Primary Citation PubMed: 1585175
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CSA: comprehensive comparison of pairwise protein structure alignments.
(2012) Nucleic Acids Res 40
PubMed: 22553365 | PubMedCentral: PMC3394275 | DOI: 10.1093/nar/gks362
( A ) The two calmodulin conformers (PDB IDs 4cln and 2bbm) superpositioned according to the TM-alignment, which aligns only one of the two regions that move relative to each other.
Comparing flexible and rigid scoring schemes We align two conformations of the calmodulin protein (PDB IDs 4cln, chain A and 2bbm, chain A, with a length of 148 residues).
Publication Year: 2012
Munc13-like skMLCK variants cannot mimic the unique calmodulin binding mode of Munc13 as evidenced by chemical cross-linking and mass spectrometry.
(2013) PLoS One 8
PubMed: 24130683 | PubMedCentral: PMC3794949 | DOI: 10.1371/journal.pone.0075119
Generation of protein structures and docking of apo-CaM (PDB entry 2L53, aa 1–77;  ) with holo-CaM (PDB entry 2BBM, aa 78–148;  ) was performed with open-source Pymol 0-99rc6 (... eLano Scientific, San Francisco).
We show that the distance constraints imposed by the chemical cross-links in all CaM/skMLCK peptide complexes agree well with the published NMR structure of the CaM/M13 skMLCK peptide complex (PDB entry 2BBM)  .
Distances between cross-linked amino acids are presented in the NMR structures of (A, B) the CaM/M13 skMLCK peptide complex (PDB entry 2BBM,  ; viewed from two angles) and (C) the CaM/Munc13-1 peptide complex (PDB entry 2KDU,  ).
Figure S4C in File S1 shows the distances of cross-linked amino acids in the NMR structure of the CaM/Munc13-1 peptide complex  , clearly indicating that this structure does not exist for the CaM/skMLCK peptide complex (PDB entry 2BBM).
In order to investigate whether the cross-links found at 30 nM Ca 2+ are in agreement with a half Ca 2+ -loaded CaM structure, we docked the N -terminus of apo-CaM (PDB entry 2L53,  ) with the C -terminus of holo-CaM (PDB entry 2BBM,  ).
Distances between cross-linked amino acids (at 1 mM Ca 2+ ) are presented in the NMR structures of (A, B) CaM/M13 skMLCK peptide complex (PDB entry 2BBM,  ; viewed from two angles and (C) CaM/Munc13-1 peptide complex (PDB entry 2KDU,  ).
Distances between cross-linked amino acids are presented in the NMR structures of (A, B) the CaM/M13 kMLCK peptide complex (PDB entry 2BBM,  ; viewed from two angles) and (C) the CaM/Munc13-1 peptide complex (PDB entry 2KDU,  ).
(D) Distances of cross-linked amino acids identified at 30 nM Ca 2+ displayed in the half-loaded CaM ( N -terminal domain of apo-CaM (PDB entry 2L53  , aa 1–77; green) and C -terminal domain of holo-CaM (PDB entry 2BBM  , aa 78–147; grey)).
Publication Year: 2013
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 7 The closed state of Ca 2+ -bound calmodulin [PDB:2BBM] is obtained by another conformational change when a peptide is bound to the open state ([PDB:1CLL], shown faded), causing the two globul... r domains to "wrap" around the peptide (not shown) .
A subsequent conformational change occurs when open Ca 2+ -bound calmodulin binds a peptide; the two globular domains "wrap" around the peptide, leading to the closed state [PDB:2BBM] shown in Figure 7 .
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
EttA regulates translation by binding the ribosomal E site and restricting ribosome-tRNA dynamics.
(2014) Nat Struct Mol Biol 21
PubMed: 24389465 | PubMedCentral: PMC4143144 | DOI: 10.1038/nsmb.2741
Specifically, the missing residues of EttA arm (residues 132–140), inter-ABC-domain linker helices (residues 243–279, which we call PtIM) and missing residues of C-terminal helix (resi... ues 543–555) were modeled based on parts of PDB ID: 1UO0, 1ABZ and 2BBM, respectively.
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