The beryllium fluoride form of the Na+,K+-ATPase and the intermediates of the functional cycle

The Na+,K+-ATPase generates electrochemical gradients of Na+ and K+ across the plasma membrane. Here, we describe a 4.0 Å resolution crystal structure of the pig kidney Na+,K+-ATPase stabilized by beryllium fluoride (denoted E2-BeFx). The structure shows high resemblance to the E2P phosphoenzyme obtained by phosphorylation from inorganic phosphate (Pi) and stabilised by cardiotonic steroids, and reveals a Mg2+ bound near the ion binding site II. Anomalous Fourier analysis of the crystals soaked in Rb+ (K+ congener) followed by a low resolution rigid-body refinement (6.9-7.5 Å) revealed pre-occlusion transitions leading to activation of the desphosphorylation reaction. Mg2+ location indicates a site of an initial K+ recognition and acceptance upon binding to the outward-open E2P state after Na+ release. Despite the overall structural resemblance to the Pi-induced E2P phosphoform, BeFx inhibited enzyme is able to binds both ADP/ATP and ions, the features that relate E2-BeFx complex to an intermediate of the functional cycle of the Na+,K+-ATPase prior E2P.

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Crystal structures of Ca2+–calmodulin bound to NaV C-terminal regions suggest role for EF-hand domain in binding and inactivation

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1818618116 ◽

2019 ◽

Vol 116 (22) ◽

pp. 10763-10772 ◽

Cited By ~ 10

Author(s):

Bernd R. Gardill ◽

Ricardo E. Rivera-Acevedo ◽

Ching-Chieh Tung ◽

Filip Van Petegem

Keyword(s):

Crystal Structure ◽

Binding Sites ◽

Binding Mode ◽

Conformational Switch ◽

Channel Inactivation ◽

Dependent Inactivation ◽

Ef Hand ◽

Inherited Arrhythmia ◽

A Site

Voltage-gated sodium (NaV) and calcium channels (CaV) form targets for calmodulin (CaM), which affects channel inactivation properties. A major interaction site for CaM resides in the C-terminal (CT) region, consisting of an IQ domain downstream of an EF-hand domain. We present a crystal structure of fully Ca2+-occupied CaM, bound to the CT of NaV1.5. The structure shows that the C-terminal lobe binds to a site ∼90° rotated relative to a previous site reported for an apoCaM complex with the NaV1.5 CT and for ternary complexes containing fibroblast growth factor homologous factors (FHF). We show that the binding of FHFs forces the EF-hand domain in a conformation that does not allow binding of the Ca2+-occupied C-lobe of CaM. These observations highlight the central role of the EF-hand domain in modulating the binding mode of CaM. The binding sites for Ca2+-free and Ca2+-occupied CaM contain targets for mutations linked to long-QT syndrome, a type of inherited arrhythmia. The related NaV1.4 channel has been shown to undergo Ca2+-dependent inactivation (CDI) akin to CaVs. We present a crystal structure of Ca2+/CaM bound to the NaV1.4 IQ domain, which shows a binding mode that would clash with the EF-hand domain. We postulate the relative reorientation of the EF-hand domain and the IQ domain as a possible conformational switch that underlies CDI.

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Crystal Structure Refinements of Four Monazite Samples from Different Localities

Minerals ◽

10.3390/min10111028 ◽

2020 ◽

Vol 10 (11) ◽

pp. 1028 ◽

Cited By ~ 1

Author(s):

M. Mashrur Zaman ◽

Sytle M. Antao

Keyword(s):

Crystal Structure ◽

Electron Probe ◽

Unit Cell Volume ◽

Unit Cell ◽

X Ray Diffraction ◽

Unit Cell Parameters ◽

X Ray ◽

Cell Parameters ◽

Large Unit Cell ◽

A Site

This study investigates the crystal chemistry of monazite (APO4, where A = Lanthanides = Ln, as well as Y, Th, U, Ca, and Pb) based on four samples from different localities using single-crystal X-ray diffraction and electron-probe microanalysis. The crystal structure of all four samples are well refined, as indicated by their refinement statistics. Relatively large unit-cell parameters (a = 6.7640(5), b = 6.9850(4), c = 6.4500(3) Å, β = 103.584(2)°, and V = 296.22(3) Å3) are obtained for a detrital monazite-Ce from Cox’s Bazar, Bangladesh. Sm-rich monazite from Gunnison County, Colorado, USA, has smaller unit-cell parameters (a = 6.7010(4), b = 6.9080(4), c = 6.4300(4) Å, β = 103.817(3)°, and V = 289.04(3) Å3). The a, b, and c unit-cell parameters vary linearly with the unit-cell volume, V. The change in the a parameter is large (0.2 Å) and is related to the type of cations occupying the A site. The average <A-O> distances vary linearly with V, whereas the average <P-O> distances are nearly constant because the PO4 group is a rigid tetrahedron.

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β-Li0.37Na0.63Fe(MoO4)2

Acta Crystallographica Section E Structure Reports Online ◽

10.1107/s1600536814000646 ◽

2014 ◽

Vol 70 (2) ◽

pp. i9-i10 ◽

Cited By ~ 6

Author(s):

Amira Souilem ◽

Mohamed Faouzi Zid ◽

Ahmed Driss

Keyword(s):

Crystal Structure ◽

Solid State ◽

Solid State Reaction ◽

Title Compound ◽

General Position ◽

Site Occupancy ◽

The Other ◽

Main Structure ◽

Axis Direction ◽

A Site

The title compound, lithium/sodium iron(III) bis[orthomolybdate(VI)], was obtained by a solid-state reaction. The main structure units are an FeO6octahedron, a distorted MoO6octahedron and an MoO4tetrahedron sharing corners. The crystal structure is composed of infinite double MoFeO11chains along theb-axis direction linked by corner-sharing to MoO4tetrahedra so as to form Fe2Mo3O19ribbons. The cohesion between ribbonsviamixed Mo—O—Fe bridges leads to layers arranged parallel to thebcplane. Adjacent layers are linked by corners shared between MoO4tetrahedra of one layer and FeO6octahedra of the other layer. The Na+and Li+ions partially occupy the same general position, with a site-occupancy ratio of 0.631 (9):0.369 (1). A comparison is made withAFe(MoO4)2(A= Li, Na, K and Cs) structures.

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Multi-scale structural analysis of the A-site and oxygen deficient perovskite Sr11Mo4O23

Dalton Transactions ◽

10.1039/c7dt02087b ◽

2017 ◽

Vol 46 (37) ◽

pp. 12466-12473 ◽

Cited By ~ 3

Author(s):

Graham King ◽

Maxim Avdeev ◽

Ilyas Qasim ◽

Qingi Zhou ◽

Brendan J. Kennedy

Keyword(s):

Crystal Structure ◽

Structural Analysis ◽

Multi Scale ◽

Local Correlations ◽

A Site

The crystal structure of Sr11Mo4O23 and the local correlations between the disordered sites are examined.

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Crystal structure of the DENR-MCT-1 complex revealed zinc-binding site essential for heterodimer formation

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1809688116 ◽

2018 ◽

Vol 116 (2) ◽

pp. 528-533 ◽

Cited By ~ 6

Author(s):

Ivan B. Lomakin ◽

Sergey E. Dmitriev ◽

Thomas A. Steitz

Keyword(s):

Crystal Structure ◽

Binding Site ◽

Translation Initiation ◽

Zinc Ion ◽

Zinc Binding ◽

Ion Binding ◽

Binding Interface ◽

Zinc Binding Site ◽

Reading Frames ◽

Zinc Ion Binding

The density-regulated protein (DENR) and the malignant T cell-amplified sequence 1 (MCT-1/MCTS1) oncoprotein support noncanonical translation initiation, promote translation reinitiation on a specific set of mRNAs with short upstream reading frames, and regulate ribosome recycling. DENR and MCT-1 form a heterodimer, which binds to the ribosome. We determined the crystal structure of the heterodimer formed by human MCT-1 and the N-terminal domain of DENR at 2.0-Å resolution. The structure of the heterodimer reveals atomic details of the mechanism of DENR and MCT-1 interaction. Four conserved cysteine residues of DENR (C34, C37, C44, C53) form a classical tetrahedral zinc ion-binding site, which preserves the structure of the DENR’s MCT-1–binding interface that is essential for the dimerization. Substitution of all four cysteines by alanine abolished a heterodimer formation. Our findings elucidate further the mechanism of regulation of DENR-MCT-1 activities in unconventional translation initiation, reinitiation, and recycling.

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Route, mechanism, and implications of proton import during Na+/K+ exchange by native Na+/K+-ATPase pumps

The Journal of General Physiology ◽

10.1085/jgp.201311148 ◽

2014 ◽

Vol 143 (4) ◽

pp. 449-464 ◽

Cited By ~ 45

Author(s):

Natascia Vedovato ◽

David C. Gadsby

Keyword(s):

Binding Site ◽

Single Molecule ◽

Conformational Changes ◽

Outward Current ◽

Side Chain ◽

Ion Binding ◽

Inward Current ◽

Na Release ◽

K Transport ◽

External K

A single Na+/K+-ATPase pumps three Na+ outwards and two K+ inwards by alternately exposing ion-binding sites to opposite sides of the membrane in a conformational sequence coupled to pump autophosphorylation from ATP and auto-dephosphorylation. The larger flow of Na+ than K+ generates outward current across the cell membrane. Less well understood is the ability of Na+/K+ pumps to generate an inward current of protons. Originally noted in pumps deprived of external K+ and Na+ ions, as inward current at negative membrane potentials that becomes amplified when external pH is lowered, this proton current is generally viewed as an artifact of those unnatural conditions. We demonstrate here that this inward current also flows at physiological K+ and Na+ concentrations. We show that protons exploit ready reversibility of conformational changes associated with extracellular Na+ release from phosphorylated Na+/K+ pumps. Reversal of a subset of these transitions allows an extracellular proton to bind an acidic side chain and to be subsequently released to the cytoplasm. This back-step of phosphorylated Na+/K+ pumps that enables proton import is not required for completion of the 3 Na+/2 K+ transport cycle. However, the back-step occurs readily during Na+/K+ transport when external K+ ion binding and occlusion are delayed, and it occurs more frequently when lowered extracellular pH raises the probability of protonation of the externally accessible carboxylate side chain. The proton route passes through the Na+-selective binding site III and is distinct from the principal pathway traversed by the majority of transported Na+ and K+ ions that passes through binding site II. The inferred occurrence of Na+/K+ exchange and H+ import during the same conformational cycle of a single molecule identifies the Na+/K+ pump as a hybrid transporter. Whether Na+/K+ pump–mediated proton inflow may have any physiological or pathophysiological significance remains to be clarified.

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Mn-Mg disordering in cummingtonite: a high-temperature neutron powder diffraction study

Mineralogical Magazine ◽

10.1180/002646100549166 ◽

2000 ◽

Vol 64 (2) ◽

pp. 255-266 ◽

Cited By ~ 10

Author(s):

J. J. Reece ◽

S. A. T. Redfern ◽

M. D. Welch ◽

C. M. B. Henderson

Keyword(s):

Crystal Structure ◽

Phase Transition ◽

New York ◽

High Temperature ◽

Powder Diffraction ◽

Elevated Temperatures ◽

Neutron Powder Diffraction ◽

Site Preference ◽

A Site

AbstractThe crystal structure of a manganoan cummingtonite, composition [M4](Na0.13Ca0.41Mg0.46Mn1.00) [M1,2,3](Mg4.87Mn0.13)(Si8O22)(OH)2, (Z = 2), a = 9.5539(2) Å, b = 18.0293(3) Å, c = 5.2999(1) Å, β = 102.614(2)° from Talcville, New York, has been refined at high temperature using in situ neutron powder diffraction. The P21/m to C2/m phase transition, observed as spontaneous strains +ε1 = −ε2, occurs at ˜107°C. Long-range disordering between Mg2+ and Mn2+ on the M(4) and M(2) sites occurs above 550°C. Mn2+ occupies the M(4) and M(2) sites preferring M(4) with a site-preference energy of 24.6±1.5 kJ mol−1. Disordering induces an increase in XMnM2 and decrease in XMnM4 at elevated temperatures. Upon cooling, the ordered states of cation occupancy are ‘frozen in’ and strains in lattice parameters are maintained, suggesting that re-equilibration during cooling has not taken place.

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Spontaneous ribosomal translocation of mRNA and tRNAs into a chimeric hybrid state

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1901310116 ◽

2019 ◽

Vol 116 (16) ◽

pp. 7813-7818 ◽

Cited By ~ 18

Author(s):

Jie Zhou ◽

Laura Lancaster ◽

John Paul Donohue ◽

Harry F. Noller

Keyword(s):

Crystal Structure ◽

Elongation Factor ◽

Intermediate Complex ◽

Reading Frame ◽

Hybrid State ◽

Head Domain ◽

30S Subunit ◽

A Site ◽

Insight Into ◽

Factor G

The elongation factor G (EF-G)–catalyzed translocation of mRNA and tRNA through the ribosome is essential for vacating the ribosomal A site for the next incoming aminoacyl-tRNA, while precisely maintaining the translational reading frame. Here, the 3.2-Å crystal structure of a ribosome translocation intermediate complex containing mRNA and two tRNAs, formed in the absence of EF-G or GTP, provides insight into the respective roles of EF-G and the ribosome in translocation. Unexpectedly, the head domain of the 30S subunit is rotated by 21°, creating a ribosomal conformation closely resembling the two-tRNA chimeric hybrid state that was previously observed only in the presence of bound EF-G. The two tRNAs have moved spontaneously from their A/A and P/P binding states into ap/P and pe/E states, in which their anticodon loops are bound between the 30S body domain and its rotated head domain, while their acceptor ends have moved fully into the 50S P and E sites, respectively. Remarkably, the A-site tRNA translocates fully into the classical P-site position. Although the mRNA also undergoes movement, codon–anticodon interaction is disrupted in the absence of EF-G, resulting in slippage of the translational reading frame. We conclude that, although movement of both tRNAs and mRNA (along with rotation of the 30S head domain) can occur in the absence of EF-G and GTP, EF-G is essential for enforcing coupled movement of the tRNAs and their mRNA codons to maintain the reading frame.

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