Dimer ribbons in the three-dimensional structure of sarcoplasmic reticulum

Castellani, Loriana; Hardwicke, Peter M.D.; Vibert, Peter

doi:10.1016/0022-2836(85)90073-7

Cited by 81 publications

(51 citation statements)

References 36 publications

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“…1 and Ref. 25), consistent with the size of the Ca-ATPase (25,35,36). The second scallop muscle fraction (B 1 ), which was used later in the studies, is enriched in SL (29).…”

Section: Resultssupporting

confidence: 61%

A Ca2+-dependent Tryptic Cleavage Site and a Protein Kinase A Phosphorylation Site Are Present in the Ca2+ Regulatory Domain of Scallop Muscle Na+-Ca2+ Exchanger

Chen¹,

Zhang

Tawiah-Boateng

et al. 2000

Journal of Biological Chemistry

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Digestion of scallop muscle membrane fractions with trypsin led to release of soluble polypeptides derived from the large cytoplasmic domain of a Na ؉ -Ca 2؉ exchanger. In the presence of 1 mM Ca 2؉ , the major product was a peptide of ϳ37 kDa, with an N terminus corresponding to residue 401 of the NCX1 exchanger. In the presence of 10 mM EGTA, ϳ16-and ϳ19-kDa peptides were the major products. Polyclonal rabbit IgG raised against the 37-kDa peptide also bound to the 16-and 19-kDa soluble tryptic peptides and to a 105-110-kDa polypeptide in the undigested membrane preparation. The 16-kDa fragment corresponded to the N-terminal part of the 37-kDa peptide. The Na ϩ -Ca 2ϩ exchangers of the plasma membrane catalyze a secondary active transport process dependent on the Na ϩ electrochemical gradient generated by the Na ϩ ,K ϩ -ATPase and play a major role in cellular Ca 2ϩ homeostasis in many tissues (1). Three Na ϩ -Ca 2ϩ exchanger proteins (NCX1, NCX2, and NCX3) have been described in vertebrates (2-5). The molecular biology of the Na ϩ -Ca 2ϩ exchanger (Calx) from Drosophila has been described (6, 7), and an exchanger from squid has been reported (8). An electroneutral Na ϩ -Ca 2ϩ antiporter has also been found in mitochondria, where it may be involved in modulating matrix Ca 2ϩ in response to changes in cytoplasmic Ca 2ϩ concentration (9, 10). The protein moieties of the plasma membrane Na ϩ -Ca 2ϩ exchanger proteins are close in overall size (ϳ103-106 kDa) (4, 11) to the SERCA 1 -type Ca 2ϩ -ATPase pumps, which have a molecular mass of ϳ110 kDa (12). In the case of NCX1, a signal sequence of 32 amino acid residues at the N terminus of the protein is removed post-translationally (13-15). From the N terminus, structure prediction algorithms suggest that five transmembrane segments lead to a large cytoplasmic, followed by four C-terminal transmembrane helices (14 -16 [17][18][19][20]. This binds Ca 2ϩ cooperatively and provides regulation of the exchanger through the I 2 mechanism, in which increased levels of cytoplasmic Ca 2ϩ activate the enzyme (19). The regulatory Ca 2ϩ binding region involves the ␤-1 repeat and extends through the variable region between the two ␤ repeats to the beginning of ␤-2 (18). Two acidic triads, one at the C terminus of ␤-1 (Asp 478(446) -Asp-Asp) and one in the variable region, (Asp 530(498) -Asp-Asp), just N-terminal to ␤-2, are important components of this high affinity Ca 2ϩ binding site (18). The isolated cardiac exchanger shows three bands on silverstained SDS gels: a glycosylated 120-kDa species corresponding to the native exchanger, a glycosylated 160-kDa polypeptide representing oxidized exchanger, and an unglycosylated polypeptide of 70 kDa, which arises by proteolysis of the 120-kDa protein at the Asp 289(257) -Gly or Asp 303(270) -Gly bonds in the large cytoplasmic domain (11,(21)(22)(23). Digestion of the exchanger with chymotrypsin leads to a loss of regulatory function, probably through proteolysis localized in the cytoplasmic f loop (4).The study of the protein chemistr...

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“…1 and Ref. 25), consistent with the size of the Ca-ATPase (25,35,36). The second scallop muscle fraction (B 1 ), which was used later in the studies, is enriched in SL (29).…”

Section: Resultssupporting

confidence: 61%

A Ca2+-dependent Tryptic Cleavage Site and a Protein Kinase A Phosphorylation Site Are Present in the Ca2+ Regulatory Domain of Scallop Muscle Na+-Ca2+ Exchanger

Chen¹,

Zhang

Tawiah-Boateng

et al. 2000

Journal of Biological Chemistry

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“…The Ca-ATPase from the cross-striated part of the adductor muscle of the sea scallop has been the subject of a number of biochemical and structural studies (11,12). Provided the E 2 form of the scallop Ca-ATPase is stabilized against loss of activity, it adopts a dimeric type of quaternary organization (13) that is absent in the E 1 form of the enzyme (14), and in both the E 1 ϳP and E 2 -P states the enzyme is arranged in parallel instead of antiparallel helical strands in the tubular vesicles with only a single asymmetric subunit in each unit cell (p1 lattice) (15).…”

Section: Transport Camentioning

confidence: 99%

“…Recent studies have found that the E 1 (Ca 2ϩ ) 2 form of rabbit SERCa1a shows clear structural differences to the enzyme in its vanadate-stabilized Ca 2ϩ -free (E 2 ) state (7-10). In the E 1 form, the Actuator (A) domain is isolated from the nucleotide (N) and phosphorylation (P) domains, whereas in the E 2 form all three domains are clustered together.The Ca-ATPase from the cross-striated part of the adductor muscle of the sea scallop has been the subject of a number of biochemical and structural studies (11,12). Provided the E 2 form of the scallop Ca-ATPase is stabilized against loss of activity, it adopts a dimeric type of quaternary organization (13) that is absent in the E 1 form of the enzyme (14), and in both the E 1 ϳP and E 2 -P states the enzyme is arranged in parallel instead of antiparallel helical strands in the tubular vesicles with only a single asymmetric subunit in each unit cell (p1 lattice) (15).…”

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confidence: 99%

Effect of Orthophosphate, Nucleotide Analogues, ADP, and Phosphorylation on the Cytoplasmic Domains of Ca2+-ATPase from Scallop Sarcoplasmic Reticulum

Ryan

Stokes

Chen

et al. 2004

Journal of Biological Chemistry

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The effects of orthophosphate, nucleotide analogues, ADP, and covalent phosphorylation on the tryptic fragmentation patterns of the E 1 and E 2 forms of scallop Ca-ATPase were examined. Sites preferentially cleaved by trypsin in the E 1 form of the Ca-ATPase were detected in the nucleotide (N) and phosphorylation (P) domains, as well as the actuator (A) domain. These sites were occluded in the E 2 (Ca 2؉ -free) form of the enzyme, consistent with mutual protection of the A, N, and P domains through their association into a clustered structure. Similar protection of cytoplasmic Ca 2؉ -dependent tryptic cleavage sites was observed when the catalytic binding site for substrate on the E 1 form of scallop Ca-ATPase was occupied by P i , AMP-PNP, AMP-PCP, or ADP despite the presence of saturating levels of Ca 2؉ . These results suggest that occupation of the catalytic site on E 1 can induce condensation of the cytoplasmic domains to yield a unique structural intermediate that may be related to the form of the enzyme in which the active site is prepared for phosphoryl transfer. The effect of P i on the E 2 form of the scallop Ca-ATPase was also investigated, when it was found that formation of E 2 -P led to extreme resistance toward secondary cleavage by trypsin and stabilization of enzymatic activity for long periods of time.The sarco(endo)plasmic reticulum ATPases (SERCAs) 1 transport Ca 2ϩ against an electrochemical gradient from the cytoplasm into the intracellular membranous compartment of the sarcoplasmic or endoplasmic reticulum and play a major role in Ca 2ϩ homeostasis in both muscle and non-muscle cells (1, 2). In the course of transporting Ca 2ϩ , these enzymes pass through a number of relatively well defined intermediate biochemical states that can be isolated and studied. These include forms in which the ␤-carboxyl group of a specific aspartyl residue (Asp 351 in the case of rabbit SERCA1a) is present as an acylphosphate mixed anhydride. Much of the experimental data has been interpreted in terms of the enzyme being able to exist in two basic forms: the E 1 state, in which the enzyme possesses high affinity binding sites for Ca 2ϩ and can be phosphorylated by ATP but not by P i , and the E 2 state, which possesses low affinity Ca 2ϩ sites and can be phosphorylated by P i but not by ATP (3).Comparison of the tryptic digestion patterns of rabbit SERCA1a in its Ca 2ϩ -bound and -free forms has provided some of the strongest direct evidence supporting such a model where the enzyme can exist in two fundamentally different conformational states (4 -6). Recent studies have found that the E 1 (Ca 2ϩ ) 2 form of rabbit SERCa1a shows clear structural differences to the enzyme in its vanadate-stabilized Ca 2ϩ -free (E 2 ) state (7-10). In the E 1 form, the Actuator (A) domain is isolated from the nucleotide (N) and phosphorylation (P) domains, whereas in the E 2 form all three domains are clustered together.The Ca-ATPase from the cross-striated part of the adductor muscle of the sea scallop has been the subject of a ...

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“…Scallop SR Ca 2+ -ATPase was isolated and crystallized as described by Castellani et al (1985). The resultant crystals were plunge-frozen in liquid ethane and imaged at 50,000x magnification on a Philips CM200 field-emission electron microscope (FEI Corp., Eindhoven, Netherlands) under low-dose conditions (~15 electrons/Å 2 ) with an Oxford CT3500 (Gatan Corp., Pleasanton CA) cryo-holder.…”

Section: Methodsmentioning

confidence: 99%

Application of the iterative helical real-space reconstruction method to large membranous tubular crystals of P-type ATPases

Pomfret

Rice

Stokes

2007

Journal of Structural Biology

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Since the development of three-dimensional helical reconstruction methods in the 1960's, advances in Fourier-Bessel methods have facilitated structure determination to near-atomic resolution. A recently developed iterative helical real-space reconstruction (IHRSR) method provides an alternative that uses single-particle analysis in conjunction with the imposition of helical symmetry. In this work, we have adapted the IHRSR algorithm to work with frozenhydrated tubular crystals of P-type ATPases. In particular, we have implemented layer-line filtering to improve the signal-to-noise ratio, Wiener-filtering to compensate for the contrast transfer function, solvent flattening to improve reference reconstructions, out-of-plane tilt compensation to deal with flexibility in three dimensions, systematic calculation of Fourier shell correlations to track the progress of the refinement, and tools to control parameters as the refinement progresses. We have tested this procedure on datasets from Na + /K + -ATPase, rabbit skeletal Ca 2+ -ATPase and scallop Ca 2+ -ATPase in order to evaluate the potential for subnanometer resolution as well as the robustness in the presence of disorder. We found that FourierBessel methods perform better for well-ordered samples of skeletal Ca 2+ -ATPase and Na + /K + -ATPase, although improvements to IHRSR are discussed that should reduce this disparity. On the other hand, IHRSR was very effective for scallop Ca 2+ -ATPase, which was too disordered to analyze by Fourier-Bessel methods.

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Dimer ribbons in the three-dimensional structure of sarcoplasmic reticulum

Cited by 81 publications

References 36 publications

A Ca2+-dependent Tryptic Cleavage Site and a Protein Kinase A Phosphorylation Site Are Present in the Ca2+ Regulatory Domain of Scallop Muscle Na+-Ca2+ Exchanger

A Ca2+-dependent Tryptic Cleavage Site and a Protein Kinase A Phosphorylation Site Are Present in the Ca2+ Regulatory Domain of Scallop Muscle Na+-Ca2+ Exchanger

Effect of Orthophosphate, Nucleotide Analogues, ADP, and Phosphorylation on the Cytoplasmic Domains of Ca2+-ATPase from Scallop Sarcoplasmic Reticulum

Application of the iterative helical real-space reconstruction method to large membranous tubular crystals of P-type ATPases

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