Citations in PubMed

Primary Citation PubMed: 23222541 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 10

Citations in PubMed

This linkout lists citations, indexed by PubMed, to the Primary Citation for this PDB ID.

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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High-resolution crystal structure of human protease-activated receptor 1.

(2012) Nature 492

PubMed: 23222541 | PubMedCentral: PMC3531875 | DOI: 10.1038/nature11701

S.R.C. and B.K.K. initiated project, planned and analyzed experiments, supervised the research and wrote the manuscript with C.Z. Author Information Coordinates and structure factors for PAR1 are depo... ited in the Protein Data Bank (accession code 3VW7).

Publication Year: 2012


Microbial and animal rhodopsins: structures, functions, and molecular mechanisms.

(2014) Chem Rev 114

PubMed: 24364740 | PubMedCentral: PMC3979449 | DOI: 10.1021/cr4003769

In addition, density best represented by a bound octahedrally coordinated sodium ion has been found within the TM bundle of A 2A -adenosine and PAR1 receptor structures (PDB ID: 4EIY, 3VW7; shown as a... black sphere) in a similar position to a water observed in the bovine Rho structure (PDB ID: 1U19).

Publication Year: 2014


Agonist-bound structure of the human P2Y12 receptor.

(2014) Nature 509

PubMed: 24784220 | PubMedCentral: PMC4128917 | DOI: 10.1038/nature13288

The P2Y 12 R-2MeSADP complex was solved by molecular replacement with Phaser 32 using the receptor portion of PAR1 (PDB: 3VW7), converted to polyalanines, and BRIL (PDB: 1M6T) as initial models and re... ined in Refmac5 33 and Buster 34 The P2Y 12 R-2MeSATP structure was solved using P2Y 12 R in complex with 2MeSADP and BRIL (PDB: 1M6T) as starting models and refined under the same procedure.

Publication Year: 2014


PubMed ID is not available.

Published in 2014

PubMedCentral: PMC4131901

Discussion Allosteric effects of sodium on GPCR agonist binding and activation have been known for years but were recently revived by new insights provided by ultra-high-resolution (1.8–2.2 &#... 000c5;) crystallographic structures of the A2AR (PDB entry 4EIY( 22 )), the B1AR (PDB entry 4BVN( 5 )), the PAR1 (PDB entry 3VW7( 23 )), and the δ-OR (PDB entry 4N6H( 24 )), which have revealed important details of binding of sodium to GPCRs (recently reviewed in ref ( 6 )).

21 The first direct experimental evidence of binding of sodium to a GPCR came only very recently with the ultra-high-resolution crystallographic structure of the adenosine A2A receptor (A2AR; PDB entry 4EIY( 22 )), which was followed within just a few months by the very high (1.8–2.2 Å)-resolution crystallographic structures of the β1-adrenergic receptor (B1AR; PDB entry 4BVN( 5 )), protease-activated receptor 1 (PAR1; PDB entry 3VW7( 23 )), and the δ-OR (PDB entry 4N6H( 24 )).

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


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


PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4360564

CXCR4 with the cyclic peptide antagonist CVX15 (PDB code 3OE0), DOR with the morphinan antagonist naltrindole (PDB code 4EJ4), NTSR1 with the peptide agonist NTS 8-13 (PDB code 4GRV), and PAR1 with th... antagonist vorapaxar (PDB code 3VW7).

NOP (PDP code 4EA3); KOR (PDB code 4DJH); DOR (PDB code 4N6H); MOR (PDB code 4KDL); CXCR4 (PDB code 3OE0); CCR5 (PDB code 4MBS); NTSR1 (PDB code 4GRV); PAR1 (PDB code 3VW7).

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


PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4422131

The dataset consists of 18 Class A GPCR structures in their inactive state: rhodopsin (PDB id: 1GZM), adenosine A2A receptor (PDB id: 3PWH), β2-adrenergic receptor (PDB id: 2RH1), β1-a... renergic receptor (PDB id: 2VT4), squid rhodopsin (PDB id: 2Z73), histamine H1 receptor (PDB id: 3RZE), sphingosine1-phosphate receptor 1 (PDB id: 3V2Y), dopamine D3 receptor (PDB id: 3PBL), CXCR4 chemokine receptor (PDB id: 3ODU), M2 muscarinic acetylcholine receptor (PDB id: 3UON), M3 muscarinic acetylcholine Receptor (PDB id: 4DAJ), protease-activated receptor 1 (PDB id: 3VW7), kappa opioid receptor (PDB id: 4DJH), mu-opioid receptor (PDB id: 4DKL), nociceptin/orphanin FQ opioid receptor (PDB id: 4EA3), delta opioid receptor (PDB id: 4N6H), CCR5 chemokine receptor (PDB id: 4MBS), P2Y12 receptor (PDB id: 4NTJ); and 7 Class A GPCR structures in their active state: β2-adrenergic receptor (PDB id: 4LDE), metarhodopsin II (PDB id: 3PQR), adenosine A2A receptor (PDB id: 3QAK), neurotensin NTS1 receptor (PDB id: 4GRV), M2 muscarinic acetylcholine receptor (PDB id: 4MQT), serotonin 5-HT2B receptor (PDB id: 4IB4), P2Y12 receptor (PDB id: 4PY0).

Publication Year: 2015


PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4453067

3D Structure Modeling A model of the 3D structure of FFAR2 has been constructed using Modeller (v9.10) ( Martí-Renom et al. 2000 ), the alignment shown in supplementary data S7 , Supplementary... Material online, deduced from a HHpred search ( Söding et al. 2005 ) and, as template, the 3D structure of proteinase-activated receptor 1 (pdb 3vw7; Zhang et al. 2012 ).

Mapping of Amino Acids under Positive Selection on the 3D Structure of Chicken FFAR2 A model of the 3D structure of chicken FFAR2 (ENSGALP00000034780) was made, using the experimental 3D structure of the proteinase-activated receptor 1 as a template (pdb 3vw7, 25% identity, HH-Pred probability 100, E value 4.5 × 10 − 45 ).

The model was made by homology with the 3D structure of the proteinase-activated receptor 1 (pdb 3vw7).

Publication Year: 2015