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PDB ID Mentions in PubMed Central Article count: 48

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PDB ID Mentions in PubMed Central

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Crystal structure of the ?2 adrenergic receptor-Gs protein complex.

(2011) Nature 477

PubMed: 21772288 | PubMedCentral: PMC3184188 | DOI: 10.1038/nature10361

Author Information Coordinates and structure factors for the β 2 AR-Gs complex are deposited in the Protein Data Bank (accession code 3SN6).

Publication Year: 2011

Modeling of human prokineticin receptors: interactions with novel small-molecule binders and potential off-target drugs.

(2011) PLoS One 6

PubMed: 22132188 | PubMedCentral: PMC3221691 | DOI: 10.1371/journal.pone.0027990

The β1adr homology model is based on 4 different β2adr crystal structures (PDB codes – 3SN6, 2RH1, 3NY8, and 3d4S); the β2adr model is based on the crystal structures o... β1adr (2VT4, 2YCW), the Dopamine D3 receptor (3PBL), and the histamine H1 receptor (3RZE).

Publication Year: 2011

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

Stereo view of molecular overlay of helix VI within 7TM bundles: inactivated (red, PDB ID: 1U19-A) and activated (pink, PDB ID: 3PXO) bovine rhodopsin, inactivated (blue, PDB ID: 2RH1) and activated (... yan, PDB ID: 3SN6) β2 receptor, inactivated (yellow, PDB ID: 3EML) and activated (lemon, PDB ID: 3QAK) A2A receptor.

Publication Year: 2012

Action of molecular switches in GPCRs--theoretical and experimental studies.

(2012) Curr Med Chem 19

PubMed: 22300046 | PubMedCentral: PMC3343417 | DOI: null

Summary of All Available Crystal Structures of GPCRs (Based on [ 61 ]) GPCR Engineered Type of ligand Ligand name PDB ID (Resolution Å) [Reference] A 2A R (human) IC3 fusion Agonist UK-432097 ... QAK (2.71) [ 101 ] Inverse agonist ZM241385 3EML (2.6) [ 98 ] Point mutations Agonist Adenosine 2YDO (3.0) [ 105 ] Agonist NECA 2YDV (2.6) [ 105 ] Antagonist Caffeine 3RFM (3.60) [ 106 ] Antagonist XAC 3REY (3.31) [ 106 ] Inverse agonist ZM241385 3PWH (3.30) [ 106 ] β 1 AR (turkey) Point mutations Agonist Carmoterol 2Y02 (2.6) [ 104 ] Agonist Isoprenaline 2Y03 (2.85] [ 104 ] Antagonist Cyanopindolol 2VT4 (2.7) [ 74 ], 2YCX (3.25) [ 159 ], 2YCY (3.15) [ 159 ], 2YCZ (3.65) [ 159 ] Inverse agonist Carazolol 2YCW (3.0) [ 159 ] Partial agonist Dobutamine 2Y00 (2.5) [ 104 ], 2Y01 (2.6) [ 104 ] Partial agonist Salbutamol 2Y04 (3.05) [ 104 ] β 2 AR (human) IC3 fusion Agonist BI-167107, nanobody 3P0G (3.5) [ 96 ] Agonist FAUC50 3PDS (3.5) [ 96 ] Antagonist Alprenolol 3NYA (3.16) [ 97 ] Inverse agonist Carazolol 2RH1 (2.4) [ 18 ] Inverse agonist Compound #1 3NY9 (2.84) [ 97 ] Inverse agonist ICI118551 3NY8 (2.84 [ 97 ] Inverse agonist Timolol 3DS4 (2.8) [ 59 ] Inverse agonist FAB, not resolved 2R4R (3,4) [ 96 ], 2R4S (3.4) [ 96 ] Inverse agonist FAB, not resolved 3KJ6 (3.4) [ 135 ] N-terminal fusion Agonist BI-167107, Gαβγ, nanobody 3SN6 (3.2) [ 15 ] CXCR4 (human) IC3 fusion Antagonist CVX15 peptide 3OE0 (2.9) [ 33 ] Antagonist Molecule 1t 3ODU (2.5) [ 33 ], 3OE6 (3.2) [ 33 ], 3OE8 (3.1) [ 33 ], 3OE9 (3.1)[ 33 ] D 3 R (human) IC3 fusion Antagonist Eticlopride 3PBL (2.89) [ 99 ] H 1 R (human) IC3 fusion Inverse agonist Doxepin 3RZE (3.1) 36 [ 100 ] Opsin 3CAP (2.9) [ 89 ] Gα peptide 3DQB (3.2) [ 91 ] Rhodopsin (bovine) Agonist All- trans -retinal 2G87 (2.6) [ 139 ] Inverse agonist 11- cis -retinal 1F88 (2.8) [ 17 ], 1U19 (2.2) [ 83 ], 1GZM (2.65) [ 83 ], L9H (2.6) [ 83 ], 1HZX (2.8) [ 83 ], 2I37 (4.0) [ 83 ], 3OAX (2.6) [ 83 ], 3C9L (2.65) [ 83 ] Point mutations Agonist 11- trans -retinal, Ga peptide 2X72 (3.0) [ 122 ], 3PQR (2.85) [ 123 ], 3PXO (3.0) [ 123 ] 9- cis -retinal 2PED (2.95) 3385 [ 85 ] 2J4Y (3.4) 3 [ 83 ], 3C9M (3.4) [ 83 ] Rhodopsin (squid) Inverse agonist 11- cis -retinal 2ZIY (3.7) [ 86 ]

Publication Year: 2012

GDP release preferentially occurs on the phosphate side in heterotrimeric G-proteins.

(2012) PLoS Comput Biol 8

PubMed: 22829757 | PubMedCentral: PMC3400569 | DOI: 10.1371/journal.pcbi.1002595

In agreement, some parts of the X-ray structure that describes an unbound G α subunit (PDB:3SN6) would require to be rebuilt, because of some putative crystallization artifacts [9] .

Publication Year: 2012

Assessing the relative stability of dimer interfaces in g protein-coupled receptors.

(2012) PLoS Comput Biol 8

PubMed: 22916005 | PubMedCentral: PMC3420924 | DOI: 10.1371/journal.pcbi.1002649

By superimposing the TM region of one of the two protomers of the simulated B2AR dimers on the active B2AR TM region of the recent crystal structure of the B2AR- Gs complex (PDB ID: 3SN6 [22] ) we not... interactions of the second protomer with the G-protein vary, depending on the specific dimeric arrangement of B2AR ( Fig. 3 ).

The extracellular view of the B2AR-Gs protein complex (PDB ID: 3SN6) is shown with B2AR in grey cartoon representation, and the Gs heterotrimer, is shown in both cartoon and transparent surface (α is in orange, β is in cyan and γ is in pale blue).

The first protomer of each of our minimum energy dimers for B2AR (Θ2 for TM4/3) is superimposed on the B2AR from the crystal structure 3SN6, and the position of the second protomer is shown in a green cartoon representation.

Publication Year: 2012

N-terminal T4 lysozyme fusion facilitates crystallization of a G protein coupled receptor.

(2012) PLoS One 7

PubMed: 23056231 | PubMedCentral: PMC3464249 | DOI: 10.1371/journal.pone.0046039

H. ICL2 in the β 2 AR-Gs structure (pdb 3SN6).

Publication Year: 2012

Why GPCRs behave differently in cubic and lamellar lipidic mesophases.

(2012) J Am Chem Soc 134

PubMed: 22931253 | PubMedCentral: PMC3469068 | DOI: 10.1021/ja3056485

To assess this hypothesis in the context of structural information available for GPCRs, we examined crystallographic contact interfaces for 12 different structures of rhodopsin-like GPCRs obtained by ... eans of the in meso technology (β 2 receptor – PBD codes: 2RH1 , 3PDS , 3SN6 ; A2A receptor – PDB codes: 3EML , 3QAK ; Chemokine CXCR4 receptor – PDB codes: 3ODU , 3OE0 , 3OE6 , 3OE8 , 3OE9 ; Dopamine D3 receptor – PDB code: 3PBL , and Histamine H1 receptor – PDB code: 3RZE ).

Publication Year: 2012

Structure of the agonist-bound neurotensin receptor.

(2012) Nature 490

PubMed: 23051748 | PubMedCentral: PMC3482300 | DOI: 10.1038/nature11558

(c) Alignment of the inactive state of β 2 AR 40 (pale mauve, PDB code 2RH1) and its active state 32 (pale grey, PDB code 3SN6) and NTS1-GW5 (green).

(c) The same comparison for inactive β 2 AR 40 (pale mauve, PDB code 2RH1) and active β 2 AR 32 (pale grey, PDB code 3SN6) (residues E130, R131 and Y219).

Publication Year: 2012

Similarity between class A and class B G-protein-coupled receptors exemplified through calcitonin gene-related peptide receptor modelling and mutagenesis studies.

(2013) J R Soc Interface 10

PubMed: 23235263 | PubMedCentral: PMC3565703 | DOI: 10.1098/rsif.2012.0846

This interaction is born out by MD simulations, but the analogous residues in the β 2 -AR–Gs complex (PDB code 3SN6) are poorly resolved and so the interpretation should be used with c... re, despite the observations from mutagenesis experiments that implicate K 6.32 and K 6.35 in G-protein coupling in both class A [ 36 , 46 – 48 ] and class B [ 39 , 49 – 52 ] GPCRs.

The crystal structure of the active β 2 -adrenergic receptor (β 2 -AR)–G-protein complex, pdb code 3SN6, has played a key role in generating these active structures [ 20 ] and hence in interpreting the mutagenesis.

Position 2.39 contacts the G-protein in our model complex and in the structure of the β 2 -AR–Gs complex, 3SN6.

Residues 5.61 and 5.65 contact the transducin C-terminal peptide in the opsin structures [ 32 ], but a larger range of residues contact the G-protein in the β 2 -AR 3SN6 structure.

Publication Year: 2013

Towards improved quality of GPCR models by usage of multiple templates and profile-profile comparison.

(2013) PLoS One 8

PubMed: 23468878 | PubMedCentral: PMC3585245 | DOI: 10.1371/journal.pone.0056742

Right panels show results of self-docking to crystal structures (PDB id: 3SN6, 3RZE, 3ODU, 3PQR).

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 and b , The complex of β 2 -AR and Gs (PDB code 3SN6) was aligned with molecule B of the β 1 -AR dimer with the TM1-TM2-H8 interface.

The complex of β 2 -AR and Gs (PDB code 3SN6) was aligned with molecule B of the β 1 -AR dimer with the TM1-TM2-H8 interface.

Publication Year: 2013

Common and distinct mechanisms of activation of rhodopsin and other G protein-coupled receptors.

(2013) Sci Rep 3

PubMed: 23677071 | PubMedCentral: PMC3654499 | DOI: 10.1038/srep01844

Table 1 PDB entries used for this study   PDB ID receptor Inactive-like Active-like rhodopsin 1GZM-A 2X72   1U19-A 3PQR     3PXO     4A4M β 2 re... eptor 2RH1 3P0G   3D4S 3SN6   3NY8     3NY9   A 2A receptor 3EML 2YDO   3VG9 2YDV   4EIY 3QAK

Publication Year: 2013

Efficacy of the ??-adrenergic receptor is determined by conformational equilibrium in the transmembrane region.

(2012) Nat Commun 3

PubMed: 22948827 | PubMedCentral: PMC3658005 | DOI: 10.1038/ncomms2046

The crystal structures of β 2 AR have been solved in the forms bound to inverse agonists 6 7 8 9 10 , a neutral antagonist 10 , a full agonist 11 and a full agonist with a G-protein 12 or a G-... rotein-mimicking nanobody 13 (PDB accession codes: 3D4S , 2RH1 , 3PDS , 3SN6 , and 3P0G ).

The crystal structure of β 2 AR with a full agonist, BI-167107, and a G-protein (PDB accession code: 3SN6 ) 12 is shown in violet ribbons.

Publication Year: 2012

Conformation guides molecular efficacy in docking screens of activated ?-2 adrenergic G protein coupled receptor.

(2013) ACS Chem Biol 8

PubMed: 23485065 | PubMedCentral: PMC3658555 | DOI: 10.1021/cb400103f

This structure is almost identical in the binding site to a later active structure co-crystallized with BI-167107 and the G protein itself (PDB ID 3SN6) that we did not use due to lower resolution in ... he binding site.

Publication Year: 2013

Structure and activation of rhodopsin.

(2012) Acta Pharmacol Sin 33

PubMed: 22266727 | PubMedCentral: PMC3677203 | DOI: 10.1038/aps.2011.171

(B) Comparison of the binding mode of rhodopsin with the synthetic peptide and that of the β2-adrenergic receptor with intact G protein (PDB: 3SN6).

(C) The whole-complex model of the β2-adrenergic receptor with intact G protein (PDB: 3SN6).

Publication Year: 2012

Active-state models of ternary GPCR complexes: determinants of selective receptor-G-protein coupling.

(2013) PLoS One 8

PubMed: 23826246 | PubMedCentral: PMC3691126 | DOI: 10.1371/journal.pone.0067244

Materials and Methods Homology Modeling We used the crystal structure of the β 2 -adrenergic receptor (β2AR) together with a heterotrimeric G-protein [16] (PDB-ID: 3SN6) as a starting ... oint for our calculations.

(A) Intracellular view of the superposition of active-state models of D2 Down R (green) and D2 Up R (dark-red) and the crystal structures of D3R (PDB-ID 3PBL, grey) and β2AR in complex with different binding partners (violet: carazolol, PDB-ID 2RH1; dark-blue: FAUC50, PDB-ID 3PDS; blue: BI167107 and the G s protein, PDB-ID 3SN6).

The aim of the applied force is to avoid spurious conformations caused by the high flexibility of the αN-helix in the absence of both the βγ-subunit and the stabilizing acylations because the amino acids that could potentially be acylated are not resolved in the crystal structure of the ternary complex (PDB-ID: 3SN6).

” We therefore used the crystal structure of the β2AR-Gα s -complex (PDB-ID: 3SN6) as a starting point for active-state homology models of D2R in complex with the nucleotide-free state of Gα i .

Publication Year: 2013

Heterotrimeric G protein signalling in the plant kingdom.

(2013) Open Biol 3

PubMed: 23536550 | PubMedCentral: PMC3718340 | DOI: 10.1098/rsob.120186

Crystal structures shown are animal heterotrimeric G protein (PDB: 1GOT) [ 56 ], G protein and β2 adrenergic receptor (PDB: 3SN6) [ 6 ], and Arabidopsis AtGPA1 (PDB: 2XTZ) [ 41 ].

Publication Year: 2013

Orthosteric binding of ?-Da1a, a natural peptide of snake venom interacting selectively with the ?1A-adrenoceptor.

(2013) PLoS One 8

PubMed: 23935897 | PubMedCentral: PMC3723878 | DOI: 10.1371/journal.pone.0068841

Nine β 2 -AR structures are available (2RH1, 3D4S, 3KJ6, 3NY8, 3NY9, 3NYA, 3PDS, 3P0G, 3SN6) and are very similar (Cα RMSDs<1.5 Å for 253 residues).

Publication Year: 2013

Computational study on the different ligands induced conformation change of ?2 adrenergic receptor-Gs protein complex.

(2013) PLoS One 8

PubMed: 23922653 | PubMedCentral: PMC3726664 | DOI: 10.1371/journal.pone.0068138

Materials and Methods Protein Structures Preparation The agonist-bound model of β 2 AR was prepared beginning from the crystal structure (PDB ID: 3SN6) [12] by removing T4 lysozyme and nanobod... (Nb35).

Publication Year: 2013

Simulations of biased agonists in the ?(2) adrenergic receptor with accelerated molecular dynamics.

(2013) Biochemistry 52

PubMed: 23879802 | PubMedCentral: PMC3763781 | DOI: 10.1021/bi400499n

The available crystal structures of the β 2 AR with PDB codes 2RH1, 3D4S, 3NY8, 3NY9, 3NYA, 3PDS, 3P0G, and 3SN6 were used to monitor whether the simulated conformational space samples the pro... ection of available experimental structures.

Publication Year: 2013

Molecular interactions between fenoterol stereoisomers and derivatives and the ??-adrenergic receptor binding site studied by docking and molecular dynamics simulations.

(2013) J Mol Model 19

PubMed: 24043542 | PubMedCentral: PMC3825559 | DOI: 10.1007/s00894-013-1981-y

The structure of β 2 -AR co-crystalized with Nb80 nanobody was selected because no significant changes in the binding pocket were observed in comparison with the most recent one structure (PDB... ID: 3SN6).

Publication Year: 2013

Effect of intracellular loop 3 on intrinsic dynamics of human ?2-adrenergic receptor.

(2013) BMC Struct Biol 13

PubMed: 24206668 | PubMedCentral: PMC3834532 | DOI: 10.1186/1472-6807-13-29

The conformational change of ICL3 gives rise to a “very inactive” state of the receptor Figure  4 A shows the RMSD profiles of the sixth transmembrane helix (TM6) from its inac... ive (PDB:2RH1) and its active states (PDB:3SN6) in reported crystal structures.

Both RMSD values are calculated with reference to the active state (PDB:3SN6).

(A) active crystal structure (PDB id: 3SN6), snapshots taken at (B) 52.8 ns (cluster #3), (C) 524 ns (cluster #1) and (D) 806 ns (cluster #2).

However, in the known crystal structure of the active receptor (PDB:3SN6), the distance between alpha-carbons is around 16 Å as a result of a significant outward shift in the intracellular part of TM6.

Finally, the nanobody-stabilized active state of β 2 AR in complex with G-protein, has been solved by Rasmussen and his coworkers (PDB:3SN6) [ 10 , 11 ].

Figure  9 b shows the cluster profile of the intracellular part of the receptor, which consists of residues interacting with the G-protein based on the active crystal structure (PDB:3SN6) [ 29 ].

In the active crystal structure (PDB:3SN6) taken as a reference and placed on top of the figure, G protein’s helical segment nicely fits the binding cavity.

Publication Year: 2013

Structural Aspects of GPCR-G Protein Coupling.

(2013) Toxicol Res 29

PubMed: 24386514 | PubMedCentral: PMC3877993 | DOI: 10.5487/TR.2013.29.3.149

Comparison of Ras-like domains of inactive-GDP-bound Gα subunit (Grey) (PDB:1GP2) and intermediate-receptor-bound nucleotide- free Gα subunit (Green) (PDB: 3SN6).

The crystal structure of β2AR-Gs protein complex (PDB: 3SN6).

X-ray crystal structures used in the Figures Structure PDB number State Reference Gtαβγ heterotrimer with GDP 1GOT Inactive 8 Gtα subunit with GTPγS 1TND Active 13 β2AR-Gs 3SN6 Receptor-coupled intermediate 18 Giαβγ heterotrimer with GDP 1GP2 Inactive 10 Similar to α5 helix, the strand of αN helix-β1 sheet region of Gα subunit may translate receptor-induced conformational changes to the nucleotide-binding pocket.

Publication Year: 2013

Energetic analysis of the rhodopsin-G-protein complex links the ?5 helix to GDP release.

(2014) Nat Struct Mol Biol 21

PubMed: 24292645 | PubMedCentral: PMC3947367 | DOI: 10.1038/nsmb.2705

The receptor-bound model of R*–Gα i βγ is based on the crystal structure of the β 2 AR–G s complex (PDB 3SN6 7 ; alignment shown in Supplemental Figure ... ).

(a) Crystal structure of β 2 AR–Gs complex (PDB 3SN6 11 ).

Receptor-bound Gα i βγ model consistent with experimental data The crystal structure of the β 2 AR–G s complex (PDB 3SN6 7 ) was used as the template for constructing a comparative model for the rhodopsin bound state of Gα i βγ.

The sequence of metarhodopsin, bovine Gβ 1 and Gγ 1 , and Gα i were threaded on the 3SN6 7 crystal structure.

The receptor sequence was aligned using structure-structure alignment of 3SN6 7 with the structure of metarhodopsin 3PQR 34 .

Publication Year: 2014

Current progress in Structure-Based Rational Drug Design marks a new mindset in drug discovery.

(2013) Comput Struct Biotechnol J 5

PubMed: 24688704 | PubMedCentral: PMC3962124 | DOI: 10.5936/csbj.201302011

Illustration of GPCR plasticity is given with: ( b ) zoomed side view of X-ray structure of 2AR in complex with the antagonist (S)-Carazolol (2AR inactive state, PDB entry 2rh1); ( c ) X-ray structure... of 2AR in complex with a high affinity agonist (BI-167107) (2AR-Gs protein active complex, PDB entry 3sn6); ( d ) overlay of the side views ( b ) and ( c ) showing residues in close contact (< 5 Å) with the antagonist (cyanide blue) and the agonist (brown).

Publication Year: 2013

MP:PD--a data base of internal packing densities, internal packing defects and internal waters of helical membrane proteins.

(2014) Nucleic Acids Res 42

PubMed: 24194596 | PubMedCentral: PMC3965053 | DOI: 10.1093/nar/gkt1062

Otherwise, results include all entries with a match in any of the query phrases, so that the query can be used to search for multiple PDB IDs ‘3dqb 3sn6 1c3w’.

Publication Year: 2014

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

(2014) Chem Rev 114

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

(D) Crystal structure of an agonist bound β 2 AR-T4L fusion (T4L not shown) in complex with its cognate heterotrimeric G protein, Gs αβγ , and a stabilizing nanobody (n... t shown) reveals the mode of Gs binding to monomeric β 2 AR (PDB ID: 3SN6).

Publication Year: 2014

Dynamic behavior of the active and inactive states of the adenosine A(2A) receptor.

(2014) J Phys Chem B 118

PubMed: 24579769 | PubMedCentral: PMC3983344 | DOI: 10.1021/jp411618h

We also calculated the root-mean-square deviations (RMSDs) in coordinates of the corresponding residues in the fully active G-protein-coupled state of the β 2 -adrenergic receptor (pdb ID: 3SN... ) and the inactive state of the β 2 -adrenergic receptor (pdb ID: 2RH1).

Publication Year: 2014

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].

Publication Year: 2013

Alpha-bulges in G protein-coupled receptors.

(2014) Int J Mol Sci 15

PubMed: 24806342 | PubMedCentral: PMC4057707 | DOI: 10.3390/ijms15057841

The GPCR mobility issue has been reduced by adding strong binding ligands (e.g., PDBid = 3eml [ 14 ]), nanobodies (e.g., PDBid = 3p0g [ 15 ]), G proteins (e.g., PDBid = 3sn6 [ 11 ]), and by mutating t... e residues that are most involved in the activation process—for example, the β1 adrenoceptor (PDBid = 2vt4 [ 16 ]) or the adenosine A2A receptor (PDBid = 3rey [ 17 ]).

β-2 adrenoceptor in the active state (PDBid = 3sn6 [ 11 ]; red) superposed on the inactive state (PDBid = 3ny8 [ 12 ]; cyan).

Red: PDBid = 3sn6 [ 11 ]; and ( D ) Rhodopsin.

At some locations, these three groups show a systematic behavior that is illustrated in Panels B – E , which show a blow-up of three representative structures (light blue: 3ny8 bound to an inverse agonist; orange: 3nya bound to an antagonist; red: 3sn6 bound to an agonist and a trimeric G protein on the cytosolic side); ( B ) In helix II we observe a systematic motion of the area around the a-bulge towards helix III in the activated receptor; ( C ) In helix V, we observe a systematic motion of the area around the α-bulge towards helix III and helix IV in the activated receptor; ( D ) Relative to the inverse agonist bound structure (cyan) and the antagonist bound structure (orange), the cytosolic side of helix V moves outward when an agonist and a G-protein are bound as does helix VI; and ( E ) The loop between helix VII and helix VIII behaves systematically (albeit in a hard to describe way) as function of the type of ligand bound.

Publication Year: 2014

Kir3 channel signaling complexes: focus on opioid receptor signaling.

(2014) Front Cell Neurosci 8

PubMed: 25071446 | PubMedCentral: PMC4085882 | DOI: 10.3389/fncel.2014.00186

The complex was constructed from diagrams based on the published crystal structures of the Kir3.2 tetramer in association with corresponding Gβ1γ2 subunits (PDB: 4KFM) (A) and that of ... he nucleotide-free Gαsβ1γ2 trimer in association with the active β 2 adrenergic receptor (PDB: 3sn6) where the latter was replaced by the topography corresponding to the DOR crystal (PDB: 4EJ4).

Publication Year: 2014

PubMed ID is not available.

Published in 2014

PubMedCentral: PMC4131901

32 After the latter (residues 30–59, 66–96, 103–136, 147–171, 198–225, 266–298, and 306–328 in PDB entry 3SN6( 32 )) had been superposed onto th... TM Cα atoms of the δ-OR inactive structure (residues 46–75, 82–112, 118–151, 162–186, 212–239, 254–286, and 298–320 in PDB entry 4N6H( 24 )), the TM Cα atoms of δ-OR with the sodium ion at the allosteric, crystallographic site were biased toward the coordinates of 3SN6 using the mean-square deviation (MSD) between these TM Cα atoms as a reaction coordinate and an increasing elastic constant (1000 kJ/Å 2 for 70 ns, 2000 kJ/Å 2 for 30 ns, and 10000 kJ/Å 2 for 15 ns).

Because no active OR crystal structure is available yet, all-atom, adiabatic biased molecular dynamics (ABMD) simulations 31 (see details in Molecular Dynamics Simulations ) were employed to sample the conformational transition of the δ-OR TM bundle from its inactive crystal structure in the presence of a docked selective δ-OR agonist, i.e., (+)-4-{(α R )-α-[(2 S ,5 R )-4-allyl-2,5-dimethyl-1-piperazinyl]-3-methoxybenzyl}- N , N -diethylbenzamide [SNC-80 (see the docking details in the following section)], instead of naltrindole, to the corresponding atomic coordinates of the TM region of the active β2-adrenergic receptor (B2AR) crystal structure in complex with the G-protein (PDB entry 3SN6( 32 )).

Publication Year: 2014

Visualization of arrestin recruitment by a G-protein-coupled receptor.

(2014) Nature 512

PubMed: 25043026 | PubMedCentral: PMC4134437 | DOI: 10.1038/nature13430

Figure 4 Structural model of the β 2 V 2 R-βarr1-Fab30 complex a. Views of the T4L-β 2 V 2 R-βarr1-Fab30 complex 3D reconstruction with modeled T4L-β 2 AR (gree... -orange, pdb: 3SN6), βarr1 (blue, pdb: 4JQI), and Fab30 (purple, pdb: 4JQI) crystal structures.

Molecular modeling For modeling the T4L-β 2 V 2 R-βarr1-Fab30 complex we used the crystal structure of T4L-β 2 AR receptor from the T4L-β 2 AR-Gαs complex (3SN6) 6 and the crystal structure of V 2 Rpp-βarr1-Fab30 (4JQI).

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

Search for ?2 adrenergic receptor ligands by virtual screening via grid computing and investigation of binding modes by docking and molecular dynamics simulations.

(2014) PLoS One 9

PubMed: 25229694 | PubMedCentral: PMC4168136 | DOI: 10.1371/journal.pone.0107837

Materials and Methods Protein and Ligand Preparation To screen the ligands of β 2 AR, the active conformation of β 2 AR was extracted from PDB database (PDB code: 3SN6 [55] ).

Molecular Dynamics Simulations The crystal structure of β 2 AR was obtained from PDB database (PDB code: 3SN6 [55] ).

Publication Year: 2014

PubMed ID is not available.

Published in 2014

PubMedCentral: PMC4170816

Last but not least, we compared the structure of our CB2 model after MD simulation with agonist and the crystal structure of β2AR bound with Gα subunit (PDBID:3SN6), 77 as shown in Fig... re S13c .

We think the only plausible method is to construct a homology model based on the beta-2 active structure (PDBID:3SN6) 77 and relaxing it a little bit before using for docking and other studies.

Publication Year: 2014

A dynamic view of molecular switch behavior at serotonin receptors: implications for functional selectivity.

(2014) PLoS One 9

PubMed: 25313636 | PubMedCentral: PMC4196896 | DOI: 10.1371/journal.pone.0109312

Specifically, in the 5-HT 1B R, F 6.44 adopts a conformation facing helix 5 ( Figure 1B (left) active F 6.44 state), which is close to the one found in the active state of the β2-adrenergic cr... stal structure in complex with a G s protein (PDB ID: 3SN6 [20] ).

Publication Year: 2014

Graph analysis of ?2 adrenergic receptor structures: a "social network" of GPCR residues.

(2013) In Silico Pharmacol 1

PubMed: 25505660 | PubMedCentral: PMC4230308 | DOI: 10.1186/2193-9616-1-16

Although most of the structures have been solved in an inactive state, two of the crystal structures of the β 2 AR have been solved in a fully activated state, one in complex with a G protein-... eterotrimer (PDB ID: 3SN6) and one in complex with a nanobody that mimics the G protein (PDB ID: 3P0G) (Rasmussen et al.

Publication Year: 2013

Characterization of the Anopheles gambiae octopamine receptor and discovery of potential agonists and antagonists using a combined computational-experimental approach.

(2014) Malar J 13

PubMed: 25407998 | PubMedCentral: PMC4253978 | DOI: 10.1186/1475-2875-13-434

For the active conformation, a structure was obtained that was built based on the crystal structure of the β 2 -adrenergic receptor-G αs protein complex with high affinity agonist BI-1... 7107 bound [PDB:3SN6].

To obtain initial ligand poses used in grid generation, each of the conformations were first overlapped in PyMOL [ 39 ] with the top templates used by I-TASSER for their creation (2RH1 for the inactive conformation and 3SN6 for the active conformation) and the positions of the ligands found in each of the templates were first saved as a PDB file, then added using Schrodinger Suite 2011’s Maestro to their respective AgOAR45B conformation (2RH1 partial inverse agonist CAU was used for the inactive conformation and 3SN6 agonist 30G was used for the active conformation) to denote the active site of the protein.

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

sp Rhodopsin, nonvisual 9.9 MAG 1xio (2.00), 4tl3 (2.30) Channelrhodopsin (1) Chlamydomonas reinhardtii Rhodopsin, nonvisual 9.9 MAG 3ug9 (2.30) Acetabularia rhodopsin II (1) Acetabularia acetabulum R... odopsin, nonvisual 9.9 MAG + cholesterol 3am6 (3.20) Proteorhodopsin (1) Exiguobacterium sibiricum Rhodopsin, nonvisual 9.9 MAG 4hyj (2.30) Light-harvesting complex II (1) Rhodoblastus acidophilus Light-harvesting complex II 9.9 MAG 2fkw (2.45) Cytochrome caa 3 oxidase (1) Thermus thermophilus Cytochrome oxidase 7.7 MAG 2yev (2.36) Prostaglandin E2 synthase 1 (1) Homo sapiens Enzyme 8.8 MAG + DOPC 4bpm (2.08) Na + /Ca + exchanger (1) Methanocaldococcus jannaschii Exchanger 9.9 MAG 3v5u (1.90) Ca 2+ /H + exchanger (VCX1) (1) Saccharomyces cerevisiae Exchanger 9.9 MAG 4k1c (2.30) H + /Ca 2+ exchanger (1) Archaeoglobus fulgidus Exchanger 9.9 MAG 4kpp (2.30) Na + symporter MhsT (1) Bacillus halodurans Symporter 7.8 MAG 4us4 (2.60) Claudin (1) Mus musculus Junction protein 9.9 MAG 4p79 (2.40) GPCRG protein complex (1) Bos taurus , Rattus norvegicus , Homo sapiens G protein-coupled receptorG protein complex 7.7 MAG + cholesterol 3sn6 (3.20) -Barrel AlgE (3) Pseudomonas aeruginosa Transporter 7.8 MAG 4afk (1.90), 4azl (2.80), 4b61 (2.40) OmpF (3) Escherichia coli Channel 9.9 MAG 3poq (1.90), 3pou (2.80), 3pox (2.00) Vitamin B 12 transporter ButB (1) Escherichia coli Transporter 9.9 MAG 2guf (1.95) Adhesin/invasin OpcA (1) Neisseria meningitidis Adhesin 9.9 MAG 2vdf (1.95) Intimin (1) Escherichia coli Adhesin 9.9 MAG 4e1s (1.86) Invasin (1) Yersinia pseudotuberculosis Adhesin 9.9 MAG 4e1t (2.26) -Helix Gramicidin D (4) Brevibacillus brevis Channel 7.7 MAG; 8.8 MAG; 11.7 MAG; 9.9 MAG 2y5m (1.08), 2y6n (1.26), 3zq8 (1.70), 2xdc (1.70)

Publication Year: 2015