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- PDB-6r10: Thermus thermophilus V/A-type ATPase/synthase, rotational state 1R -

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Basic information

Entry
Database: PDB / ID: 6r10
TitleThermus thermophilus V/A-type ATPase/synthase, rotational state 1R
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 V-type ATPase, V0 domain / proton-transporting two-sector ATPase complex, catalytic domain / proton-transporting ATP synthase complex / proton motive force-driven plasma membrane ATP synthesis / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / ATP binding / metal ion binding
Similarity search - Function
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 / ATPase, V0 complex, c subunit / Vacuolar (H+)-ATPase G subunit / ATPase, V1 complex, subunit F, bacterial/archaeal / V-ATPase proteolipid subunit / ATPase, V0 complex, c/d subunit / V-type ATPase subunit C/d ...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 / ATPase, V0 complex, c subunit / Vacuolar (H+)-ATPase G subunit / ATPase, V1 complex, subunit F, bacterial/archaeal / V-ATPase proteolipid subunit / 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-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 N-term extension / 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 / 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 / P-loop containing nucleoside triphosphate hydrolase
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: 4.3 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
DepositionMar 13, 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 1.2Dec 18, 2019Group: Other / Category: atom_sites
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3]
Revision 1.3Sep 30, 2020Group: Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.identifier_ORCID
Revision 1.4May 15, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model
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

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Structure visualization

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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)681,54529
Polymers680,66626
Non-polymers8793
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area40090 Å2
ΔGint-174 kcal/mol
Surface area123200 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)
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)
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)
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)
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)
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)
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)
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: 13166.218 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
References: UniProt: Q5SIT5
#9: Protein
V-type ATP synthase, subunit K


Mass: 9841.714 Da / Num. of mol.: 12 / Source method: isolated from a natural source
Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
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 / Adenosine 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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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 chlorideNaClSodium chloride1
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 FIELDBright-field microscopy / 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: 1.13_2998: / Classification: refinement
EM software
IDNameVersionCategory
1RELION3.0 betaparticle selection
2EPUimage acquisition
4CTFFIND4.1.5CTF correction
7UCSF Chimera1.13.1model fitting
9RELION3.0 betainitial Euler assignment
10RELION3.0 betafinal Euler assignment
11RELION3.0 betaclassification
12RELION3.0 beta3D reconstruction
19PHENIX1.12model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 181245
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 15571 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 167.6 / 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

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