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PDB ID Mentions in PubMed Central Article count: 25

Citations in PubMed

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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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MovieMaker: a web server for rapid rendering of protein motions and interactions.

(2005) Nucleic Acids Res 33

PubMed: 15980488 | PubMedCentral: PMC1160245 | DOI: 10.1093/nar/gki485

Table 1 Summary of different simulation or animation scenarios and the CPU time taken to complete the calculation Simulation example PDB IDs Time taken (s) a Simple rotation about Z axis 4Q21 10 Motio... between two end-state conformers 1A29 & 1CLL 15 Small-scale vibrational motions 1MYF_A 16 Oligomerization (assembly/disassembly) 1C48 25 Ligand docking 1A29 & TFP 20 NMR ensemble simulation 1BQV 260 Protein folding/unfolding 1A29 215 a Times will vary according to server load and PDB file size.

Publication Year: 2005


Wiggle-predicting functionally flexible regions from primary sequence.

(2006) PLoS Comput Biol 2

PubMed: 16839194 | PubMedCentral: PMC1500818 | DOI: 10.1371/journal.pcbi.0020090

Figure 2 FF Score Identifies FFR in Bovine Pancreatic Inhibitor and Calmodulin Comparison of unweighted (dashed line) and weighted (solid line) FF scores for BPTI ([top], PDB ID: 5PTI)... and calmodulin (bottom, PDB ID: 1CLL).

Publication Year: 2006


Binding induced conformational changes of proteins correlate with their intrinsic fluctuations: a case study of antibodies.

(2007) BMC Struct Biol 7

PubMed: 17509130 | PubMedCentral: PMC1888692 | DOI: 10.1186/1472-6807-7-31

Protein ID (unbound-bound) Name of the protein Number of residues Ligand Rmsd between the structures (Å) 3chy - 1chn CheY 128 Mg 1.39 5dfr - 4dfr ^ Dihydrofolate Reductase 158 Methotrexate 0.8... 1ctr - 1cll Calmodulin 138 Trifluoperazine 14.4 2lao - 1lst K-, R-, Orn-Binding Protein 238 Lys 4.70 3tms - 2tsc Thymidylate Synthase 264 UMP, CB3 0.80 1hka - 1rao HPPK (kinase) 158 AMP 3.13 1bbs - 1rne Renin 326 CGP, NAG 6.16 2a 6j - 2a6d * Antibody-Heavy chain 222 Dodecapeptide1 0.94 2a6j - 2a6i * Antibody-Heavy chain 222 Dodecapeptide2 1.10 2a6j - 2a6k * Antibody-Heavy chain 222 Dodecapeptide3 1.00 1oaq - 1oau Antibody-Heavy chain 121 DNP-Ser 0.62 1ocw - 1oaz Antibody-Heavy chain 121 Trx-Shear3 1.91 The first column lists the unbound and bound conformations PDB codes.

Publication Year: 2007


Elucidating the mechanisms of cooperative calcium-calmodulin interactions: a structural systems biology approach.

(2008) BMC Syst Biol 2

PubMed: 18518982 | PubMedCentral: PMC2435525 | DOI: 10.1186/1752-0509-2-48

The apo (1DMO [18]) (A) and Ca 2+ bound (1CLL [19]) (B) structures of the CaM protein illustrate Ca 2+ induced conformational transitions.

(D) Structure of the Ca 2+ loop on the N-terminal of the CaM protein (1CLL [19]).

Publication Year: 2008


The unfoldomics decade: an update on intrinsically disordered proteins.

(2008) BMC Genomics 9 Suppl 2

PubMed: 18831774 | PubMedCentral: PMC2559873 | DOI: 10.1186/1471-2164-9-S2-S1

( B ) Large scale structural alterations in calmodulin induced by binding to the MoRF of GAD (PDB entries: unbound – 1CLL and bound – 1NWD ).

Publication Year: 2008


Regulation of bestrophin Cl channels by calcium: role of the C terminus.

(2008) J Gen Physiol 132

PubMed: 19029375 | PubMedCentral: PMC2585866 | DOI: 10.1085/jgp.200810056

Alignment of the four EF hands of CaM (1cll.

Molecular Modeling A three-dimensional homology model for hBest1 was built based on the coordinates of the third EF hand in human CaM (1cll.

Publication Year: 2008


Using least median of squares for structural superposition of flexible proteins.

(2009) BMC Bioinformatics 10

PubMed: 19159484 | PubMedCentral: PMC2639377 | DOI: 10.1186/1471-2105-10-29

Figure 10 Multiple level superposition for the Calmodulin structures: 1cll (light gray) and 1ctr (dark gray) .

We superimpose two conformational structures (1cll and 1ctr) of Calmodulin, where this hinge motion involves a long helix splitting into two helices and the angle between the axes of the two helical segments is about 100 degrees.

10 illustrates two level superposition for the Calmodulin structures: 1cll (light gray) and 1ctr (dark gray).

Figure 6 Superposition comparison for the Calmodulin structures: 1cll (light gray) and 1ctr (dark gray) .

Table 1 Superposition results of protein systems with conformational changes using the LMS fit Protein system PDB1 PDB2 RMSD #Res 1 #Subset Core% 2 Time(s) ER α 3erd 3ert 4.9 244 203 83.2% 0.28 RAN 1byu 1rrp 14.4 200 141 70.5% 0.19 Myosin 1b7t 1dfk 13.0 720 403 56.0% 0.58 Calmodulin 1cll 1ctr 14.7 138 72 52.2% 0.09 Topo II 1bgw 1bjt 18.4 665 389 58.5% 0.55 Pneumolysin 2bk1 2bk2 21.8 435 139 32.0% 0.39 1 "#Res" is the number of atom pairs used for superposition by removing any inappropriate residues.

Publication Year: 2009


A dynamic model of interactions of Ca2+, calmodulin, and catalytic subunits of Ca2+/calmodulin-dependent protein kinase II.

(2010) PLoS Comput Biol 6

PubMed: 20168991 | PubMedCentral: PMC2820514 | DOI: 10.1371/journal.pcbi.1000675

PDB 1CLL [56] (B) A 2.4 angstrom ribbon structure of CaM bound to a peptide (green) corresponding to the CaM binding domain of CaMKII.

PDB 1CLL [15] .

Publication Year: 2010


Structure of the gating ring from the human large-conductance Ca(2+)-gated K(+) channel.

(2010) Nature 466

PubMed: 20574420 | PubMedCentral: PMC2910425 | DOI: 10.1038/nature09252

c , The EF-hand structure of a Ca 2+ binding protein (a human Calmodulin molecule with PDB code 1CLL).

Publication Year: 2010


Exploring NMR ensembles of calcium binding proteins: perspectives to design inhibitors of protein-protein interactions.

(2011) BMC Struct Biol 11

PubMed: 21569443 | PubMedCentral: PMC3116463 | DOI: 10.1186/1472-6807-11-24

For C-CaM, the binding pocket consists of one cavity (volume 314.22 Å 3 , code 1CLL) containing residues F88, I96, L101, M105, M120, E123, M140 and M141.

(A) 31 NMR (code 2K0F; in grey cartoon) and one X-ray (code 1CLL; in green cartoon) structures of CaM.

(A) docking into the X-ray (code 1CLL) and the 31 NMR structures (code 2K0F) of CaM; (B) docking on the X-ray (code 2GGM) and the 20 NMR structures (code 2A4J ) of HsCen2.

In the case of 2K0F, including 160 models, we have chosen those 31 models giving the better superposition of the binding zone into the X-ray structure 1CLL.

(A) sequence alignment of CaM and HsCen2, the C-terminal domains are shown in blue and the pocket regions in magenta; (B) superposition of the X-ray structures of CaM (yellow cartoon, unbound form, code 1CLL) and HsCen2 (blue cartoon, bound form, code 2GGM); (C) CaM in a complex with trifluorperasine (sticks in magenta) (code 1LIN); (D) structure of HsCen2 (unbound form, code 1M39).

Methods Selection of CaM and HsCen2 structures and binding pocket analysis X-ray structures and NMR ensembles of CaM and HsCen2, all in the Ca 2+ -bound state, have been taken from the Protein Data Bank [ 56 ] and analyzed in details as follows: i) For CaM: an unliganded X-ray structure, code 1CLL at 1.7 Å resolution [ 57 ]; a NMR ensemble of 160 unliganded structures, code 2K0E [ 58 ]; a NMR ensemble of 160 structures bound to 19-mer peptide from smMLCK, code 2K0F [ 58 ]; ii) For HsCen2: a NMR ensemble of unliganded C-terminal domain, code 1M39; a X-ray structure of HsCen2 bound to the P17-XPC peptide, code 2GGM at 2.35 Å resolution [ 44 ]; a NMR ensemble of 20 structures of HsCen2 bound to P17-XPC, code 2A4J [ 48 ].

The on-line tool PCE "Protein Continuum Electrostatics" [ 59 ] was used to calculate the pKa values of the titratable groups as well as the 3D electrostatic potential distribution of the C-terminal domains on the X-ray CaM (code 1CLL) and HsCen2 (code 2GGM) structures including the Ca 2+ atoms and taking dielectric constants of the solute and solvent as 11 and 80, respectively.

The peptide P17-XPC bound to HsCen2 is shown in pink (code 2GGM); (C) surface presentation of the X-ray structure of CaM (code 1CLL); (D) surface presentation of the X-ray structure of HsCen2 (code 2GGM).

Among the twelve protein structures, 1CLL, 2K0F model 76, and 2K0F model 98 were considered as "bad" because no one of the re-scoring methods AMMOS, GBSA and X-score retrieved good docking poses.

For CaM, the X-ray structure of the human unliganded CaM (1CLL) with the highest resolution among other retrieved X-ray CaM structures (PDB codes: 1LIN, 3EWV, 1IWQ, 2VAY, 1ZUZ, 3BYA, 1YR5) has been considered for docking calculations.

Publication Year: 2011


Solution structure of the Apo C-terminal domain of the Lethocerus F1 troponin C isoform.

(2010) Biochemistry 49

PubMed: 20104876 | PubMedCentral: PMC3388720 | DOI: 10.1021/bi902094w

Table 2 Interhelical Angles in Representative EF-Hands a protein PDB entry method I−II II−III III−IV I−IV apo NCaM 1dmo NMR 128 ± 3 130 ±...  4 130 ± 4 121 ± 2 apo CCaM 1dmo NMR 137 ± 3 144 ± 3 132 ± 5 144 ± 3 apo skNTnC 1tnp NMR 130 ± 3 126 ± 5 125 ± 4 111 ± 2 apo cNTnC 1spy NMR 139 ± 3 115 ± 4 125 ± 5 117 ± 3 apo cNTnC 1a2x X-ray 138 119 136 121 holo cNTnC b 1ap4 NMR 136 ± 4 97 ± 4 119 ± 4 115 ± 2 apo F1 NTnC 2jnf NMR 133 ± 3 118 ± 2 124 ± 2 126 ± 3 apo F1 CTnC 2k2a NMR 135 ± 5 134 ± 4 132 ± 12 129 ± 7 holo F1 CTnC 2jnf NMR 103 ± 3 119 ± 2 127 ± 4 97 ± 2 holo NCaM 4cln X-ray 94 110 96 107 holo NCaM 1cll X-ray 87 112 96 99 holo NCaM 1g4y X-ray 96 111 90 115 holo NCaM 1cdl X-ray 88 112 91 104 holo CCaM 4cln X-ray 98 114 94 115 holo CCaM 1cll X-ray 97 112 95 109 apo CCaM c 1g4y X-ray 95 137 93 140 holo CCaM 1cdl X-ray 101 112 96 112 holo cCTnC 1a2x X-ray 99 120 109 112 holo cCTnC 1j1d X-ray 100 125 118 109 holo skNTnC 1tnq NMR 90 ± 3 100 ± 6 69 ± 5 109 ± 3 holo skNTnC 1ytz X-ray 105 101 94 116 apo skCTnC d 1yv0 X-ray 101 121 112 106 holo skCTnC 1ytz X-ray 106 123 111 114 apo CRLC e 1wdcB X-ray 103 146 104 144 apo CELC e 1wdcC X-ray 115 130 94 143 holo CAct e 1h8b NMR 96 ± 3 150 ± 4 93 ± 4 147 ± 3 a The values were calculated using the interhlx program freely available online ( http://nmr.uhnres.utoronto.ca/ikura/resources/data+sw/interhlx/ ).

Publication Year: 2010


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

TABLE 2 Percentage sequence identity and comparative RMSD values for Ca 2+ -bound CaBP1 (PDB codes 2LAN and 2LAP ) and CaM (PDB code 1CLL ) compared to CaBP7 NTD (PDB code 2LV7 ) Sequence identity was... calculated based on alignment of CaBP7, CaBP1, and CaM excluding non-homologous regions in the N termini or linker regions of the proteins.

Space-filling representations of Ca 2+ -bound CaBP7 NTD (PDB code 2LV7 , residues 30–100) ( A ), Ca 2+ -bound CaBP1 (PDB code 2LAP ) ( B ), and Ca 2+ -bound CaM (PDB code 1CLL , residues 80–147) ( C ).

B and C , ribbon representation of Ca 2+ -bound CaBP7 NTD (PDB code 2LV7 , residues 30–100) lowest energy conformer ( purple ) superposed with Ca 2+ -bound CaBP1 CTD ( cyan , PDB code 2LAP ) ( B ) and Ca 2+ -bound CaM CTD ( yellow , PDB code 1CLL , residues 80–147) ( C ).

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


Structural characterization of the interaction of human lactoferrin with calmodulin.

(2012) PLoS One 7

PubMed: 23236421 | PubMedCentral: PMC3516504 | DOI: 10.1371/journal.pone.0051026

B) Ribbon representation of Ca 2+ -CaM with the side chain of Lys-75 highlighted (PDB code 1CLL).

CaM amino acid residues experiencing a significant change in chemical shift or cross-saturation upon binding apo-Lf are mapped on the structure of B) free Ca 2+ -CaM (PDB code 1CLL) or C) Ca 2+ -CaM bound to the CBD of CaMKK (PDB code: 1IQ5).

PDB codes 1CLL, 1B0L, and 1H76, respectively.

Publication Year: 2012


Protein analysis by time-resolved measurements with an electro-switchable DNA chip.

(2013) Nat Commun 4

PubMed: 23839273 | PubMedCentral: PMC3719012 | DOI: 10.1038/ncomms3099

Upon calcium binding ( K D =1–10 μM 27 28 29 ) (refs 27 , 28 , 28 ), CaM changes its structure from a globular to a dumb-bell-shaped form by rearranging hydrophobic methyl grou... s from methionine residues ( cf. pdb entries 1QX5 and 1CLL ) 30 31 .

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

The C-terminal domain of calcium-bound calmodulin (PDB ID: 1CLL) is shown on the left.

Publication Year: 2013


SCEDS: protein fragments for molecular replacement in Phaser.

(2013) Acta Crystallogr D Biol Crystallogr 69

PubMed: 24189233 | PubMedCentral: PMC3817695 | DOI: 10.1107/S0907444913021811

  Target Target Template Template   PDB code Conformer PDB code Conformer Training set  Alcohol dehydrogenase 6adh Closed 8adh Open  Alcohol dehydrogenase 8adh Open 6ad... Closed  cAMP-dependent protein kinase 1atp Open 1ctp Closed  Citrate synthase 6csc Closed 5csc Open  Diptheria toxin 1mdt Closed 1ddt Open  Diptheria toxin 1ddt Open 1mdt Closed  Glutamine-binding protein 1wdn Closed 1ggg Open  Immunoglobulin 1hil , chain B Unbound 1him , chain M Bound  Lactoferrin 1flg Closed 1flh Open  Lactoferrin 1flh Open 1flg Closed  LAO binding protein 2lao Open 1lst Closed  Maltodextrin-binding protein 1anf Closed 1omp Open  Thymine synthase 2tsc Closed 3tms Open Test set  Adenylate kinase 1ake Open 2eck Closed  Adenylate kinase 2eck Closed 1ake Open  cAMP-dependent protein kinase 1ctp Open 1atp Closed  Calmodulin, closed 1ctr Closed 1cll Open  Calmodulin, open 1cll Open 1ctr Closed  Citrate synthase 6csc Closed 5csc Open  Glutamine-binding protein 1wdn Closed 1ggg Open  Maltodextrin-binding protein 1omp Open 1anf Closed  Pyruvate phosphate dikinase 1kbr Active 2t82 Inactive  Pyruvate phosphate dikinase 2t82 Inactive 1kbr Active Table 2 R values/ R free after ten cycles of REFMAC (Murshudov et al. , 2011 ▶ ) for structures of the whole template superimposed on the target (template) and after MR with the template divided into SCEDS fragments using the value of NDOM given The conformational change for calmodulin between the closed and open forms is too large to allow the whole template in one conformation to be superimposed on the target in the other conformation.

  PDB code Modes NDOM Fragment 1 Fragment 2 Fragment 3 Fragment 4 Fragment 5 Excluded ( a ) Adenylate kinase, closed 2eck , chain B 7, 9 3 1–35, 68–124, 155–214 (CORE) 36–67 (NMP) 125–154 (LID) — — None ( b ) Adenylate kinase, open 4ake , chain A 7, 8 3 1–34, 68–117, 164–214 (CORE) 118–163 (LID) 35–67 (NMP) — — None ( c ) Calmodulin, closed 1ctr 9, 10 2 9–83 84–147 — — — 4–8 ( d ) Calmodulin, open 1cll 9, 10 2 12–72 88–147 — — — 1–11, 73–73, 81–87 ( e ) cAMP-dependent protein kinase 1atp , chain E 7, 8 2 15–35, 125–328 36–124, 222–350 — — — 329–332 ( f ) Citrate synthase 5csc , chain A 7, 8 2 1–82, 84–276, 385–433 277–291, 295–384 — — — None ( g ) Glutamine-binding protein 1ggg , chain A 8 2 5–82, 189–224 89–183 — — — 83–88, 184–188 ( h ) Maltodextrin-binding protein 1anf 7, 9 2 113–258, 319–370 8–112, 259–303 — — — 1–7 ( i ) Pyruvate phosphate dikinase 1kbl 11 4 566–828 6–243 244–380, 515–565, 829–873 381–514 — 2–5 ( j ) Pyruvate phosphate dikinase, triple mutant 2r82 7, 10 5 6–242 709–873 539–699 379–515 243–338 2–5, 340–370, 516–538, 700–708

( d ) Calmodulin, PDB entry 1cll .

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.

For 11 of the PDBs (1hhp, 1rx1, 1lst, 1kc7, 2afi, 1f88, 3cap, 2brd, 2fmq, 1k9k, 1cll), excluding weaker H-bonds resulted in higher B-cubed scores than KINARI v1.0, in a few cases, quite substantially.

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


Structure-function of proteins interacting with the ?1 pore-forming subunit of high-voltage-activated calcium channels.

(2014) Front Physiol 5

PubMed: 24917826 | PubMedCentral: PMC4042065 | DOI: 10.3389/fphys.2014.00209

PDB files are as follows: apoCaM: 1QX5, free Ca 2+ CaM: 1CLL, CaM with Ca V 1.2 IQ: 2BE6, CaM with Ca V 2.2 IQ 3DVE, dimer CaM with Ca V 1.2 IQ: 3G43.

Publication Year: 2014


A real-time all-atom structural search engine for proteins.

(2014) PLoS Comput Biol 10

PubMed: 25079944 | PubMedCentral: PMC4117414 | DOI: 10.1371/journal.pcbi.1003750

We begin from an EF-hand from calmodulin (PDB ID  =  1CLL) and search for only two aspartate side-chains from the motif, each of which coordinates the calcium ion once.

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

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; c... osed) 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.

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) .

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 globular domains to "wrap" around the peptide (not shown) .

The resulting conformation is Ca 2+ -bound calmodulin in its open state [PDB:1CLL], depicted in Figure 6 .

Indeed, our analysis assigns a twist purity value of around 150, indicating a more general "screw" motion; the open conformation [PDB:1CLL] is shown faded, aligned along residues 64-75.

Publication Year: 2014


PubMed ID is not available.

Published in 2014

PubMedCentral: PMC4174990

The diffusion tensor for the rigid dumbbell structure of calmodulin, calculated from PDB file 1CLL, has principal values D xx = 9.77 × 10 6 s –1 , D yy = 10.2 × 10 6 s –... 1 , and D zz = 20.4 × 10 6 s –1 .

39 , 40 Figure 7 Fitted 15 N spin relaxation data for calmodulin acquired at 800 MHz and 316 K. (a) Structure of the rigid dumbbell structure from PDB file 1CLL.

Publication Year: 2014


PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4349623

Modeling The model structures of chimeras were generated and optimized with Swiss-Model Automatic Program Modeling Severs ( http://swissmodel.expasy.org/ ) [ 42 , 43 ] using 1CFC and 1CLL as the templ... tes for apo and holo CaM forms, respectively.

Modeling and solvent-accessible calculations To rationalize the experimental data on hydrophobic exposure upon Ca 2+ binding, we modeled the chimera structures in the apo- and Ca 2+ -bound forms by aligning the sequences of chimeras to the models of apo-CaM (PDB: 1CFC) and Ca 2+ -CaM (PDB: 1CLL) as described in the experimental section, assuming that all chimera proteins adopt a similar structure to that of CaM.

In fact, the structural alignment of CaM (PDB: 1CLL) and sTnC (4TnC) indicated that both structures cannot be aligned well given the root-mean square-deviation (RMSD) value of 6.8181 Å for all atoms.

Publication Year: 2015


PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4392415

The high-resolution structures of the protein calmodulin, a Ca 2+ -binding protein with a myriad of cellular functions dependent on its conformational state, were used to test the power of EOM 2.0 to ... iscriminate between open [PDB entry 1cll (Chattopadhyaya et al. , 1992 ▶ ), R g = 22.6 Å] and closed [PDB entry 1ctr (Cook et al .

Publication Year: 2015