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PDB ID Mentions in PubMed Central Article count: 2

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PDB ID Mentions in PubMed Central

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Schiff base switch II precedes the retinal thermal isomerization in the photocycle of bacteriorhodopsin.

(2013) PLoS One 8

PubMed: 23922839 | PubMedCentral: PMC3726731 | DOI: 10.1371/journal.pone.0069882

Additional simulations were performed based on three M state x-ray crystal structures (PDBids 1KG8, 1F4Z and 1C8S) ( Table S1 ).

We also investigated three M state x-ray crystal structures [10] – [12] (PDBID 1KG8, 1F4Z and 1C8S).

Materials and Methods BR Structures and Modeling The N’ intermediate state x-ray crystal structure (PDB code 1P8U) [42] , the M1 intermediate state structure (PDB code 1KG8) [10] , the M2 intermediate structure (PDB code 1F4Z) [11] and the Mn intermediate state structure (PDB code 1C8S) [12] were used in our simulations.

We therefore performed similar simulations based on three crystal structures of M intermediate state (1KG8, 1F4Z and 1C8S).

In the N’ structure, there are four such crystal water molecules while two, three, and two are present in 1KG8, 1F4Z, and 1C8S, respectively.

Figure S5 Time development of the number of the water molecules in the D96-K216 cavity, starting from four crystal structures 1p8u, 1kg8 1f4z and 1c8s.

g005 Figure 5 Percent occupancies of the 15-anti /CP-pointing (lower panel) and 15-syn /EC-pointing (upper panel) configurations of the SB C15 = NZ bond in each of 48 simulations based on crystal structure of 1p8u, 1kg8, 1f4z and 1c8s.

Publication Year: 2013


A comprehensive review of the lipid cubic phase or in meso method for crystallizing membrane and soluble proteins and complexes.

(2015) Acta Crystallogr F Struct Biol Commun 71

PubMed: 25615961 | PubMedCentral: PMC4304740 | DOI: 10.1107/S2053230X14026843

Type Name (PDB record count) Organism Function Host and additive lipids PDB entry (resolution, ) -Helical GPCR (54) Homo sapiens , Rattus norvegicus , Mus musculus , Meleagris gallopavo G protein-coup... ed receptor 9.9 MAG + cholesterol; 7.7 MAG + cholesterol; 9.9 MAG 4phu (2.33), 3eml (2.60), 4eiy (1.80), 3qak (2.70), 4gbr (3.99), 2rh1 (2.40), 3d4s (2.80), 3ny9 (2.84), 3ny8 (2.84), 3nya (3.16), 3pds (3.50), 3p0g (3.50), 3odu (2.50), 3oe0 (2.90), 3oe6 (3.20), 3oe8 (3.10), 3oe9 (3.10), 4k5y (2.98), 3pbl (2.89), 4oo9 (2.60), 3rze (3.10), 3uon (3.00), 4mqs (3.50), 4mqt (3.70), 3vw7 (2.20), 4jkv (2.45), 4o9r (3.20), 4n4w (2.80), 4qim (2.61), 4qin (2.06), 3v2w (3.35), 3v2y (2.80), 4djh (2.90), 4lde (2.79), 4ldl (3.10), 4ldo (3.20), 4qkx (3.30), 4iaq (2.80), 4iar (2.70), 4ib4 (2.70), 4nc3 (2.80), 4n6h (1.80), 4l6r (3.30), 4ntj (2.62), 4pxz (2.50), 4py0 (3.10), 4ea3 (3.01), 4or2 (2.80), 4mbs (2.71), 4daj (3.40), 4grv (2.80), 4dkl (2.80), 4ej4 (3.40), 4bvn (2.10) Bacteriorhodopsin (39) Halobacterium salinarum Rhodopsin, nonvisual 9.9 MAG; -XylOC 16+4 ; 95% monomethyl-DOPE, 5% DOPE-mPEG350 1ap9 (2.35), 1brx (2.30), 1qhj (1.90), 1c3w (1.55), 1c8r (1.80), 1c8s (2.00), 1cwq (2.25), 1qko (2.10), 1qkp (2.10), 1f4z (1.80), 1f50 (1.70), 1e0p (2.10), 1jv6 (2.00), 1jv7 (2.25), 1kg8 (2.00), 1kg9 (1.81), 1kgb (1.65), 1m0k (1.43), 1m0l (1.47), 1m0m (1.43), 1o0a (1.62), 1mgy (2.00), 1p8h (1.52), 1p8i (1.86), 1p8u (1.62), 1vjm (2.30), 1s8j (2.30), 1s8l (2.30), 2i1x (2.00), 2i20 (2.08), 2i21 (1.84), 2ntu (1.53), 2ntw (1.53), 2wjk (2.30), 2wjl (2.15), 3mbv (2.00), 3ns0 (1.78), 3nsb (1.78), 4fpd (2.65) Cytochrome ba 3 oxidase (13) Thermus thermophilus Cytochrome oxidase 9.9 MAG 3s8f (1.80), 3s8g (1.80), 4fa7 (2.50), 4faa (2.80), 4gp4 (2.80), 4gp5 (2.70), 4gp8 (2.80), 4g7r (3.05), 4g70 (2.60), 4g71 (2.90), 4g72 (3.19), 4g7q (2.60), 4g7s (2.00) Diacylglycerol kinase (7) Escherichia coli K-12 Enzyme 7.8 MAG; 7.9 MAG 3ze3 (2.05), 3ze4 (3.70), 3ze5 (3.10), 4bpd (3.30), 4brb (2.55), 4brr (2.44), 4d2e (2.28) MATE transporters (7) Pyrococcus furiosus Transporter 9.9 MAG 3vvn (2.40), 3vvo (2.50), 3vvp (2.91), 3vvr (3.00), 3vvs (2.60), 3w4t (2.10), 3wbn (2.45) Photosynthetic reaction centre (6) Blastochloris viridis Reaction centre 9.9 MAG 2wjm (1.95), 2wjn (1.86), 2x5u (3.00), 2x5v (3.00), 4ac5 (8.2), 4cas (3.50) Sensory rhodopsin II (6) Natronomonas pharaonis Rhodopsin, nonvisual 9.9 MAG 1jgj (2.40), 1gu8 (2.27), 1gue (2.27), 1h68 (2.10), 3qap (1.90), 3qdc (2.50) Photosynthetic reaction centre (5) Rhodobacter sphaeroides Reaction centre 9.9 MAG 1ogv (2.35), 2bnp (2.70), 2bns (2.50), 2gnu (2.00), 4tqq (2.50) Peptide (POT) transporter (5) Geobacillus kaustophilus Transporter 9.9 MAG 4ikv (1.90), 4ikw (2.00), 4ikx (2.30), 4iky (2.10), 4ikz (2.40) CDP-alcohol phosphotranspherase (4) Archaeoglobus fulgidus Enzyme 9.9 MAG 4o6m (1.90), 4o6n (2.10), 4q7c (3.10), 4mnd (2.66) Sensory rhodopsin IItransducer complex (4) Natronomonas pharaonis Rhodopsin, nonvisual 11.7 MAG 1h2s (1.93), 2f93 (2.00), 2f95 (2.20), 4gyc (2.05) Halorhodopsin (3) Halobacterium salinarum Rhodopsin, nonvisual 9.9 MAG 1e12 (1.80), 2jag (1.93), 2jaf (1.70) Peptide (POT) transporter (3) Streptococcus thermophilus Transporter 7.8 MAG 4d2b (2.35), 4d2c (2.47), 4d2d (2.52) Na + /bile acid symporter (2) Yersinia frederiksenii Transporter 9.9 MAG 4n7w (2.80), 4n7x (1.95) Sugar (SWEET) transporter (2) Leptospira biflexa , Vibrio sp.

Publication Year: 2015