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PDB ID Mentions in PubMed Central Article count: 5

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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phenix.model_vs_data: a high-level tool for the calculation of crystallographic model and data statistics.

(2010) J Appl Crystallogr 43

PubMed: 20648263 | PubMedCentral: PMC2906258 | DOI: 10.1107/S0021889810015608

  R work and R free   R work and R free PDB code PDB file header Recomputed with model_vs_data PDB code PDB file header Recomputed with model_vs_data 1gu8 23.0/25.6 23.0/25.7 2g0v 5.1/... .4 18.5/n.a. 1htq 20.4/22.3 20.7/n.a. 2g0x 5.5/5.3 18.5/n.a. 1l2g 27.8/29.7 25.7/28.7 2g0z 5.8/7.0 18.4/n.a. 1mz0 15.0/17.3 14.6/16.7 2g10 4.5/4.9 17.3/n.a. 1n6j 24.3/26.8 28.5/31.2 2g11 5.1/5.7 17.4/n.a. 1ohh 23.2/28.0 21.7/n.a. 2g12 5.3/6.2 17.4/n.a. 1ot6 14.4/16.1 14.6/n.a. 2g14 5.1/5.8 17.3/n.a. 1ot9 13.4/16.1 13.5/n.a. 2g32 23.9/25.8 25.1/27.3 1t3n 26.5/28.6 25.6/28.0 2gn0 18.8/22.2 23.1/25.9 1u0c 21.4/27.7 28.6/n.a. 2gpm n.a./27.0 24.8/33.0 1u0d 21.7/25.7 37.8/38.5 2gq4 n.a./27.0 25.1/28.4 1vjm 25.2/29.8 24.7/29.3 2gq5 n.a./31.8 26.5/31.7 1wte 17.1/22.3 21.2/26.3 2gq6 n.a./29.5 27.4/28.5 1x0i 23.8/28.2 25.2/28.9 2gq7 n.a./31.0 24.8/31.2 1yk0 24.0/28.4 23.5/23.8 2grz 10.6/10.9 56.9/58.8 1yrq 17.1/22.0 22.4/26.0 2j9j 14.2/19.1 15.3/n.a. 1zbl 21.7/25.3 26.0/28.2 2je4 14.3/18.4 21.4/n.a. 1zev 21.8/27.9 29.0/33.1 2ntw 15.3/19.5 14.4/n.a. 1zy8 20.8/27.6 20.9/27.1 2q3m 15.7/21.7 15.7/21.2 2aaz 29.0/30.5 27.8/29.4 2q3o 18.0/23.5 17.9/23.1 2ce2 14.4/16.3 21.8/23.3 2q3p 18.2/22.4 18.1/21.9 2cl6 14.6/18.6 23.8/27.4 2q3u 13.5/17.1 14.3/17.4 2cl7 14.8/17.0 20.3/23.4 2ull 16.5/19.2 50.1/n.a. 2clc 14.9/18.0 23.7/27.0 2vtu 27.2/31.0 30.7/26.6 2cld 14.9/17.6 21.9/24.8 3c5f 22.4/26.3 22.2/26.1 2d6b 18.2/21.3 17.3/n.a. 3cmy 17.2/21.3 22.4/25.1 2e1c 20.6/23.0 31.1/31.4 3cye 19.3/23.1 18.1/22.0 2evw 15.6/23.6 20.9/23.6 406d 26.2/29.4 33.6/35.8 Table 5 Crystal structures solved using neutron data R work and R free as extracted from PDB file header (second column), and as recalculated using phenix.model_vs_data (third column).

Publication Year: 2010


Structural and functional similarities between osmotin from Nicotiana tabacum seeds and human adiponectin.

(2011) PLoS One 6

PubMed: 21311758 | PubMedCentral: PMC3032776 | DOI: 10.1371/journal.pone.0016690

Our research has evidenced that the structure of archeal ( Natronomonas pharaonis ) phototaxis protein rhodopsin II (PDB code: 1GU8) presented similar lengths of helices and loops between the helices ... espect to ADIPOR1 and, thus, suggested that this protein was the correct template for predicting the three-dimensional structure of ADIPOR1 by comparative modelling strategy.

We have also modeled yeast PHO36 (UniProt code: Q12442, region: 80–300) using the same procedure described for human ADIPOR1 and as template the structure of archeal ( Natronomonas pharaonis ) phototaxis protein rhodopsin II (PDB code: 1GU8).

Publication Year: 2011


The evolutionary relationship between microbial rhodopsins and metazoan rhodopsins.

(2013) ScientificWorldJournal 2013

PubMed: 23476135 | PubMedCentral: PMC3583139 | DOI: 10.1155/2013/435651

PDB number Protein name Species Classification 1U19 Rhodopsin Bos taurus (bovine) Eukaryota (Animalia) 2Z73 Rhodopsin Todarodes pacificus (Japanese flying squid) Eukaryota (Animalia) 1GU8 Sensory rhod... psin II Natronobacterium pharaonis Archaea (Halobacteria) 1JV6 Bacteriorhodopsin Halobacterium salinarum Archaea (Halobacteria) 1XIO Anabaena sensory rhodopsin Nostoc sp.

, University of Washington, Seattle, Wash, USA, 1993 36 Doolittle RF Convergent evolution: the need to be explicit Trends in Biochemical Sciences 1994 19 1 15 18 2-s2.0-0027983037 8140615 37 Luecke H Schobert B Richter HT Cartailler JP Lanyi JK Structure of bacteriorhodopsin at 1.55 A resolution Journal of Molecular Biology 1999 291 4 899 911 2-s2.0-0033609904 10452895 38 Edman K Royant A Nollert P Early structural rearrangements in the photocycle of an integral membrane sensory receptor Structure 2002 10 4 473 482 2-s2.0-0036230849 11937052 39 Okada T Sugihara M Bondar AN Elstner M Entel P Buss V The retinal conformation and its environment in rhodopsin in light of a new 2.2 A crystal structure Journal of Molecular Biology 2004 342 2 571 583 2-s2.0-4344581120 15327956 40 Vogeley L Sineshchekov OA Trivedi VD Sasaki J Spudich JL Luecke H Anabaena sensory rhodopsin: a photochromic color sensor at 2.0 A Science 2004 306 5700 1390 1393 2-s2.0-8844250818 15459346 41 Murakami M Kouyama T Crystal structure of squid rhodopsin Nature 2008 453 7193 363 367 2-s2.0-43749109187 18480818 42 Nei M Gu X Sitnikova T Evolution by the birth-and-death process in multigene families of the vertebrate immune system Proceedings of the National Academy of Sciences of the United States of America 1997 94 7799 7806 9223266 43 Knoll AH Carroll SB Early animal evolution: emerging views from comparative biology and geology Science 1999 284 5423 2129 2137 2-s2.0-0033603541 10381872 44 Gu X Early metazoan divergence was about 830 million years ago Journal of Molecular Evolution 1998 47 3 369 371 2-s2.0-0031685054 9732464 45 Marti T Rosselet SJ Otto H Heyn MP Khorana HG The retinylidene Schiff base counterion in bacteriorhodopsin Journal of Biological Chemistry 1991 266 28 18674 18683 2-s2.0-0026059269 1917991 46 Luecke H Schobert B Stagno J Crystallographic structure of xanthorhodopsin, the light-driven proton pump with a dual chromophore Proceedings of the National Academy of Sciences of the United States of America 2008 105 43 16561 16565 2-s2.0-55949126022 18922772 47 Bofkin L Goldman N Variation in evolutionary processes at different codon positions Molecular Biology and Evolution 2007 24 2 513 521 2-s2.0-33846799228 17119011 48 Katritch V Cherezov V Stevens RC Diversity and modularity of G protein-coupled receptor structures Trends in Pharmacological Sciences 2012 33 1 17 27 22032986 49 Nordström KJ Sällman Almén M Edstam MM Fredriksson R Schiöth HB Independent HHsearch, Needleman—Wunsch-based, and motif analyses reveal the overall hierarchy for most of the G protein-coupled receptor families Molecular Biology and Evolution 2011 28 9 2471 2480 21402729 Figure 1 Structure alignment of squid rhodopsin (2Z73:A | PDB, metazoan rhodopsin), bovine rhodopsin (1U19:A | PDB, metazoan rhodopsin), Anabaena sensory rhodopsin (1XIO:A | PDB, microbial rhodopsin), Natronomonas sensory rhodopsin II (1GU8:A | PDB, microbial rhodopsin), Halobacterium salinarum bacteriorhodopsin (1JV6:A | PDB, microbial rhodopsin), Natronomonas halorhodopsin (3A7 K:A | PDB, microbial rhodopsin), and Salinibacter ruber xanthorhodopsin (3DDL:A | PDB, microbial rhodopsin).

Publication Year: 2013


A Saccharomyces cerevisiae assay system to investigate ligand/AdipoR1 interactions that lead to cellular signaling.

(2013) PLoS One 8

PubMed: 23762377 | PubMedCentral: PMC3676391 | DOI: 10.1371/journal.pone.0065454

In brief, the 3D-homology model of human AdipoR1 was built for amino acids 135–364 with the Schrödinger suite 2011 using archeal ( Natronomonos pharaonis ) phototaxis protein rhodopsin... II (PDB id: 1GU8) as template structure [39] .

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