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- PDB-7tdo: Cryo-EM structure of transmembrane AAA+ protease FtsH in the ADP state -

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Basic information

Entry
Database: PDB / ID: 7tdo
TitleCryo-EM structure of transmembrane AAA+ protease FtsH in the ADP state
ComponentsATP-dependent zinc metalloprotease FtsH
KeywordsHYDROLASE / AAA+ ATPase / protease / hexamer / ADP-bound state
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / ATP-dependent peptidase activity / protein catabolic process / metalloendopeptidase activity / ATP hydrolysis activity / proteolysis / zinc ion binding / ATP binding / identical protein binding / plasma membrane
Similarity search - Function
Peptidase M41, FtsH extracellular / FtsH Extracellular / Peptidase M41 / Peptidase, FtsH / Peptidase M41-like / Peptidase family M41 / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. ...Peptidase M41, FtsH extracellular / FtsH Extracellular / Peptidase M41 / Peptidase, FtsH / Peptidase M41-like / Peptidase family M41 / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ATP-dependent zinc metalloprotease FtsH
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.15 Å
AuthorsLiu, W. / Schoonen, M. / Wang, T. / McSweeney, S. / Liu, Q.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States) United States
CitationJournal: Commun Biol / Year: 2022
Title: Cryo-EM structure of transmembrane AAA+ protease FtsH in the ADP state.
Authors: Wu Liu / Martien Schoonen / Tong Wang / Sean McSweeney / Qun Liu /
Abstract: AAA+ proteases regulate numerous physiological and cellular processes through tightly regulated proteolytic cleavage of protein substrates driven by ATP hydrolysis. FtsH is the only known family of ...AAA+ proteases regulate numerous physiological and cellular processes through tightly regulated proteolytic cleavage of protein substrates driven by ATP hydrolysis. FtsH is the only known family of membrane-anchored AAA+ proteases essential for membrane protein quality control. Although a spiral staircase rotation mechanism for substrate translocation across the FtsH pore has been proposed, the detailed conformational changes among various states have not been clear due to absence of FtsH structures in these states. We report here the cryo-EM structure for Thermotoga maritima FtsH (TmFtsH) in a fully ADP-bound symmetric state. Comparisons of the ADP-state structure with its apo-state and a substrate-engaged yeast YME1 structure show conformational changes in the ATPase domains, rather than the protease domains. A reconstruction of the full-length TmFtsH provides structural insights for the dynamic transmembrane and the periplasmic domains. Our structural analyses expand the understanding of conformational switches between different nucleotide states in ATP hydrolysis by FtsH.
History
DepositionJan 2, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

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MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATP-dependent zinc metalloprotease FtsH
B: ATP-dependent zinc metalloprotease FtsH
C: ATP-dependent zinc metalloprotease FtsH
D: ATP-dependent zinc metalloprotease FtsH
E: ATP-dependent zinc metalloprotease FtsH
F: ATP-dependent zinc metalloprotease FtsH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)413,50112
Polymers410,9386
Non-polymers2,5636
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "B"
d_2ens_1chain "A"
d_3ens_1chain "C"
d_4ens_1chain "D"
d_5ens_1chain "E"
d_6ens_1chain "F"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1VALGLUC1 - 420
d_12ens_1ADPADPD
d_21ens_1VALGLUA1 - 420
d_22ens_1ADPADPB
d_31ens_1VALGLUE1 - 420
d_32ens_1ADPADPF
d_41ens_1VALGLUG1 - 420
d_42ens_1ADPADPH
d_51ens_1VALGLUI1 - 420
d_52ens_1ADPADPJ
d_61ens_1VALGLUK1 - 420
d_62ens_1ADPADPL

NCS oper:
IDCodeMatrixVector
1given(0.50499224617, -0.863123319315, -0.000983342297714), (0.863117787315, 0.504984073573, 0.00433251176336), (-0.00324291973495, -0.00303662507512, 0.999990131141)186.078202718, -50.4443458873, 0.777178408693
2given(0.502827439761, 0.86435996762, -0.00681264996627), (-0.864381074282, 0.50283720718, -0.000318590164432), (0.00315027729832, 0.00604892157326, 0.99997674288)-49.6715698802, 186.337582237, -0.880777941869
3given(-0.498785076565, 0.866651484946, -0.0113424440078), (-0.866722058867, -0.498702308283, 0.00942763954287), (0.00251397480111, 0.0145331123342, 0.999891228373)87.4700755009, 322.788188903, -1.7935436301
4given(-0.484549743677, -0.87474191904, 0.00617421867571), (0.874750891725, -0.484568782289, -0.00199315255773), (0.00473532771857, 0.00443512173133, 0.999978952962)322.697523872, 84.1579140692, -0.895147255916
5given(-0.999870434111, -0.0138028114017, -0.00828235397391), (0.0137208973982, -0.999857181259, 0.00986681610723), (-0.0084173609004, 0.00975189637534, 0.999917020834)275.713095848, 271.386334814, -0.257990490516

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Components

#1: Protein
ATP-dependent zinc metalloprotease FtsH


Mass: 68489.664 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: ftsH, TM_0580 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9WZ49, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases
#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Hexameric FtsH in the ADP-bound state / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Thermotoga maritima (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 700 nm
Image recordingElectron dose: 65 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

Software
NameVersionClassification
phenix.real_space_refine1.18.2_3874refinement
PHENIX1.18.2_3874refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.15 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 86652 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 3.66 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002719848
ELECTRON MICROSCOPYf_angle_d0.542426850
ELECTRON MICROSCOPYf_chiral_restr0.04273102
ELECTRON MICROSCOPYf_plane_restr0.0043492
ELECTRON MICROSCOPYf_dihedral_angle_d10.2252778
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2CELECTRON MICROSCOPYNCS constraints6.21791961374E-13
ens_1d_3CELECTRON MICROSCOPYNCS constraints4.02360686189E-11
ens_1d_4CELECTRON MICROSCOPYNCS constraints9.2471605283E-12
ens_1d_5CELECTRON MICROSCOPYNCS constraints1.67825177661E-12
ens_1d_6CELECTRON MICROSCOPYNCS constraints1.88438669785E-10

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