Primary Citation PubMed: 22437502
Citations in PubMed
This linkout lists citations, indexed by PubMed, to the Primary Citation for this PDB ID.
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.
Comparative analysis of the heptahelical transmembrane bundles of G protein-coupled receptors.
(2012) PLoS One 7
PubMed: 22545139 | PubMedCentral: PMC3335790 | DOI: 10.1371/journal.pone.0035802
Note Added in Proof After revision of this paper, four new entries (five chains) in the PDB have been released, namely, two inactivated chains of human kappa opioid receptor (PDBID: 4DJH), one inactiv... ted chain of mouse mu opioid receptor (4DKL), and two inactivated chains of A2A receptor (3UZA, 3UZC).
Publication Year: 2012
Crystal structure of the µ-opioid receptor bound to a morphinan antagonist.
(2012) Nature 485
PubMed: 22437502 | PubMedCentral: PMC3523197 | DOI: 10.1038/nature10954
Coordinates and structure factors for μOR-T4L are deposited in the Protein Data Bank (accession code 4DKL).
High-resolution crystal structure of human protease-activated receptor 1.
(2012) Nature 492
PubMed: 23222541 | PubMedCentral: PMC3531875 | DOI: 10.1038/nature11701
The simulation of the µ-opioid receptor (MOR) dimer was based on the crystal structure of MOR bound to the irreversible antagonist β-funaltrexamine (PDB code 4DKL).
Structural Characterization of an LPA1 Second Extracellular Loop Mimetic with a Self-Assembling Coiled-Coil Folding Constraint.
(2013) Int J Mol Sci 14
PubMed: 23434648 | PubMedCentral: PMC3588015 | DOI: 10.3390/ijms14022788
Rhodopsin (1F88 [ 21 ], orange), β2-adrenoceptor (2RH1 [ 19 ], magenta), β1-adrenoceptor (2VT4 [ 18 ], cyan), adenosine A2a (3EML [ 17 ], pink), dopamine D3 (3PBL [ 15 ], brown), chemo... ine CXCR4 (3Oe0 [ 16 ], green), histamine H1 (3RZE [ 14 ], mustard), muscarinic acetylcholine M2 (3UON [ 22 ], brick red), muscarinic acetylcholine M3 (4DAJ [ 33 ], grey), κ-opioid (4DJH [ 23 ], red), μ-opioid (4DKL [ 24 ], purple), and S1P 1 (3V2Y [ 25 ], blue) are shown using ribbon representations.
Publication Year: 2013
Crystal structure of oligomeric ?1-adrenergic G protein-coupled receptors in ligand-free basal state.
(2013) Nat Struct Mol Biol 20
PubMed: 23435379 | PubMedCentral: PMC3618578 | DOI: 10.1038/nsmb.2504
a , β 1 -AR is in green and μ-opioid receptor (PDB code 4DKL) is in magenta.
Insights into the molecular evolution of oxytocin receptor ligand binding.
(2013) Biochem Soc Trans 41
PubMed: 23356283 | PubMedCentral: PMC3634130 | DOI: 10.1042/BST20120256
Figure 3 Mapping of GPCR ligand-binding sites on to the structural model of the human OTR Sequences of the OTR and the opioid receptor were aligned with muscle [ 34 ] and a model of the human OTR was ... uilt using MODELLER v9.8 [ 35 ] applying the automodel procedure, of the mouse μ-opioid receptor crystal structure as a template (PDB ID: 4DKL) [ 21 ].
Orvinols with mixed kappa/mu opioid receptor agonist activity.
(2013) J Med Chem 56
PubMed: 23438330 | PubMedCentral: PMC3646402 | DOI: 10.1021/jm301543e
Docking: the 4DJH crystal structure of the KOR and the 4DKL crystal structure of the MOR were prepared for docking work by running them through the Protein Preparation Wizard tool of the Schrö... inger software.
A computationally designed water-soluble variant of a G-protein-coupled receptor: the human mu opioid receptor.
(2013) PLoS One 8
PubMed: 23799068 | PubMedCentral: PMC3682944 | DOI: 10.1371/journal.pone.0066009
g002 Figure 2 (A) Sequences of the crystal structure of the mouse mu opioid receptor (PDB code 4DKL; top) (1) and the human water-soluble variant wsMUR-TM (bottom).
GOMoDo: A GPCRs online modeling and docking webserver.
PubMed: 24058518 | PubMedCentral: PMC3772745 | DOI: 10.1371/journal.pone.0074092
Model template is the mouse μ-opioid receptor (PDB structure: 4DKL, UniProt ID: P42866).
Human ? Opioid Receptor Models with Evaluation of the Accuracy Using the Crystal Structure of the Murine ? Opioid Receptor.
(2012) J Anesth Clin Res 3
PubMed: 24527268 | PubMedCentral: PMC3920553 | DOI: 10.4172/2155-6148.1000218
The X-ray crystallographic structure murine μ opioid receptor (PDB accession code: 4DKL) was used to evaluate these models.
The representative models from the comparative modeling procedure were compared with the crystal structure of murine μ opioid receptor (PDB accession code: 4DKL).
Differential stability of the crystallographic interfaces of mu- and kappa-opioid receptors.
(2014) PLoS One 9
PubMed: 24651466 | PubMedCentral: PMC3944890 | DOI: 10.1371/journal.pone.0090694
Materials and Methods System Setup Missing loop segments from the crystallographic structures of the mouse MOPr (PDB ID: 4DKL)  (residues 263–270) and chain A of the human KOPr (PDB ID: 4DJ... )  (residues 262 and 301–307) were built using ROSETTA version 2.2  .
MOPr protomers interacting at a TM1,2,H8/TM1,2,H8 interface colored in red and pink from PDB ID: 4DKL.
MOPr protomers interacting at a TM5,6/TM5,6 interface in blue and light blue, also from PDB ID 4DKL, and KOPr protomers interacting at a TM1,2,H8/TM1,2,H8 interface are shown in green and light green, from PDB ID: 4DJH.
Publication Year: 2014
PubMed ID is not available.
Published in 2014
Thus, we conducted all-atom, microsecond-scale MD simulations of ligand-free δ-OR, μ-OR, and κ-OR crystallographic structures (PDB entries 4N6H, 24 4DKL, 27 and 4DJH, 28 respec... ively) embedded in a hydrated POPC/10% cholesterol bilayer, and in the presence of physiological concentrations of sodium.
Materials and Methods Simulation System Setups and Force Field The inactive crystal structures of mouse μ-OR, human κ-OR, and human δ-OR corresponding to PDB entries 4DKL, 27 4DJH, 28 and 4N6H, 24 respectively, were used as starting conformations for all-atom MD simulations in an explicit lipid–water environment.
Figure 1 Vertical views of the representative structures from the microsecond simulations of (A) δ-OR (PDB entry 4N6H), (B) μ-OR (PDB entry 4DKL), and (C) κ-OR (PDB entry 4DJH) in cartoon representation with negatively charged (Asp and Glu) residues shown as sticks.
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 ).
Sequence alignments of sstr2 and the known crystal structure of GPCR revealed that sstr2 has a moderate sequence identity similarity: ∼40% to nociceptin/orphanin FQ receptor (NOP, PDB entry: 4... A3, resolution: 3.01), ∼44% to μ-opioid receptor (MOR, PDB entry: 4DKL, resolution: 2.80), ∼41% to κ-opioid receptor (KOR, PDB entry: 4DJH, resolution: 3.01), 42% to δ-opioid receptor (DOR, PDB entry: 4EJ4, resolution: 3.40), ∼34% to chemokine receptor CXCR4 (PDB entry: 3ODU, resolution: 2.50), ∼28% todopamine D3 receptor (D3R, PDB entry: 3PBL, resolution: 2.89), 27% to human beta2-adrenergic receptor (PDB entry: 2RH1, resolution: 2.40), ∼28% to chemokine receptor CXCR1 (PDB entry: 2LNL, solid-state NMR), ∼22% to human A2A receptor (A2AAR, PDB entry: 2YDO, resolution: 3.00), ∼26% to human histamine H1 receptor (H1R, PDB entry: 3RZE, resolution: 3.10), ∼25% to sphingosine 1-phosphate receptor (S1P, PDB entry: 3V2W, resolution: 3.35), and ∼31% to human beta1-adrenergic receptor (PDB entry: 2Y00, resolution: 2.50).
These receptors and their structures used in our studies are nociceptin/orphanin FQ receptor (NOP, PDB entry: 4EA3, resolution: 3.01), μ-opioid receptor (MOR, PDB entry: 4DKL, resolution: 2.80), κ-opioid receptor (KOR, PDB entry: 4DJH, resolution: 3.01), and δ-opioid receptor (DOR, PDB entry: 4EJ4, resolution: 3.40).
On the modularity of the intrinsic flexibility of the µ opioid receptor: a computational study.
PubMed: 25549261 | PubMedCentral: PMC4280117 | DOI: 10.1371/journal.pone.0115856
Methods A. Molecular dynamics simulations The 3D structure of the µ OR was built from the coordinates obtained by X-ray diffraction structure  that are available in the PDB (ID: 4DKL).
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
Published in 2015
Materials and Methods System Preparation The atomic coordinates of non-protein molecules were removed from the PDB files of the crystallographic structures of the mouse δ-OR (PDB ID: 4EJ4 [ 15... ]), mouse μ-OR (PDB ID: 4DKL [ 12 ]), and chain A of the human κ-OR (PDB ID: 4DJH [ 13 ]) receptors.
While no cholesterol molecules were resolved in the κ-OR or δ-OR crystal structures, electron density was attributed to a cholesterol molecule in the μ-OR crystal structure (4DKL), at the same location between TM6 and TM7 as seen in the A2A crystal structure 4EIY.
is consistent with the location of cholesterol molecules found in the ultra-high-resolution adenosine A2A crystal structure 4EIY and in the μ-OR crystal structure 4DKL.
Specifically, in κ-OR, this interface is 8.56 Å apart from the putative TM5,6-TM5,6 dimer interface inferred from the μ-OR crystal structure (after overlapping the dimer from simulation with chain A of 4DKL and its periodic image).
The closest crystal structure to the TM1,2,H8/TM1,2,H8 interface that forms during μ-OR simulations is not the one inferred by the μ-OR crystal structure (4DKL [ 12 ]), but rather the one suggested by a β1-adrenergic receptor (B1AR) crystal structure (4GPO [ 23 ]).
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 ]].
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).
(A) Intracellular view of the CB 1 R-5-HT 2A R heteromer (blue and green protomers) bound to DOI (green surface) and rimonabant (red surface), modeled from the crystal structure of the μ-opioi... receptor (PDB id 4DKL) [ 1 ].
Our calculations are based on the X-ray structure of mouse μOR covalently bound with β-funaltrexamine (β-FNA), a semisynthetic opioid antagonist derived from morphine, resolved... at 2.8 Å resolution (PDB entry: 4DKL) [ 18 ].
The RCSB PDB (citation) is managed by two members of the Research Collaboratory for Structural Bioinformatics:
RCSB PDB is a member of the
The RCSB PDB is funded by a grant (DBI-1338415) from the
National Science Foundation, the
National Institutes of Health, and the
US Department of Energy.