Sandbox 5Y5Y Assignment

From Proteopedia

---

Revision as of 15:56, 30 November 2025

proteopedia linkproteopedia link

Contents 1 Structure 2 Function 3 Relevance 4 Structural highlights 5 PyMOL Scripts 6 References

Structure

spinqualitylabelsall models Cryo-EM structure of Thermus thermophilus V/A-type H+-ATPase/synthase Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image The V/A-type ATPase from Thermus thermophilus is a membrane-embedded rotary enzyme complex responsible for ATP synthesis driven by proton translocation. The 3D cryo-EM structures of the intact enzyme were resolved at 4.7–7.5 Å resolution capturing three rotational states of the central rotor subunit (DF shaft). The enzyme consists of two major sectors : a soluble V1 domain that hydrolyzes or synthesizes ATP via three catalytic AB pairs arranged in open, closed, and semi-closed conformations, and a membrane-bound Vo domain that translocates protons through a c12 ring and an a-subunit. Two peripheral EG stalks connect the V1 and Vo regions forming a stator apparatus, while the central DF shaft and d-subunit constitute the rotor complex. The V/A-ATPase structure reveals detailed interactions critical for mechanical torque transmission, proton pathway formation, and catalytic cooperativity. The structure also identifies ADP-bound sites consistent with an ADP-inhibited resting state. The overall architecture of the Thermus thermophilus ATPase is shown in [5y5y]. Explore the rotation and subunit arrangement interactively by clicking the green link.

Function

The complex couples ATP hydrolysis or synthesis in the V1 domain with proton flow through Vo, driving rotary catalysis. Proton motive force causes rotation of the central rotor (c12 ring, d-subunit and DF shaft) which induces conformational changes in the three catalytic sites, enabling cooperative synthesis of ATP from ADP and inorganic phosphate. Conversely, ATP hydrolysis in V1 drives rotation of the shaft, pumping protons across the membrane. The enzyme exhibits discrete 120° steps in V1 coupled with 30° steps in Vo, reflecting its structural symmetry mismatches and elastic coupling through flexible peripheral stalks.

Relevance

This structure elucidates the fundamental mechanism of rotary ATPases, a class of enzymes essential for cellular energy conversion across all domains of life. Understanding how proton translocation is coupled to ATP synthesis provides insights relevant to bioenergetics, antibiotic targeting, and design of molecular machines.

Structural highlights

Three rotational states captured by cryo-EM demonstrate the rotary catalytic mechanism.

The A3B3 catalytic head shows three conformations of nucleotide binding sites: open, closed, and semi-closed, with bound ADP at closed and semi-closed sites indicating an inhibited state.

The membrane-embedded a-subunit and c12 ring create two aqueous half-channels for protons, with a conserved Arg-Glu salt bridge critical for proton translocation.

The d-subunit forms a socket that tightly interfaces with the DF shaft’s short helix, transmitting torque efficiently.

Peripheral EG stalks exhibit flexible coiled-coil conformations allowing elastic energy coupling between V1 and Vo regions, accommodating the symmetry mismatch in rotational steps.

This is a sample scene created with SAT to by Group, and another to make of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

PyMOL Scripts

1. IMAGE 1: Overall V/A-ATPase

fetch 5y5y, ATP_synthase bg_color white hide everything show cartoon, ATP_synthase color red, (ATP_synthase and ss h) # helices color yellow, (ATP_synthase and ss s) # beta strands color green, (ATP_synthase and not ss h and not ss s) # coils/other orient ATP_synthase zoom ATP_synthase label (ATP_synthase and name CA and resi 1), "Start" show surface, ATP_synthase set transparency, 0.3 ray 1200, 1200 png 5y5y_overall_structure.png

1. IMAGE 2: Catalytic A3B3 head with nucleotides

fetch 5y5y, ATP_synthase bg_color white hide everything show cartoon, (ATP_synthase and chain A) show cartoon, (ATP_synthase and chain B) color cyan, (ATP_synthase and chain A) color limon, (ATP_synthase and chain B) select nucleotides, (ATP_synthase and (resn ADP+ATP)) show sticks, nucleotides color magenta, nucleotides label nucleotides, "ADP" select open_site, (ATP_synthase and chain B and resi 1-50) select closed_site, (ATP_synthase and chain A and resi 50-100) select semiclosed_site, (ATP_synthase and chain B and resi 100-150) show surface, open_site show surface, closed_site show surface, semiclosed_site set transparency, 0.4, open_site set transparency, 0.4, closed_site set transparency, 0.4, semiclosed_site orient ATP_synthase zoom ATP_synthase, 1.5 ray 1200, 1200 png 5y5y_catalytic_sites.png

References

Nakanishi, A., Kishikawa, J., Tamakoshi, M., Mitsuoka, K., & Yokoyama, K. (2018). Cryo EM structure of intact rotary H+-ATPase/synthase from Thermus thermophilus. Nature Communications, 9, 89. https://doi.org/10.1038/s41467-017-02553-6