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- PDB-6fki: Chloroplast F1Fo conformation 3 -

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Basic information

Entry
Database: PDB / ID: 6fki
TitleChloroplast F1Fo conformation 3
Components(ATP synthase ...) x 9
KeywordsMEMBRANE PROTEIN / ATP synthase / membrane protein complex / molecular motor
Function / homology
Function and homology information


mitochondrial proton-transporting ATP synthase complex / chloroplast thylakoid membrane / proton motive force-driven mitochondrial ATP synthesis / proton-transporting ATP synthase complex, coupling factor F(o) / proton motive force-driven ATP synthesis / proton transmembrane transporter activity / proton-transporting ATP synthase complex, catalytic core F(1) / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism ...mitochondrial proton-transporting ATP synthase complex / chloroplast thylakoid membrane / proton motive force-driven mitochondrial ATP synthesis / proton-transporting ATP synthase complex, coupling factor F(o) / proton motive force-driven ATP synthesis / proton transmembrane transporter activity / proton-transporting ATP synthase complex, catalytic core F(1) / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / ADP binding / lipid binding / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
ATP synthase, F0 complex, subunit b' / ATP synthase delta/epsilon subunit, C-terminal domain / ATP synthase, Delta/Epsilon chain, long alpha-helix domain / ATP synthase, F0 complex, subunit A, bacterial/chloroplast / ATP synthase, F0 complex, subunit b/b', bacterial/chloroplast / ATP synthase B/B' CF(0) / ATP synthase, F0 complex, subunit C, bacterial/chloroplast / ATPase, OSCP/delta subunit, conserved site / ATP synthase delta (OSCP) subunit signature. / F1F0 ATP synthase OSCP/delta subunit, N-terminal domain superfamily ...ATP synthase, F0 complex, subunit b' / ATP synthase delta/epsilon subunit, C-terminal domain / ATP synthase, Delta/Epsilon chain, long alpha-helix domain / ATP synthase, F0 complex, subunit A, bacterial/chloroplast / ATP synthase, F0 complex, subunit b/b', bacterial/chloroplast / ATP synthase B/B' CF(0) / ATP synthase, F0 complex, subunit C, bacterial/chloroplast / ATPase, OSCP/delta subunit, conserved site / ATP synthase delta (OSCP) subunit signature. / F1F0 ATP synthase OSCP/delta subunit, N-terminal domain superfamily / ATP synthase, F0 complex, subunit A / ATP synthase, F0 complex, subunit A, active site / ATP synthase, F0 complex, subunit A superfamily / ATP synthase A chain / ATP synthase a subunit signature. / ATPase, OSCP/delta subunit / ATP synthase delta (OSCP) subunit / ATP synthase, F1 complex, delta/epsilon subunit / ATP synthase, F1 complex, delta/epsilon subunit, N-terminal / F0F1 ATP synthase delta/epsilon subunit, N-terminal / ATP synthase, Delta/Epsilon chain, beta-sandwich domain / ATP synthase, F0 complex, subunit C / F1F0 ATP synthase subunit C superfamily / ATP synthase, F0 complex, subunit C, DCCD-binding site / ATP synthase c subunit signature. / ATP synthase, F1 complex, gamma subunit conserved site / ATP synthase gamma subunit signature. / ATP synthase, F1 complex, beta subunit / ATP synthase, alpha subunit, C-terminal domain superfamily / ATP synthase, F1 complex, gamma subunit / ATP synthase, F1 complex, gamma subunit superfamily / ATP synthase / ATP synthase, alpha subunit, C-terminal / ATP synthase, F1 complex, alpha subunit / ATP synthase, F1 complex, alpha subunit nucleotide-binding domain / ATP synthase alpha/beta chain, C terminal domain / 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 / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / ATP synthase subunit beta, chloroplastic / ATP synthase epsilon chain, chloroplastic / ATP synthase gamma chain, chloroplastic / ATP synthase subunit alpha, chloroplastic / ATP synthase subunit a, chloroplastic / ATP synthase subunit b, chloroplastic / ATP synthase delta chain, chloroplastic / ATP synthase subunit b', chloroplastic / ATP synthase subunit c, chloroplastic
Similarity search - Component
Biological speciesSpinacia oleracea (spinach)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsHahn, A. / Vonck, J. / Mills, D.J. / Meier, T. / Kuehlbrandt, W.
CitationJournal: Science / Year: 2018
Title: Structure, mechanism, and regulation of the chloroplast ATP synthase.
Authors: Alexander Hahn / Janet Vonck / Deryck J Mills / Thomas Meier / Werner Kühlbrandt /
Abstract: The chloroplast adenosine triphosphate (ATP) synthase uses the electrochemical proton gradient generated by photosynthesis to produce ATP, the energy currency of all cells. Protons conducted through ...The chloroplast adenosine triphosphate (ATP) synthase uses the electrochemical proton gradient generated by photosynthesis to produce ATP, the energy currency of all cells. Protons conducted through the membrane-embedded F motor drive ATP synthesis in the F head by rotary catalysis. We determined the high-resolution structure of the complete cFF complex by cryo-electron microscopy, resolving side chains of all 26 protein subunits, the five nucleotides in the F head, and the proton pathway to and from the rotor ring. The flexible peripheral stalk redistributes differences in torsional energy across three unequal steps in the rotation cycle. Plant ATP synthase is autoinhibited by a β-hairpin redox switch in subunit γ that blocks rotation in the dark.
History
DepositionJan 24, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 23, 2018Provider: repository / Type: Initial release
Revision 2.0Oct 3, 2018Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations
Category: atom_site / pdbx_nonpoly_scheme ...atom_site / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_seq_id / _struct_site_gen.auth_asym_id / _struct_site_gen.auth_seq_id
Revision 2.1Oct 2, 2019Group: Data collection / Other / Category: atom_sites / cell
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.length_a / _cell.length_b / _cell.length_c
Revision 2.2Oct 23, 2019Group: Data collection / Other / Category: cell / Item: _cell.Z_PDB

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Structure visualization

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Assembly

Deposited unit
a: ATP synthase subunit a, chloroplastic
b: ATP synthase subunit b, chloroplastic
d: ATP synthase delta chain, chloroplastic
p: ATP synthase subunit b', chloroplastic
e: ATP synthase epsilon chain, chloroplastic
g: ATP synthase gamma chain, chloroplastic
S: ATP synthase subunit c, chloroplastic
N: ATP synthase subunit c, chloroplastic
O: ATP synthase subunit c, chloroplastic
P: ATP synthase subunit c, chloroplastic
Q: ATP synthase subunit c, chloroplastic
R: ATP synthase subunit c, chloroplastic
M: ATP synthase subunit c, chloroplastic
T: ATP synthase subunit c, chloroplastic
G: ATP synthase subunit c, chloroplastic
H: ATP synthase subunit c, chloroplastic
L: ATP synthase subunit c, chloroplastic
K: ATP synthase subunit c, chloroplastic
J: ATP synthase subunit c, chloroplastic
I: ATP synthase subunit c, chloroplastic
E: ATP synthase subunit alpha, chloroplastic
F: ATP synthase subunit beta, chloroplastic
A: ATP synthase subunit alpha, chloroplastic
B: ATP synthase subunit beta, chloroplastic
C: ATP synthase subunit alpha, chloroplastic
D: ATP synthase subunit beta, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)597,23636
Polymers594,73826
Non-polymers2,49710
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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ATP synthase ... , 9 types, 26 molecules abdpegSNOPQRMTGHLKJIEACFBD

#1: Protein ATP synthase subunit a, chloroplastic / / ATP synthase F0 sector subunit a / F-ATPase subunit IV


Mass: 27102.680 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P06451
#2: Protein ATP synthase subunit b, chloroplastic / / ATP synthase F(0) sector subunit b / ATPase subunit I


Mass: 21013.904 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P06453
#3: Protein ATP synthase delta chain, chloroplastic / F-ATPase delta chain


Mass: 27708.582 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P11402
#4: Protein ATP synthase subunit b', chloroplastic / / ATP synthase F(0) sector subunit b' / ATPase subunit II


Mass: 24487.596 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P31853
#5: Protein ATP synthase epsilon chain, chloroplastic / ATP synthase F1 sector epsilon subunit / F-ATPase epsilon subunit


Mass: 14715.707 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P00833
#6: Protein ATP synthase gamma chain, chloroplastic / F-ATPase gamma subunit


Mass: 40119.066 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P05435
#7: Protein
ATP synthase subunit c, chloroplastic / / ATP synthase F(0) sector subunit c / ATPase subunit III / F-type ATPase subunit c / F-ATPase ...ATP synthase F(0) sector subunit c / ATPase subunit III / F-type ATPase subunit c / F-ATPase subunit c / Lipid-binding protein


Mass: 7977.366 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P69447
#8: Protein ATP synthase subunit alpha, chloroplastic / / ATP synthase F1 sector subunit alpha / F-ATPase subunit alpha


Mass: 55505.199 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach)
References: UniProt: P06450, H+-transporting two-sector ATPase
#9: Protein ATP synthase subunit beta, chloroplastic / / ATP synthase F1 sector subunit beta / F-ATPase subunit beta


Mass: 53797.367 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach)
References: UniProt: P00825, H+-transporting two-sector ATPase

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Non-polymers , 3 types, 10 molecules

#10: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#11: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#12: 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: Chloroplast ATP synthase / Type: COMPLEX / Entity ID: #1-#9 / Source: NATURAL
Molecular weightValue: 0.6 MDa
Source (natural)Organism: Spinacia oleracea (spinach)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
130 mMHEPES1
22 mMMgCl21
30.5 mMEDTAEthylenediaminetetraacetic acid1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 70 % / Chamber temperature: 283 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: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 75000 X / Calibrated magnification: 132953 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm / Calibrated defocus min: 1500 nm / Calibrated defocus max: 2500 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 62 sec. / Electron dose: 25 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of real images: 6254

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Processing

SoftwareName: PHENIX / Version: 1.12_2829: / Classification: refinement
EM software
IDNameVersionCategory
1RELION2particle selection
2EPUimage acquisition
4CTFFIND4CTF correction
9RELION2.1initial Euler assignment
10RELION2.1final Euler assignment
11RELION2.1classification
12RELION2.13D reconstruction
EM 3D crystal entity∠α: 90 ° / ∠β: 90 ° / ∠γ: 90 ° / A: 1 Å / B: 1 Å / C: 1 Å / Space group name: P1 / Space group num: 1
CTF correctionType: PHASE FLIPPING ONLY
Particle selectionNum. of particles selected: 670614
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 14409 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Details: rigid body fit from structure build in complex in conformation 1
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01727823
ELECTRON MICROSCOPYf_angle_d1.25137702
ELECTRON MICROSCOPYf_dihedral_angle_d8.40217061
ELECTRON MICROSCOPYf_chiral_restr0.0734438
ELECTRON MICROSCOPYf_plane_restr0.0084901

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