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Comparative mapping of sequence-based and structure-based protein domains.
(2005) BMC Bioinformatics 6
PubMed: 15790427 | PubMedCentral: PMC1087832 | DOI: 10.1186/1471-2105-6-77
The PDB proteins 1a6d and 1iokG are used for the illustration.
Publication Year: 2005
Mechanism of lid closure in the eukaryotic chaperonin TRiC/CCT.
(2008) Nat Struct Mol Biol 15
PubMed: 18536725 | PubMedCentral: PMC2546500 | DOI: 10.1038/nsmb.1436
TRiC open-state comparative modeling and domain docking The thermosome structure from T. acidophilum (PDB 1A6D) and the N and C termini of the thermosome from the Thermococcus strain KS-1 (PDB 1Q3R) w... re chosen as templates.
The structure of the closed ATP-induced TRiC state, assessed at 15-Å resolution using the 0.5 Fourier Shell Correlation (FSC) criterion, was notably similar to the X-ray structures of related archaeal chaperonins (for example, PDB 1A6D and 1A6E 25 ).
Publication Year: 2008
Chaperonin genes on the rise: new divergent classes and intense duplication in human and other vertebrate genomes.
(2010) BMC Evol Biol 10
PubMed: 20193073 | PubMedCentral: PMC2846930 | DOI: 10.1186/1471-2148-10-64
The first 16 N-terminal residues of ThsA, predicted to contain a strand, are not included in the 1a6d crystal structure (top line).
(b) The three-dimensional fold of the secondary structure elements in the thermosome structure 1a6d chain A. Red cylinders represent helices and yellow arrows represent strands.
We identified potential contact positions in these families based on homology to the positions involved in inter-monomer contacts in the crystal structure of the T. acidophilum thermosome complex (PDB code 1a6d ).
The results of these predictions are schematically represented in Figure 6a , in relation to the secondary structure description of the PDB structure 1a6d chain A of the thermosome subunit ThsA from Thermoplasma acidophilum [ 36 ] (see additional file 15 : Figure S10, additional file 16 : Figure S11, additional file 17 : Figure S12, additional file 18 : Figure S13, additional file 19 : Figure S14, and additional file 20 : Figure S15 for detailed representations of multiple alignments, secondary structure predictions and alignments to the secondary-structure elements of ThsA).
In Figure 6a , the secondary structure description of ThsA is shown (line " 1a6d ") in relation to the position of the equatorial, intermediate, and apical domains.
(a) Secondary structure predictions of Thermoplasma acidophilum thermosome alpha subunit ThsA (line Ta_ThsA), human CCTs, mammal CCT8Ls and vertebrate BBSs (lines MKKS, BBS10 and BBS12) compared to the secondary structure description of ThsA (top line 1a6d ) determined from its crystal structure (PDB code 1a6d , chain A).
Secondary structure elements in 1a6d are labeled in succession with numbers (strands) or letters (helices).
Publication Year: 2010
CCTalpha and CCTdelta chaperonin subunits are essential and required for cilia assembly and maintenance in Tetrahymena.
(2010) PLoS One 5
PubMed: 20502701 | PubMedCentral: PMC2872681 | DOI: 10.1371/journal.pone.0010704
The model of the partial CCTα structure obtained was based on the coordinates of the subunit α of the chaperonin thermosome from T. acidphilum (Pubmed accession numbers: 1a6e, 1a6d and... 1q2v).
Symmetry-free cryo-EM structures of the chaperonin TRiC along its ATPase-driven conformational cycle.
(2012) EMBO J 31
PubMed: 22045336 | PubMedCentral: PMC3273382 | DOI: 10.1038/emboj.2011.366
Since the current reconstructions were completed at relatively low resolution, we began with a homology model corresponding to the CCT2 subunit using thermosome (1A6D) as template and fit it as rigid ... ody to all the subunits in the closed TRiC–ATP-AlFx map.
Publication Year: 2012
Mapping the mutual information network of enzymatic families in the protein structure to unveil functional features.
(2012) PLoS One 7
PubMed: 22848494 | PubMedCentral: PMC3405127 | DOI: 10.1371/journal.pone.0041430
A) 3DCN of the Pfam family PF00118 (pdb code: 1A6D).
ATP-driven molecular chaperone machines.
(2013) Biopolymers 99
PubMed: 23877967 | PubMedCentral: PMC3814418 | DOI: 10.1002/bip.22361
Cryo-EM maps of the Group 2 chaperonin from Methanococcus maripaludis in the open (top row), partially closed (middle row) and closed conformation shown in side view, cut away side view and top view (... M Databank and PDB ID: EMD-1396, EMD-1397, and EMD-1398/1A6D).
Publication Year: 2013
PubMed ID is not available.
Published in 2015
Table 2 RPD2 partial domains corresponding to CATH structural domains Family Pfam CATH CATH length Accession (Pfam) length class (1st to 3rd quartile) UniProt/PDB PF00079 372 3.30.497.10 109 (54 ... 3;172) Q7TP87/1YXA |A PF00118 485 22.214.171.124 177 (181–181) F0YNJ0/1A6D |B 3.30.260.10 47 (38–56) 1.10.560.10 125 (115–134) PF00285 356 126.96.36.199 109 (104–115) Q98FC2/2H12 |A PF00316 325 3.30.540.10 179 (191–192) P00637/1BK4 |A 188.8.131.52 132 (132–135) PF00476 383 1.20.1060.10 126 (115-182) A2WDN6/1KFS |A PF00710 313 184.108.40.2060 214 (214–216) C7ZQZ8/1HFJ |A PF01544 292 3.30.460.20 149 (147–151) D2C657/2BBJ |A 220.127.116.110 76 (76–76) a 18.104.22.1680 118 (118–118) PF01571 211 22.214.171.1240 88 (87–88) Q83E96/1NRK |A PF03441 277 126.96.36.199 90 (85–88) Q4V935/1TEZ |A PF03598 412 3.30.1650.10 173 (155–178) B8FZT4/3GIT |A 3.40.970.20 133 (129–146) 3.40.1470.10 93 (89–98) PF03917 370 3.30.1490.80 28 (12–45) Q1RL06/2HGS |A 3.30.470.20 166 (135–193) 1.10.1080.10 41 (33–47) a The CATH:188.8.131.520 domain is annotated to two adjacent locations covered by PF01544 in [PDB:2BBJ |A].
In other cases, e.g., [Pfam:PF00118] (TCP-1/cpn60 chaperonin)/[UniProt:F0YNJ0] vs [PDB:1A6D |B], the Pfam domain aligns with portions of structures with multiple CATH domains, some of which are discontinuous in sequence.
Publication Year: 2015
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