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PDB ID Mentions in PubMed Central Article count: 3

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PDB ID Mentions in PubMed Central

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Protein conformational changes in the bacteriorhodopsin photocycle: comparison of findings from electron and X-ray crystallographic analyses.

(2009) PLoS One 4

PubMed: 19488399 | PubMedCentral: PMC2685002 | DOI: 10.1371/journal.pone.0005769

Eight coordinates (1CWQ(B), 1IW9, 1F4Z, 1C8S, 1P8U(1), 1JV7, 1X0I and 1FBK) are used.

To investigate the conformational differences among the various sets of coordinates in the regions where the largest changes occur, we superimposed the regions containing residues 171–186 of helix F from the structures reported as models for the M 1 to N′ states (1P8H(1), 1P8U(1), 1C8S, and 1FBK) ( Fig. 4A ).

Residues 171–186 of 1P8H(1), 1P8U(1), 1C8S, and 1FBK are extracted and displayed as “lines” modeled in Pymol.

Publication Year: 2009


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

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 inte... mediate structure (PDB code 1F4Z) [11] and the Mn intermediate state structure (PDB code 1C8S) [12] were used in our simulations.

To characterize the behavior of the retinal and SB during switch II and the effects of the key ionizable residues D212 and D96, we started by investigating the high-resolution x-ray structure of an N’ photointermediate [42] (PDBid 1P8U) that was determined by photoconverting crystals of the V49A mutant at pH 5.6.

The first set of the simulations were based on the x-ray crystal structure in the N’ state (PDBid 1P8U).

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