 300 min Type 2 - - - 298 s - Type 3 - - - 225 s - Figure 12 Superpositions of the final structures obtained on the simulation process (red) with the data structures (green) for 1k20 protein (a), 1zac protein (b) and 3cln protein (c).
Table 2 Results of the procedure for the detection of secondary structures in the selected proteins Protein Molecular mass (Da) % of detected residues in secondary structures % of residues in secondary structures (PDB) α -helix β -sheet α -helix β -sheet 1zac 9.98 64.4 3.3 70 6 1k9p 10.27 54.4 6.6 60 6 3cln 16.88 54.5 6.2 59 5 1k20 67.75 35.2 24.5 40 20 2peq 30.56 80.5 0 72 0 4fkx 55.13 34.8 19.7 42 16 3sza 104.76 34 22 44 16 It can be conclude that the strategy requires a very low computational cost, needing only 8 m s to complete the secondary structure detection on the biggest protein, 3sza.
Effect of Calcium Ion Removal, Ionic Strength, and Temperature on the Conformation Change in Calmodulin Protein at Physiological pH.
(2014) J Biophys 2014
PubMed: 25548559 | PubMedCentral: PMC4274857 | DOI: 10.1155/2014/329703
This structure can be obtained from the Protein Data Bank (PDB code 3CLN), as shown in Figure 1 .
Published in 2015
To explore structural determinants of the preferential affinity of CaM NL for P1a compared with CaM CL , we generated a model of the P1aABD Δ22 /CaM CL complex, by superimposing CaM CL (82... 013;146 aa; PDB, 3CLN [ Babu et al., 1988 ]) on the crystal structure of the P1aABD Δ22 /CaM NL complex (rmsd, 0.50 Å over 53 equivalent Cα atoms out of 65).
The structure was solved by molecular replacement using human plectin ABD (PDB, 1MB8 ) ( Garcia-Alvarez et al., 2003 ) and the N-ter lobe of Ca 2+ -CaM (PDB, 3CLN ) ( Babu et al., 1988 ) as search models.
Comparison of CaM NL with the crystal structure of unbound Ca 2+ -CaM (Protein Data Bank [PDB], 3CLN ) ( Babu et al., 1988 ) (root-mean-square deviation (rmsd), 0.40 Å over 62 equivalent Cα atoms in N-lobe) showed that CaM NL did not change the conformation upon binding to plectin.
Publication Year: 2015
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