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- PDB-6qum: Thermus thermophilus V/A-type ATPase/synthase, rotational state 1 -

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Basic information

Entry
Database: PDB / ID: 6qum
TitleThermus thermophilus V/A-type ATPase/synthase, rotational state 1
Components
  • (V-type ATP synthase ...) x 7
  • (V-type ATP synthase, subunit ...) x 2
KeywordsMEMBRANE PROTEIN / ATP hydrolysis/synthesis / proton translocation / rotary catalysis
Function / homology
Function and homology information


proton-transporting two-sector ATPase complex, catalytic domain / proton-transporting V-type ATPase, V0 domain / vacuolar proton-transporting V-type ATPase complex / vacuolar acidification / proton motive force-driven plasma membrane ATP synthesis / proton-transporting ATPase activity, rotational mechanism / H+-transporting two-sector ATPase / proton-transporting ATP synthase complex / proton-transporting ATP synthase activity, rotational mechanism / ATPase binding ...proton-transporting two-sector ATPase complex, catalytic domain / proton-transporting V-type ATPase, V0 domain / vacuolar proton-transporting V-type ATPase complex / vacuolar acidification / proton motive force-driven plasma membrane ATP synthesis / proton-transporting ATPase activity, rotational mechanism / H+-transporting two-sector ATPase / proton-transporting ATP synthase complex / proton-transporting ATP synthase activity, rotational mechanism / ATPase binding / ATP binding / metal ion binding
Similarity search - Function
ATP synthase (C/AC39) subunit, domain 3 / V-type ATP synthase subunit C domain / V-type ATP synthase subunit C fold / F1F0 ATP synthase subunit B, membrane domain / ATP synthase, E subunit, C-terminal / Rossmann fold - #12240 / ATPase, V0 complex, c subunit / : / V-type ATP synthase subunit I, N-terminal / Vacuolar ATPase subunit I, N-terminal proximal lobe ...ATP synthase (C/AC39) subunit, domain 3 / V-type ATP synthase subunit C domain / V-type ATP synthase subunit C fold / F1F0 ATP synthase subunit B, membrane domain / ATP synthase, E subunit, C-terminal / Rossmann fold - #12240 / ATPase, V0 complex, c subunit / : / V-type ATP synthase subunit I, N-terminal / Vacuolar ATPase subunit I, N-terminal proximal lobe / Vacuolar ATPase Subunit I N-terminal proximal lobe / V-type ATPase subunit I, N-terminal domain / hypothetical protein PF0899 fold / Vacuolar (H+)-ATPase G subunit / ATPase, V1 complex, subunit F, bacterial/archaeal / F1F0 ATP synthase subunit C / F1FO ATP Synthase / Bovine Mitochondrial F1-ATPase, ATP Synthase Beta Chain; Chain D, domain3 / Bovine Mitochondrial F1-atpase; Atp Synthase Beta Chain; Chain D, domain 3 / ATPase, V0 complex, c/d subunit / V-type ATPase subunit C/d / V-type ATP synthase subunit c/d subunit superfamily / V-type ATP synthase c/d subunit, domain 3 superfamily / ATP synthase (C/AC39) subunit / V-ATPase proteolipid subunit / V-type ATPase, V0 complex, 116kDa subunit family / V-type ATPase 116kDa subunit family / V-type ATPase subunit E / V-type ATPase subunit E, C-terminal domain superfamily / ATP synthase (E/31 kDa) subunit / ATPase, V1 complex, subunit D / ATPase, V1 complex, subunit F / ATPase, V1 complex, subunit F superfamily / ATP synthase subunit D / ATP synthase (F/14-kDa) subunit / V-type ATP synthase regulatory subunit B/beta / V-type ATP synthase catalytic alpha chain / ATPsynthase alpha/beta subunit, N-terminal extension / ATPsynthase alpha/beta subunit barrel-sandwich domain / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / Topoisomerase I; Chain A, domain 4 / V-ATPase proteolipid subunit C-like domain / F/V-ATP synthase subunit C superfamily / ATP synthase subunit C / : / ATPase, F1/V1 complex, beta/alpha subunit, C-terminal / C-terminal domain of V and A type ATP synthase / ATP synthase subunit alpha, N-terminal domain-like superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain / ATP synthase alpha/beta family, beta-barrel domain / ATPase, alpha/beta subunit, nucleotide-binding domain, active site / ATP synthase alpha and beta subunits signature. / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase alpha/beta family, nucleotide-binding domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / P-loop containing nucleotide triphosphate hydrolases / Up-down Bundle / Beta Barrel / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / V-type ATP synthase subunit D / V-type ATP synthase subunit E / V-type ATP synthase subunit C / V-type ATP synthase subunit F / V-type ATP synthase alpha chain / V-type ATP synthase beta chain / V-type ATP synthase, subunit (VAPC-THERM) / V-type ATP synthase subunit I / V-type ATP synthase, subunit K
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.25 Å
AuthorsZhou, L. / Sazanov, L.
CitationJournal: Science / Year: 2019
Title: Structure and conformational plasticity of the intact V/A-type ATPase.
Authors: Long Zhou / Leonid A Sazanov /
Abstract: V (vacuolar)/A (archaeal)-type adenosine triphosphatases (ATPases), found in archaea and eubacteria, couple ATP hydrolysis or synthesis to proton translocation across the plasma membrane using the ...V (vacuolar)/A (archaeal)-type adenosine triphosphatases (ATPases), found in archaea and eubacteria, couple ATP hydrolysis or synthesis to proton translocation across the plasma membrane using the rotary-catalysis mechanism. They belong to the V-type ATPase family, which differs from the mitochondrial/chloroplast F-type ATP synthases in overall architecture. We solved cryo-electron microscopy structures of the intact V/A-ATPase, reconstituted into lipid nanodiscs, in three rotational states and two substates. These structures indicate substantial flexibility between V and V in a working enzyme, which results from mechanical competition between central shaft rotation and resistance from the peripheral stalks. We also describe details of adenosine diphosphate inhibition release, V-V torque transmission, and proton translocation, which are relevant for the entire V-type ATPase family.
History
DepositionFeb 27, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 28, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed ..._citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Sep 30, 2020Group: Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.identifier_ORCID
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / em_admin / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_admin.last_update

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Structure visualization

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  • EMDB-4640
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Assembly

Deposited unit
A: V-type ATP synthase alpha chain
B: V-type ATP synthase alpha chain
C: V-type ATP synthase alpha chain
D: V-type ATP synthase beta chain
E: V-type ATP synthase beta chain
F: V-type ATP synthase beta chain
G: V-type ATP synthase subunit D
H: V-type ATP synthase subunit F
I: V-type ATP synthase, subunit (VAPC-THERM)
J: V-type ATP synthase subunit E
K: V-type ATP synthase, subunit (VAPC-THERM)
L: V-type ATP synthase subunit E
M: V-type ATP synthase subunit C
N: V-type ATP synthase subunit I
O: V-type ATP synthase, subunit K
P: V-type ATP synthase, subunit K
Q: V-type ATP synthase, subunit K
R: V-type ATP synthase, subunit K
S: V-type ATP synthase, subunit K
T: V-type ATP synthase, subunit K
U: V-type ATP synthase, subunit K
V: V-type ATP synthase, subunit K
W: V-type ATP synthase, subunit K
X: V-type ATP synthase, subunit K
Y: V-type ATP synthase, subunit K
Z: V-type ATP synthase, subunit K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)647,95629
Polymers647,07726
Non-polymers8793
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area104280 Å2
ΔGint-746 kcal/mol
Surface area226440 Å2
MethodPISA

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Components

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V-type ATP synthase ... , 7 types, 12 molecules ABCDEFGHJLMN

#1: Protein V-type ATP synthase alpha chain / V-ATPase subunit A


Mass: 63699.980 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579
References: UniProt: Q56403, H+-transporting two-sector ATPase
#2: Protein V-type ATP synthase beta chain / V-ATPase subunit B


Mass: 53219.500 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q56404
#3: Protein V-type ATP synthase subunit D / V-ATPase subunit D


Mass: 24715.566 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: O87880
#4: Protein V-type ATP synthase subunit F / V-ATPase subunit F


Mass: 11294.904 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P74903
#6: Protein V-type ATP synthase subunit E / V-ATPase subunit E


Mass: 20645.582 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P74901
#7: Protein V-type ATP synthase subunit C / V-ATPase subunit C


Mass: 35968.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P74902
#8: Protein V-type ATP synthase subunit I


Mass: 72204.289 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SIT6

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V-type ATP synthase, subunit ... , 2 types, 14 molecules IKOPQRSTUVWXYZ

#5: Protein V-type ATP synthase, subunit (VAPC-THERM)


Mass: 11564.303 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SIT5
#9: Protein
V-type ATP synthase, subunit K


Mass: 7309.625 Da / Num. of mol.: 12 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SIT7

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Non-polymers , 2 types, 3 molecules

#10: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#11: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM

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Details

Has protein modificationY

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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: Thermus thermophilus V/A-type ATPase/ATP synthase / Type: COMPLEX / Entity ID: #1-#9 / Source: NATURAL
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
110.65 MDaNO
210.45 MDaNO
310.20 MDaNO
410.35 MDaNO
5135.8 kDa/nmNO
6164.0 kDa/nmNO
7194.2 MDaNO
Source (natural)Organism: Thermus thermophilus HB8 (bacteria)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMTrisNH2C(CH2OH)31
2100 mMsodium chlorideNaCl1
35 mMmagnesium chlorideMgCl21
40.1 %CHAPSC32H58N2O7S1
SpecimenConc.: 5.4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R0.6/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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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: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal magnification: 75000 X / Calibrated magnification: 129032 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm / Calibrated defocus min: 500 nm / Calibrated defocus max: 1780 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 63 sec. / Electron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2700
Image scansSampling size: 14 µm / Width: 4096 / Height: 4096

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Processing

SoftwareName: PHENIX / Version: 1.12_2829: / Classification: refinement
EM software
IDNameVersionCategory
2EPUimage acquisition
4CTFFIND4.1.5CTF correction
7UCSF Chimera1.13.1model fitting
9PHENIX1.12model refinement
10RELION3.0 betainitial Euler assignment
11RELION3.0 betafinal Euler assignment
12RELION3.0 betaclassification
13RELION3.0 beta3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 181245
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.25 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 39429 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 91.2 / Space: REAL
Atomic model building

3D fitting-ID: 1 / Source name: PDB / Type: experimental model

IDPDB-IDPdb chain-IDAccession codeInitial refinement model-IDPdb chain residue range
15Y5Y

5y5y

A5Y5Y11-578
25Y5Y

5y5y

B5Y5Y11-578
35Y5Y

5y5y

C5Y5Y11-578
45Y5Y

5y5y

D5Y5Y15-474
55Y5Y

5y5y

E5Y5Y13-471
65Y5Y

5y5y

F5Y5Y13-472
75Y5Y

5y5y

G5Y5Y13-209
85Y5Y

5y5y

H5Y5Y11-104
95Y5Y

5y5y

I5Y5Y160-120
105Y5Y

5y5y

J5Y5Y12-188
115Y5Y

5y5y

K5Y5Y160-120
125Y5Y

5y5y

L5Y5Y12-188
135Y5Y

5y5y

M5Y5Y13-322
145Y5X

5y5x

N5Y5X21-649
155Y5X

5y5x

O5Y5X28-80
165Y5X

5y5x

P5Y5X28-80
175Y5X

5y5x

Q5Y5X28-80
185Y5X

5y5x

R5Y5X28-80
195Y5X

5y5x

S5Y5X28-80
205Y5X

5y5x

T5Y5X28-80
215Y5X

5y5x

U5Y5X28-80
225Y5X

5y5x

V5Y5X28-80
235Y5X

5y5x

W5Y5X28-80
245Y5X

5y5x

X5Y5X28-80
255Y5X

5y5x

Y5Y5X28-80
265Y5X

5y5x

Z5Y5X28-80
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00745669
ELECTRON MICROSCOPYf_angle_d1.08661839
ELECTRON MICROSCOPYf_dihedral_angle_d13.48127575
ELECTRON MICROSCOPYf_chiral_restr0.0617079
ELECTRON MICROSCOPYf_plane_restr0.0088046

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