Sandbox 5Y5Y Assignment: Difference between revisions

From Proteopedia
Jump to navigationJump to search
Student (talk | contribs)
students
33,923 edits
Thermus thermophilus V/A-ATPase (5Y5Y): cryo-EM based structure, function, and key features
 
Student (talk | contribs)
students
33,923 edits
Thermus thermophilus V/A-ATPase (5Y5Y): cryo-EM based structure, function, and key features
 
Line 1: Line 1:
== Structure ==
== Structure ==
[[Image:Overall_VA-ATPase_5y5y.png|300px|left|thumb|Overall spacefill view of Thermus thermophilus V/A-type H+-ATPase/synthase, [[5y5y]], showing the intact rotary complex.]]
<StructureSection load='1stp' size='340' side='right' caption='Cryo-EM structure of Thermus thermophilus V/A-type H+-ATPase/synthase' scene=''>
<StructureSection load='1stp' size='340' side='right' caption='Cryo-EM structure of Thermus thermophilus V/A-type H+-ATPase/synthase' scene=''>
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 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.
Line 40: Line 41:
ray 1200, 1200
ray 1200, 1200
png 5y5y_overall_structure.png
png 5y5y_overall_structure.png
# 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 ==
== 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
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
Retrieved from "https://proteopedia.org/Sandbox_5Y5Y_Assignment"