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Primary Citation PubMed: 23636324 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 8

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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An analysis of oligomerization interfaces in transmembrane proteins.

(2013) BMC Struct Biol 13

PubMed: 24134166 | PubMedCentral: PMC4015793 | DOI: 10.1186/1472-6807-13-21

core-rim core-surface 2i35 A + A 316.6 0 + 0 2 + 2 105 0.39* -0.20* 2i36 C + C 684.5 1 + 1 1 + 1 105 0.47 (b) -0.35 (x)   A... 09;+ B 509.9 1 + 1 2 + 2 105 1.08* 0.50* 2i37 A + B 418.2 0 + 0 2 + 2 105 0.45* -0.23*   C + C 413.2 0 + 0 2 + 2 105 0.41* -0.25* 3odu A + B 1209.3(797.9) 0 + 0   52 1.28 (x) 1.55 (x) 3oe0 A + A 1089.4(1086.8) 0 + 0   83 1.55 (x) 1.71 (x) 3oe6 A + A 1037.6(764.8) 0 + 0   94 1.67 (x) 2.80 (x) 3oe8 B + C 665.2(591.9) 0 + 0 3 + 4 83 0.83* 0.32* 3oe9 A + B 959.4(877.4) 0 + 0   102 1.46 (x) 1.70 (x) 4djh A + B 1024.0 1 + 1   106 1.42 (x) 0.85 (x) 4gpo A + B 833.5 0 + 0   71 1.74 (x) 2.79 (x) 4jkv A + B 1237.7 6 + 6   16 0.43 (b) -1.90 (b) 3sn6 A + R 1263.1 2 + 6   103,136 0.34 (b) -2.41 (b) Analysis of a set of class A GPCR dimer interfaces proposed in the literature plus the proposed dimer interface for the human Smoothened receptor [PDB: 4jkv] and the β2 adrenergic receptor to G-protein interface [PDB: 3sn6].

Recently a structure of a class F GPCR, human Smoothened receptor [PDB: 4jkv], was solved [ 55 ] showing yet again the very well conserved 7-TM bundle.

Publication Year: 2013


Potential smoothened inhibitor from traditional Chinese medicine against the disease of diabetes, obesity, and cancer.

(2014) Biomed Res Int 2014

PubMed: 25136636 | PubMedCentral: PMC4127221 | DOI: 10.1155/2014/873010

Data Collection The X-ray crystallography structure of the human smoothened receptor (Smo) was obtained from RCSB Protein Data Bank with PDB ID: 4JKV [ 39 ].

Publication Year: 2014


The recombinant expression systems for structure determination of eukaryotic membrane proteins.

(2014) Protein Cell 5

PubMed: 25119489 | PubMedCentral: PMC4145085 | DOI: 10.1007/s13238-014-0086-4

Protein Species PDB code Reference Insect cell S. frugiperda 1 β 2 AR (Fab) Homo sapiens 2R4R 2R4S Rasmussen et al., 2007 2 β 2 AR (T4L) Homo sapiens 2RH1 Cherezov et al., 2007 3 �... b2; 2 AR-agonist complex Homo sapiens 3PDS Rosenbaum et al., 2011 4 β 2 AR-GS complex Homo sapiens 3SN6 Rasmussen et al., 2011a , b 5 A 2A adenosine receptor Homo sapiens 3EML Jaakola et al., 2008 6 CXCR4 Homo sapiens 3ODU 3OE8 Wu et al., 2010 7 Dopamine D3 receptor Homo sapiens 3PBL Chien et al., 2010 8 Sphingosine 1-phosphate receptor subtype 1 Homo sapiens 3V2 W 3V3Y Hanson et al., 2012 9 M2 muscarinic acetylcholine receptor Homo sapiens 3UON Haga et al., 2012 10 M3 muscarinic acetylcholine receptor Rattus norvegicus 4DAJ Kruse et al., 2012 11 κ-Opioid receptor Homo sapiens 4DJH Wu et al., 2012 12 μ-Opioid receptor Mus musculus 4DKL Manglik et al., 2012 13 δ-Opioid receptor Mus musculus 4EJ4 Granier et al., 2012 14 N/OFQ receptor Homo sapiens 4EA3 Thompson et al., 2012 15 CCR5 Homo sapiens 4MBS Tan et al., 2013 16 PAR1 Homo sapiens 3VW7 Zhang et al., 2012 17 5-HT 1B/2B serotonin receptor Homo sapiens 4IAR 4IB4 Wang et al., 2013a , b ; Wacker et al., 2013 18 Smoothened receptor Homo sapiens 4JKV Wang et al., 2013a , b 19 Glucagon receptor Homo sapiens 4L6R Siu et al., 2013 20 Metabotropic glutamate receptor1 Homo sapiens 4OR2 Wu et al., 2014 21 P2X 4 Danio rerio (Zebra fish) 3I5D 3H9 V 4DW1 Kawate et al., 2009 ; Hattori and Gouaux, 2012 22 ASIC1 Gallus gallus 2QTS 3HGC Jasti et al., 2007 ; Gonzales et al., 2009 23 GluA2 Rat 3KG2 3KGC Sobolevsky et al., 2009 24 GLuClα Caenorhabditis elegans 3RHW, 3RIF, 3RI5 3RIA Hibbs and Gouaux, 2011 25 CX26 Homo sapiens 2ZW3 Maeda et al., 2009 26 UT-B Bos taurus 4EZC 4EZD Levin et al., 2012 27 ZMPSTE24 Homo sapiens 4AW6 Quigley et al., 2013 28 ABCB10 Homo sapiens 4AYT Shintre et al., 2013 29 Caludin-15 Mus Musculus 4P79 Suzuki et al., 2014 30 NRT1.1 Arabidopsis thaliana 4OH3 Sun et al., 2014 Trichoplusia ni 31 β1 adrenergic receptor Meleagris gallopavo 2VT4 Warne et al., 2008 32 NTS1 Neurotensin Receptor Rattus norvegicus 4GRV White et al., 2012 33 CmClC Cyanidioschyzonmerolae 3ORG Feng et al., 2010 34 Corticotropin-releasing factor receptor Homo sapiens 4K5Y Hollenstein et al., 2013 35 GLUT1 Homo sapiens 4PYP Deng et al., 2014 * For some proteins like GPCR and potassium channel, only the representative ones are listed After the protein IL-2 was first expressed in large scale with the baculovirus-infected insect cells in 1985, this system has been quickly accepted and widely used (Smith et al., 1983 ; Maeda et al., 1985 ).

Publication Year: 2014


PubMed ID is not available.

Published in 2014

PubMedCentral: PMC4170816

Table 1 Information of 10 Crystal Structures of GPCRs Used in the Present Work a   SMO bovine rhodopsin CXCR4 M2MAR D3R β2AR A 2A AR H1R S1P β1AR PDB entry 4JKV 1F88 3ODU 3UON ... PBL 2RH1 2YDO 3RZE 3V2W 2Y00 resolution (Å) 2.45 2.40 2.50 3.00 2.89 2.40 3.00 3.10 3.35 2.50 whole sequence identity (±2%) 14.4 17.4 19.1 20.9 23.5 24.4 25.1 25.2 28.5 28.5 sequence identity in TM (±2%) 18 25 21 27 28 28 29 30 34 35 proSA-web Z-score –2.80 –2.82 –3.54 –3.24 –2.72 –4.21 –4.87 –3.36 –3.49 –4.33 ref ( 35 ) ( 19 ) ( 37 ) ( 31 ) ( 38 ) ( 30 ) ( 33 ) ( 34 ) ( 32 ) ( 36 ) a We listed the information on 10 GPCRs used in the present work, including PDB entry, resolution, sequence identity to CB2, and the related references.

Publication Year: 2014


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


Molecular docking approaches in identification of High affinity inhibitors of Human SMO receptor.

(2014) Bioinformation 10

PubMed: 25670876 | PubMedCentral: PMC4312366 | DOI: 10.6026/97320630010737

The three-dimensional structure of SMO [PDB: 4JKV] was retrieved from the Protein Data Bank [ 31 ].

All the selected SMO inhibitors were docked into inhibitor binding site of SMO in reference to coordinates of bound ligand 1KS_601 (C 26 H 24 F 4 N 6 O) in the crystal structure of 4JKV as shown in Figure 1 .

Publication Year: 2014


PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4361874

The 7TM bundle of the smoothened receptor (PDB ID: 4JKV) aligned to rhodopsin-like receptors was assumed to lack a residue at the amino terminal of helix IV (4.39).

Publication Year: 2015


PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4399913

In case that several crystal structures were available for one receptor, we chose the one with highest available resolution for data analysis [respective PDB IDs: rhodopsin (OPSD): 1U19 [ 36 ]; ... 2; 2 adrenergic receptor (ADBR2): 2RH1 [ 37 ]; β 1 adrenergic receptor (ADBR1): 2YCW [ 6 ]; A 2A adenosine receptor (AA2AR): 4EIY [ 20 ]; D3 dopamine receptor (D3DR): 3PBL [ 8 ]; H1 histamine receptor (H1HR): 3RZE [ 10 ]; (S1PR1): 3V2Y [ 11 ]; chemokine receptor CXCR4 (CXCR4): 3OE0 [ 9 ]; chemokine receptor CCR5 (CCR5): 4MBS [ 26 ]; δ-opioid receptor (OPRD): 4EJ4 [ 17 ]; μ-opioid (OPRM): 4DKL [ 14 ]; κ-opioid (OPRK): 4DJH [ 15 ]; N/OFQ opioid (OPRX): 4EA3 [ 16 ]; M2 muscarinic receptor (ACM2): 3UON [ 12 ]; M3 muscarinic receptor (ACM3): 4DAJ [ 13 ],; neurotensin receptor 1 (NTR1): 4GRV [ 18 ]; protease-activated receptor 1 (PAR1): 3VW7 [ 19 ]; serotonine receptor 1B (5HT1B): 4IAR [ 21 ]; serotonine receptor 2B (5HT2B): 4IB4 [ 21 ]; purine receptor P2Y12 (P2Y12): 2PXZ [ 27 ]; glucagon receptor (GLR): 4L6R [ 23 ]; smoothened receptor (SMO): 4JKV [ 24 ]; corticotropin-releasing factor receptor 1 (CRFR1): 4K5Y [ 25 ]; metabotropic glutamate receptor 1 (GRM1): 4OR2 [ 28 ]].

Publication Year: 2015