Primary Citation PubMed: 10580496
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Predicting transmembrane helix packing arrangements using residue contacts and a force-directed algorithm.
(2010) PLoS Comput Biol 6
PubMed: 20333233 | PubMedCentral: PMC2841610 | DOI: 10.1371/journal.pcbi.1000714
Helical packing arrangement prediction Count Resembles two-dimensional slice from crystal structure 9 No observed helix-helix interactions 3 Incorrect due to linear configuration 3 Incorrect helix pla... ement 2 Arrangements were compared to a two-dimensional slice taken from the respective crystal structures and assessed based on the alignment between the helices in the predicted arrangement and in the slice; in 9 cases there was overlap for all helices (2F95:A, 1E12:A, 1XIO:A, 2D57:A, 1FFT:C, 1JB0:L, 1C17:A, 1R3J:C, 2AHY:A).
Publication Year: 2010
The dynamic stator stalk of rotary ATPases.
(2012) Nat Commun 3
PubMed: 22353718 | PubMedCentral: PMC3293630 | DOI: 10.1038/ncomms1693
PDB codes of coordinates used are: 3a5d: T. thermophilus (AB) 3 DF complex 9 , 1r5z: T. thermophilus subunit C 58 , 3k5b: T. thermophilus EG complex (PS1) 26 , 3rrk: Myotis ruber soluble I 59 and 1c17... E. coli subunit c 12 -ring model 60 .
As there is currently no structure for the L-ring available in the protein data bank, we modified the theoretical model of a NMR-derived E. coli c 12 -ring (pdb entry: 1c17) to give a symmetrical c 12 -ring.
Publication Year: 2012
Survey of human mitochondrial diseases using new genomic/proteomic tools.
(2001) Genome Biol 2
PubMed: 11423010 | PubMedCentral: PMC33397 | DOI: null
The structure comes from the Protein Data Bank (code: 1C17).
Publication Year: 2001
Rotary ATPases: models, machine elements and technical specifications.
PubMed: 23369889 | PubMedCentral: PMC3639240 | DOI: 10.4161/bioa.23301
1, nucleotide binding stator subunits (“cylinders”) (F: 2WPD | A: 3A5C | V: 3A5C); 2, central stalk (“crankshaft”) (F: 2WPD | A: 3A5C | V: 3AON); 3, A/V rotor subunit (... #x0201c;adapter”) (A: 1R5Z | V: 1R5Z); 4, rotor ring (“turbine”) (F: 4B2Q | A: 1C17 | V: 2BL2); 5, ion channel forming subunit (no structure available); 6, peripheral stalk (“pushrod”) (F: 4B2Q [2B05/2CLY/2WSS] | A: 3K5B | V: 4DL0 and 4EFA); 7a and b, A/V peripheral stalk connector subunits (“rockers”) (A: 3RRK | V: 3RRK and 1U7L); 8, small central stalk subunit (“ratchet” in prokaryotes) (F: 2WPD | A: 3A5C | V: 3AON); 9, eukaryotic additional central stalk subunit (“lock”) (2WPD); 10, IF 1 (“brake”) (1OHH); 11, eukaryotic V-type additional peripheral stalk subunit (“brake”) (1HO8).
Publication Year: null
The four-transmembrane protein IP39 of Euglena forms strands by a trimeric unit repeat.
(2013) Nat Commun 4
PubMed: 23612307 | PubMedCentral: PMC3644091 | DOI: 10.1038/ncomms2731
After selection by manual inspection, 12 models were selected: F 1 F O ATP synthase subunit A (PDB: 1C17), neurotransmitter-gated ion-channel transmembrane pore (PDB: 1OED), heme-binding four-helical ... undle (PDB: 1PPJ, 1KQF, 1Q16, 2BS2, 1NEK), MAPEG domain-like (PDB: 2Q7R, 2H8A, 2UUI), connexin26 (PDB: 2ZW3) and V-ATPase K-ring (PDB: 2BL2).
Publication Year: 2013
Structural analysis of mitochondrial mutations reveals a role for bigenomic protein interactions in human disease.
(2013) PLoS One 8
PubMed: 23874847 | PubMedCentral: PMC3706435 | DOI: 10.1371/journal.pone.0069003
The models for each complex were derived from the following X-ray crystallographic data; Complex I (NADH dehydrogenase) 4HEA and 3M9S  ,  , Thermus thermophilus ; II (succinate dehydrogenase) 1... OY  ; Sus scrofa , III (cytochrome bc 1 ) 1BE3  , Bos taurus ; IV (cytochrome c oxidase) 1OCC  , Bos taurus ; V (ATP synthase) 1C17  , Escherichia coli and 1H8E, Bos Taurus  .
PubMed ID is not available.
Published in 2014
A 3D model of the a-subunit is from 1999 (PDB ID: 1c17) and was computed using five helical–helical interactions that were inferred from second suppressor mutation experiments, and then impose... as distance restraints for TMH2-5 , revealing a four helical bundle (with no information for TMH1).
Rastogi V.K , Girvin M.E , 1999 , A1C12 SUBCOMPLEX OF F1FO ATP SYNTHASE , 1C17 ; http://dx.doi.org/10.2210/pdb1C17/pdb , Publicly available at the RCSB Protein Data Bank.
Publication Year: 2014
Published in 2015
Based on a homology model of H V 1 in the open state 14 and the crystal structure of F 1 -F o ATPase (PDB ID 1C17), Asp112 in H V 1 was superimposed onto Asp61 of F 1 -F o subunit c using Chimera, whi... h minimizes the root-mean-square deviations of superimposed atoms.
Publication Year: 2015
Structural Analysis Protein Data Bank (PDB) files 2YBB (supercomplex of I, III, and IV), 4HEA (complex I), 1PPJ (complex III), 1V54 (complex IV), and 1E79 with 1C17 (complex V) were rendered and color... d with the Visual Molecular Dynamics viewer 1.9.1 ( Humphrey et al. 1996 ).
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