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- PDB-3j0j: Fitted atomic models of Thermus thermophilus V-ATPase subunits in... -

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Basic information

Entry
Database: PDB / ID: 3j0j
TitleFitted atomic models of Thermus thermophilus V-ATPase subunits into cryo-EM map
Components
  • (V-type ATP synthase ...) x 6
  • V-type ATP synthase, subunit (VAPC-THERM)
KeywordsHYDROLASE / flexible fitting / rigid body fitting / membrane protein complex
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
ATPase, V0 complex, c subunit / Vacuolar (H+)-ATPase G subunit / ATPase, V1 complex, subunit F, bacterial/archaeal / 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 subunit E / V-type ATPase subunit E, C-terminal domain superfamily ...ATPase, V0 complex, c subunit / Vacuolar (H+)-ATPase G subunit / ATPase, V1 complex, subunit F, bacterial/archaeal / 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 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 / 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)
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 9.7 Å
AuthorsLau, W.C.Y. / Rubinstein, J.L.
CitationJournal: Nature / Year: 2011
Title: Subnanometre-resolution structure of the intact Thermus thermophilus H+-driven ATP synthase.
Authors: Wilson C Y Lau / John L Rubinstein /
Abstract: Ion-translocating rotary ATPases serve either as ATP synthases, using energy from a transmembrane ion motive force to create the cell's supply of ATP, or as transmembrane ion pumps that are powered ...Ion-translocating rotary ATPases serve either as ATP synthases, using energy from a transmembrane ion motive force to create the cell's supply of ATP, or as transmembrane ion pumps that are powered by ATP hydrolysis. The members of this family of enzymes each contain two rotary motors: one that couples ion translocation to rotation and one that couples rotation to ATP synthesis or hydrolysis. During ATP synthesis, ion translocation through the membrane-bound region of the complex causes rotation of a central rotor that drives conformational changes and ATP synthesis in the catalytic region of the complex. There are no structural models available for the intact membrane region of any ion-translocating rotary ATPase. Here we present a 9.7 Å resolution map of the H(+)-driven ATP synthase from Thermus thermophilus obtained by electron cryomicroscopy of single particles in ice. The 600-kilodalton complex has an overall subunit composition of A(3)B(3)CDE(2)FG(2)IL(12). The membrane-bound motor consists of a ring of L subunits and the carboxy-terminal region of subunit I, which are equivalent to the c and a subunits of most other rotary ATPases, respectively. The map shows that the ring contains 12 L subunits and that the I subunit has eight transmembrane helices. The L(12) ring and I subunit have a surprisingly small contact area in the middle of the membrane, with helices from the I subunit making contacts with two different L subunits. The transmembrane helices of subunit I form bundles that could serve as half-channels across the membrane, with the first half-channel conducting protons from the periplasm to the L(12) ring and the second half-channel conducting protons from the L(12) ring to the cytoplasm. This structure therefore suggests the mechanism by which a transmembrane proton motive force is converted to rotation in rotary ATPases.
History
DepositionAug 24, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2012Group: Database references
Revision 1.2Jan 25, 2012Group: Database references
Revision 1.3Jul 17, 2013Group: Other
Revision 1.4Jul 18, 2018Group: Data collection / Category: em_image_scans / em_software / Item: _em_software.image_processing_id / _em_software.name

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Structure visualization

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  • Imaged by UCSF Chimera
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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)488,23415
Polymers487,38013
Non-polymers8542
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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V-type ATP synthase ... , 6 types, 11 molecules ABCDEFGHJLM

#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 (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 (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 (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 (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P74903
#6: Protein V-type ATP synthase subunit E / V-ATPase subunit E


Mass: 20699.693 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (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 (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P74902

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Protein / Non-polymers , 2 types, 4 molecules IK

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


Mass: 11621.355 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SIT5
#8: 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

Component
IDNameTypeParent-ID
1Detergent solubilized membrane protein complexCOMPLEX0
2Subunit A of V-ATPase1
3Subunit B of V-ATPase1
4Subunit D of V-ATPase1
5Subunit F of V-ATPase1
6Subunit E of V-ATPase1
7Subunit G of V-ATPase1
8Subunit C of V-ATPase1
Buffer solutionName: 50 mM Tris-HCl, 150 mM NaCl, 5 mM MgCl2, 0.02% DDM, pH 8.0
pH: 8
Details: 50 mM Tris-HCl, 150 mM NaCl, 5 mM MgCl2, 0.02% DDM, pH 8.0
SpecimenConc.: 2.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Details: Vitrification from 4 degree Celsius environment / Method: Blot 20 seconds before plunging

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20 / Date: Jan 1, 2010
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 50000 X / Calibrated magnification: 50000 X / Nominal defocus max: 4500 nm / Nominal defocus min: 2500 nm / Cs: 2 mm
Specimen holderTemperature: 100 K / Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingElectron dose: 0.18 e/Å2 / Film or detector model: GENERIC FILM / Details: Scanned with Intergraph Photoscan densitometer
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategoryDetails
1iMODFITmodel fitting
2UCSF Chimeramodel fittingUCSF Chimera (rigid) and Imodfit (flexible)
3Build_Fspace3D reconstruction
4FREALIGN3D reconstruction
5Refine_Fspace3D reconstruction
CTF correctionDetails: Each particle
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: Fourier sinc interpolation (Build_fspace) / Resolution: 9.7 Å / Num. of particles: 46105 / Nominal pixel size: 1.4 Å / Actual pixel size: 1.4 Å
Magnification calibration: Graphite imaging and Rosenthal apoferritin method (Publication In Preparation)
Details: Frealign and new software used for refinement and reconstruction
Symmetry type: POINT
Atomic model building
IDProtocolSpaceTarget criteriaDetails
1FLEXIBLE FITREALcorrelation coefficient (UCSF chimera, rigid) and imodfit (flexible)REFINEMENT PROTOCOL--rigid (subunit A, B, D, F, E, and G) and flexible fitting (subunit C)
2
3
Atomic model building
IDPDB-ID 3D fitting-ID
13A5C

3a5c

1
23K5B

3k5b

2
31R5Z

1r5z

3
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms22672 0 54 0 22726

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