Citations in PubMed

Primary Citation PubMed: 7552748 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 13

Citations in PubMed

This linkout lists citations, indexed by PubMed, to the Primary Citation for this PDB ID.

PDB ID Mentions in PubMed Central

Data mentions are occurrences of PDB IDs in the full text articles from the PubMedCentral Open Access Subset of currently about 1 million articles. For each article, the sentences containing the PDB ID are listed. Article titles can be filtered by keywords and sorted by year.

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Crystal structures of the GCaMP calcium sensor reveal the mechanism of fluorescence signal change and aid rational design.

(2009) J Biol Chem 284

PubMed: 19098007 | PubMedCentral: PMC2649101 | DOI: 10.1074/jbc.M807657200

Subsequently searching for the calcium-free N-terminal or C-terminal lobes of CaM (PDB code 1CFD ( 24 )) did not reveal any clear solutions.

Publication Year: 2009

Fast optimization of statistical potentials for structurally constrained phylogenetic models.

(2009) BMC Evol Biol 9

PubMed: 19740424 | PubMedCentral: PMC2754480 | DOI: 10.1186/1471-2148-9-227

C ALM 36-444 is made of 36 calmodulin sequences taken from eukaryotes, with a protein structure defined by the PDB file 1CFD and the tree topology estimated using phyML [ 40 ] under the model JTT + F ... Γ [ 41 , 42 ].

Publication Year: 2009

The effect of macromolecular crowding, ionic strength and calcium binding on calmodulin dynamics.

(2011) PLoS Comput Biol 7

PubMed: 21829336 | PubMedCentral: PMC3145654 | DOI: 10.1371/journal.pcbi.1002114

The most probable structure in M1 represents an extended, dumbbell-like conformation and it is similar to the PDB structure of apoCaM (PDBID: 1CFD).

The matrix elements at the upper triangle denote the contacts of a structure modeled from apoCaM's PDB structure (PDBID: 1CFD), while those in the lower triangle denote the contacts found in the states other than the PDB one (nonnative contacts).

There is a high probability of contact formation of these two regions in the M1 state, indicating the contacts between Helix A and D in the N-lobe and the contacts between Helix E and G in the C-lobe are highly similar to the structure modeled from apoCaM's PDB structure (PDBID: 1CFD).

The structure of apoCaM (1CFD) was employed as a template and the coarse-grained SCM structure of holoCaM (3GOF) was used to restrain the positions of C α and side-chain beads.

Publication Year: 2011

Characterization and functional analysis of the calmodulin-binding domain of Rac1 GTPase.

(2012) PLoS One 7

PubMed: 22905193 | PubMedCentral: PMC3419704 | DOI: 10.1371/journal.pone.0042975

The Apo-CaM (PDB id: 1CFD) was docked with Rac1 151–164 amino acids of Rac1 WT (PDB id: 1FOE), Rac1 K153A, Rac1 R163A, and K153A/R163A using ZDock server ( ).

The Apo-CaM (PDB id: 1CFD) was docked with Rac1 151–164 amino acids of Rac1 WT (PDB id: 1FOE), Rac1 K153A, Rac1 R163A, and K153A and R163A using Z DOCK server ( ).

Publication Year: 2012

Solution NMR structure of the Ca2+-bound N-terminal domain of CaBP7: a regulator of golgi trafficking.

(2012) J Biol Chem 287

PubMed: 22989873 | PubMedCentral: PMC3488092 | DOI: 10.1074/jbc.M112.402289

Sequence identity RMSD % Å CaM NTD 47.8 1.66 CaM CTD 47.2 1.35 CaBP1 NTD 47.8 3.54 CaBP1 CTD 43 2.12 TABLE 3 Interhelical angles of the EF-hands in CaM, CaBP1, and CaBP7 NTD The PDB codes were... as follows: apo-CaM, 1CFD ; Ca 2+ -bound CaM, 1CLL ; Mg 2+ -bound CaBP1, 2K7B and 2K7C ; Ca 2+ -bound CaBP1, 2LAN and 2LAP ; Ca 2+ -bound CaBP7 NTD, 2LV7.

Publication Year: 2012

The Ca(2+) influence on calmodulin unfolding pathway: a steered molecular dynamics simulation study.

(2012) PLoS One 7

PubMed: 23145050 | PubMedCentral: PMC3492193 | DOI: 10.1371/journal.pone.0049013

Models and Methods System Preparation and Equilibration The initial structures of Ca 2+ -loaded and Ca 2+ -free CaM are obtained form the Protein Data Bank (Ca 2+ -loaded CaM coded by 1CLL [9] , Ca 2+... -free CaM coded by 1CFD [10] ), which have the same sequences.

Publication Year: 2012

Cooperative binding.

(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).

Publication Year: 2013

Structural analysis of autoinhibition in the Ras-specific exchange factor RasGRP1.

(2013) Elife 2

PubMed: 23908768 | PubMedCentral: PMC3728621 | DOI: 10.7554/eLife.00813

Comparison to apo calmodulin (PDB ID: 1CFD) (middle) shows that calcium (purple sphere) induces a dramatic rearrangement in the helix orientations for both EF hands.

Publication Year: 2013

Towards accurate modeling of noncovalent interactions for protein rigidity analysis.

(2013) BMC Bioinformatics 14 Suppl 18

PubMed: 24564209 | PubMedCentral: PMC3817810 | DOI: 10.1186/1471-2105-14-S18-S3

Their data set was composed of: CAPK, 1ctp, 1atp; Bence-Jones protein, 4bjl; LAO-binding protein, 2lao, 1lst; adenylate kinase, 2ak3, 1ake; glutamine binding protein, 1ggg, 1wdn; DNA polymerase ... 2; , 2bpg, 1bpd; calmodulin, 1cfd, 1cll; inorganic pyrophosphatase, 1k23, 1k20; ribose binding protein, 1urp, 2dri; Ig domain of protein G, 1pdb; hydropterin pyrophosphokinase, 1hka; cyclophilin A, 1bck; rhizopuspepsin, 2apr, 3apr; chloramphenicol acetyltransferase, 2cla, 3cla; and proteinase A, 2sga, 5sga.

Publication Year: 2013

Dynamic switching of calmodulin interactions underlies Ca2+ regulation of CaV1.3 channels.

(2013) Nat Commun 4

PubMed: 23591884 | PubMedCentral: PMC3856249 | DOI: 10.1038/ncomms2727

Accordingly, we appose the atomic structure of the N-lobe (1CFD) to this segment of the PCI model, initially using a shape-complementarity docking algorithm 52 ( PatchDock ), followed by refinement wi... h docking protocols of Rosetta ( Supplementary Note 20 ).

Publication Year: 2013

Elucidating the ensemble of functionally-relevant transitions in protein systems with a robotics-inspired method.

(2013) BMC Struct Biol 13 Suppl 1

PubMed: 24565158 | PubMedCentral: PMC3952944 | DOI: 10.1186/1472-6807-13-S1-S8

These states are documented under PDB ids 1cfd (apo), 1cll (holo), and 2f3y (collapsed).

Publication Year: 2013

Calmodulin regulation (calmodulation) of voltage-gated calcium channels.

(2014) J Gen Physiol 143

PubMed: 24863929 | PubMedCentral: PMC4035741 | DOI: 10.1085/jgp.201311153

The atomic structure of the apoCaM N-lobe (1CFD) was interfaced with shape-complementarity docking algorithms.

Publication Year: 2014

Computational prediction of hinge axes in proteins.

(2014) BMC Bioinformatics 15 Suppl 8

PubMed: 25080829 | PubMedCentral: PMC4120148 | DOI: 10.1186/1471-2105-15-S8-S2

Figure 5 Rosetta scores computed with PyRosetta for 1000 samples of apo calmodulin [PDB:1CFD]; each sample is represented by a (very thin) horizontal bar, whose length corresponds to its score .

The calcium-free structure [PDB:1CFD] is shown faded, with the two structures aligned on the central helix residues (65-77) of the pinned cluster (shown in red).

We wish to find the minimum number of samples to generate, as this is the most time-consuming step; a sample set of 100 for calmodulin [PDB:1CFD] seemed to exhibit the same behavior as the sample set of 1000.

To illustrate the treatment of a typical protein from our dataset, we present the results for calcium-free calmodulin [PDB:1CFD] in Figure 5 with each sample represented as a (very thin) horizontal bar.

Figure 6 The open state of Ca 2+ -bound calmodulin [PDB:1CLL] is a result of a conformational change from calcium-free calmodulin ([PDB:1CFD], shown faded) .

Protein PDB ID KINARI cutoff Pinned cluster Moving cluster Twist purity Calmodulin (calcium-free) 1CFD default 0 1 77.1269 Calmodulin (Ca 2+ -bound; open) 1CLL -2 0 1 95.435 Calmodulin (Ca2+ -bound; closed) 2BBM(A) default 4 7 150.339 LAO binding protein (open) 1LST default 0 1 91.5669 LAO binding protein (closed) 2LAO default 0 1 98.1407 Bence-Jones protein (open) 4BJL(B) -1.25 0 1 97.0153 Bence-Jones protein (closed) 4BJL(A) -1.25 0 1 99.0822 cAMP-dependent protein kinase (open) 1CTP -1.9 0 2 89.7223 cAMP-dependent protein kinase (closed) 1ATP -1.9 0 1 93.2537 Adenylate kinase (open) 2AK3(A) default 0 1 95.2801 Adenylate kinase (closed) 1AKE(A) -2.5 1 0 91.4916 Glutamine binding protein (open) 1GGG(A) default 1 0 105.321 Glutamine binding protein (closed) 1WDN -2 0 1 90 DNA polymerase β (open) 2BPG(A) default 0 1 109.657 DNA polymerase β (closed) 1BPD default 0 1 86.6385 Inorganic pyrophosphatase (open) 1K23(A) default 0 1 91.6584 Inorganic pyrophosphatase (closed) 1K20(A) -3 1 0 80.6779 Ribose binding protein (open) 1URP(C) -2 0 1 75.4811 Ribose binding protein (closed) 2DRI -2.65 1 0 89.4672 For structures where the PDB contains more than one chain, the analyzed chain is indicated within parentheses.

Publication Year: 2014