Three-dimensional structure of the type 1 inositol 1,4,5-trisphosphate receptor at 24 A resolution

Jiang, Qiu Xing; Thrower, Edwin C.; Chester, David W.; Ehrlich, Barbara E.; Sigworth, Fred J.

doi:10.1093/emboj/cdf380

Cited by 109 publications

(88 citation statements)

References 52 publications

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“…This potential problem is accentuated if the signal-to-noise ratio is low, as frequently occurs in cryo-EM images, and no prior knowledge of the 3D structure exists. Our IP 3 R structure shows a level of detail consistent with the 3-nm resolution estimated, whereas less detail is observed by Jiang et al (33). Furthermore, our map has allowed us to assign specific functional domains, which are consistent with secondary structure predictions and biochemical studies, and show similarities to related cation channels (see below).…”

Section: Comparison With Previous Structural Data On the Ip3rsupporting

confidence: 88%

“…During the preparation of this manuscript, another 3D map of the type 1 IP 3 R was reported based on cryo-electron microscopy (cryo-EM) and single-particle image analysis at a reported resolution of 2.4 nm (33). The overall size (Ϸ18 ϫ 18 ϫ 17 nm) and shape of this 3D structure are broadly consistent with our results but there is little detailed agreement between the two studies.…”

Section: Comparison With Previous Structural Data On the Ip3rsupporting

confidence: 74%

See 1 more Smart Citation

Domain organization of the type 1 inositol 1,4,5-trisphosphate receptor as revealed by single-particle analysis

Fonseca¹,

Morris²,

Nerou³

et al. 2003

Proc. Natl. Acad. Sci. U.S.A.

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Materials and Methods Purification of IP3R.A membrane fraction was prepared from rat cerebella (17), resuspended (50 mg͞ml in 50 mM Tris͞1 mM EDTA, pH 8.3), and solubilized by the addition of 1% Triton X-100. After centrifugation (100,000 ϫ g for 60 min), the supernatant, supplemented with 250 mM NaCl, was loaded onto an Econopac heparin column (1 ml, Bio-Rad), washed with 25 ml of medium A (50 mM Tris͞250 mM NaCl͞10% glycerol, pH 8.3), supplemented with 1 mM EDTA, 1% Surfact-Amps X-100 (Pierce), and then with medium A supplemented with 0.1% Surfact-Amps X-100 (50 ml). IP 3 R was eluted from the heparin column directly onto a 2-ml Con A-agarose column (Sigma) by using medium A supplemented with 0.1% Surfact-Amps X-100 and 50 M decavanadate (18). After washing with 150 ml of medium B (50 mM Tris͞100 mM NaCl͞10% glycerol͞0.1% Surfact-Amps X-100, pH 8.3), IP 3 R was eluted by overnight incubation with 4 ml of medium B containing 800 mM methyl mannopyranoside (17). To assess the quaternary structure of the purified receptor, 0.2-ml fractions of the final eluate were loaded onto linear 10-30% sucrose gradients (10 ml) in 50 mM Tris͞1 mM EDTA͞0.1% Surfact-Amps X-100, pH 8.3, and centrifuged (134,000 ϫ g for 60 min). Gradients were calibrated by using a high-molecular-weight gel filtration standards kit (Amersham Biosciences). Size-exclusion HPLC was preformed by using a Zorbax GF-450 column (Jones Chromatography, Lakewood, CO) coupled to a Kontron system (Kontron Instruments, Watford, U.K.). All media included the following mixture of protease inhibitors: 150 nM aprotinin, 1 M pepstatin, 20 g͞ml soybean trypsin inhibitor, 1 mM benzamidine, 250 M PMSF, 250 M captopril, and 1 M bestatin.

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Section: Comparison With Previous Structural Data On the Ip3rsupporting

confidence: 88%

Section: Comparison With Previous Structural Data On the Ip3rsupporting

confidence: 74%

Domain organization of the type 1 inositol 1,4,5-trisphosphate receptor as revealed by single-particle analysis

Fonseca¹,

Morris²,

Nerou³

et al. 2003

Proc. Natl. Acad. Sci. U.S.A.

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“…Functional IP 3 Rs are tetrameric, assembled either from identical subunits or from mixtures of the three subtypes and their many splice variants Foskett et al 2007). Several structures of the entire IP 3 R1 have been published, each derived from single particle analysis of images from electron microscopy (Hamada and Mikoshiba 2002;Jiang et al 2002a;da Fonseca et al 2003;Hamada et al 2003;Serysheva et al 2003;Sato et al 2004). These studies confirm the tetrameric state of IP 3 R, but variability between the structures and their relatively low resolution ( 30 Å ) have, so far, limited any realistic interpretation of the structural basis of IP 3 R activation (Fig.…”

Section: Structural Determinants Of Ip 3 R Activationmentioning

confidence: 99%

IP3 Receptors: Toward Understanding Their Activation

Taylor¹,

Tovey²

2010

Cold Spring Harbor Perspectives in Biology

264

190

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Inositol 1,4,5-trisphosphate receptors (IP 3 R) and their relatives, ryanodine receptors, are the channels that most often mediate Ca 2þ release from intracellular stores. Their regulation by Ca 2þ allows them also to propagate cytosolic Ca 2þ signals regeneratively. This brief review addresses the structural basis of IP 3 R activation by IP 3 and Ca 2þ . IP 3 initiates IP 3 R activation by promoting Ca 2þ binding to a stimulatory Ca 2þ -binding site, the identity of which is unresolved. We suggest that interactions of critical phosphate groups in IP 3 with opposite sides of the clam-like IP 3 -binding core cause it to close and propagate a conformational change toward the pore via the adjacent N-terminal suppressor domain. The pore, assembled from the last pair of transmembrane domains and the intervening pore loop from each of the four IP 3 R subunits, forms a structure in which a luminal selectivity filter and a gate at the cytosolic end of the pore control cation fluxes through the IP 3 R.

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“…Since this reconstruction was also performed using EMAN (without EMANЈs CTF correction) with some initial analysis in IMAGIC, it seems unlikely that this is a software problem but probably represents a fundamental difference in the raw data. The receptor purification strategy used in this study uses single-step chromatography over an immunoaffinity matrix with Triton X-100 while Jiang et al (7) used CHAPS. Additionally da Fonseca (8) used essentially the same strategy as Jiang et al (7) with the only major difference being the use of Triton X-100 and Surfact-Amps X-100.…”

Section: Biochemical Purity and Functional Integrity Of The Purifiedmentioning

confidence: 99%

“…It is possible that the apparent discrepancies between the structures are a consequence of the different detergents. Additionally our protein isolation was performed at pH 7.4, whereas the other preparations (7,8) were made at alkaline pH. These pH changes may induce additional conformational transitions of the channel.…”

Section: Biochemical Purity and Functional Integrity Of The Purifiedmentioning

confidence: 99%

Structure of the Type 1 Inositol 1,4,5-Trisphosphate Receptor Revealed by Electron Cryomicroscopy

Serysheva

Bare

Ludtke

et al. 2003

Journal of Biological Chemistry

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The three-dimensional structure of the type 1 inositol 1,4,5-trisphosphate receptor (InsP 3 R1) has been determined by electron cryomicroscopy and single-particle reconstruction. The receptor was immunoaffinity-purified and formed functional InsP 3 -and heparin-sensitive channels with a unitary conductance similar to native InsP 3 Rs. The channel structure exhibits the expected 4-fold symmetry and comprises two morphologically distinct regions: a large pinwheel and a smaller square. The pinwheel region has four radial curved spokes interconnected by a central core. The InsP 3 -binding core domain has been localized within each spoke of the pinwheel region by fitting its x-ray structure into our reconstruction. A structural mapping of the amino acid sequences to several functional domains is deduced within the structure of the InsP 3 R1 tetramer.The inositol 1,4,5-trisphosphate receptor (InsP 3 R) 1 is a ligand-gated ion channel that modulates Ca 2ϩ release from intracellular stores. The InsP 3 R is widely distributed in metazoans and plays a key role in diverse physiological functions. In mammals, three different InsP 3 R isoforms are expressed; each is encoded by a distinct gene. The three isoforms are homologous and share ϳ70% amino acid identity. Functional channels are composed of four subunits that tetramerize via determinants localized within the transmembrane regions and the cytosolic C terminus (1-3). Individual cell types often express more than one isoform, which may be present as homo-or heterotetrameric populations. The most characterized type 1 InsP 3 R (InsP 3 R1) forms largely homotetramers in cerebellum with M r of 313,000 (2749 residues) for the monomer. Based on biochemical, molecular biological, and electrophysiological studies, each monomer subunit of the InsP 3 R1 is organized into three principal functional regions: an N-terminal InsP 3 -binding region (residues 226 -578), a central (ϳ1,700-residue) modulatory/coupling region, and a channel-forming region near the C terminus. The channel region contains six transmembrane segments interspersed within residues 2276 -2590 that are critical for membrane targeting, oligomerization, and formation of the ion permeation pathway (1-4). Thus, both ends, the large N-terminal region (residues 1-2275) and the C-terminal region (residues 2590 -2749), are exposed to the cytoplasm.Electron micrographs of the negatively stained detergentsolubilized InsP 3 R1 and freeze-fracture deep etching electron microscopy of endoplasmic reticulum have been used to characterize the morphology of the InsP 3 R1 channel (5, 6). But the three-dimensional shape and dimensions of the channel particles were not determined. Two three-dimensional maps of the InsP 3 R1 were reported recently based on single-particle reconstruction from specimens prepared by ice embedding (7) and negative staining (8). There is a poor agreement between these two maps with respect to the overall appearance and dimensions of the channel structure. In this study, we present a 30-Å three-dimensional s...

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Three-dimensional structure of the type 1 inositol 1,4,5-trisphosphate receptor at 24 A resolution

Cited by 109 publications

References 52 publications

Domain organization of the type 1 inositol 1,4,5-trisphosphate receptor as revealed by single-particle analysis

Domain organization of the type 1 inositol 1,4,5-trisphosphate receptor as revealed by single-particle analysis

IP3 Receptors: Toward Understanding Their Activation

Structure of the Type 1 Inositol 1,4,5-Trisphosphate Receptor Revealed by Electron Cryomicroscopy

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