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- PDB-22vl: Cryo-EM structure of Chlamydomonas reinhardtii chloroplast F1Fo-A... -

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Basic information

Entry
Database: PDB / ID: 22vl
TitleCryo-EM structure of Chlamydomonas reinhardtii chloroplast F1Fo-ATP synthase
Components(ATP synthase ...) x 10
KeywordsELECTRON TRANSPORT / Chlamydomonas reinhardtii / chloroplast / F1Fo-ATP synthase
Function / homology
Function and homology information


proton transmembrane transporter activity / proton motive force-driven ATP synthesis / chloroplast thylakoid membrane / proton-transporting two-sector ATPase complex, proton-transporting domain / proton motive force-driven mitochondrial ATP synthesis / H+-transporting two-sector ATPase / proton-transporting ATP synthase complex / proton-transporting ATP synthase activity, rotational mechanism / ADP binding / lipid binding ...proton transmembrane transporter activity / proton motive force-driven ATP synthesis / chloroplast thylakoid membrane / proton-transporting two-sector ATPase complex, proton-transporting domain / proton motive force-driven mitochondrial ATP synthesis / H+-transporting two-sector ATPase / proton-transporting ATP synthase complex / proton-transporting ATP synthase activity, rotational mechanism / ADP binding / lipid binding / mitochondrion / 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. ...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, alpha subunit nucleotide-binding domain / 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 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 / C-terminal domain of V and A type ATP synthase / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain superfamily / ATP synthase subunit alpha, N-terminal domain-like 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'-TRIPHOSPHATE / ATP synthase subunit b', chloroplastic / ATP synthase subunit a, chloroplastic / ATP synthase subunit beta, chloroplastic / ATP synthase epsilon chain, chloroplastic / ATP synthase gamma chain, chloroplastic / ATP synthase subunit alpha, chloroplastic / ATP synthase subunit c, chloroplastic / ATP synthase delta chain, chloroplastic / ATP synthase subunit b, chloroplastic
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsLiu, J. / Li, D.Y. / Guan, Z.Y. / Yin, P. / Yan, J.J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Biochem Biophys Res Commun / Year: 2026
Title: Cryo-EM structure of Chlamydomonas reinhardtii chloroplast FF-ATP synthase.
Authors: Jian Liu / Danyang Li / Qiang Wang / Ping Yin / Zeyuan Guan / Junjie Yan /
Abstract: FF-ATP synthase is a multi-subunit energy-producing macromolecular machine, consisting of hydrophilic F and hydrophobic F segments, which utilize transmembrane electrochemical potential to synthesize ...FF-ATP synthase is a multi-subunit energy-producing macromolecular machine, consisting of hydrophilic F and hydrophobic F segments, which utilize transmembrane electrochemical potential to synthesize ATP from ADP and inorganic phosphate. ATP synthases are widely distributed in the inner membrane of mitochondria, the thylakoid membrane of chloroplasts, and the plasma membrane of bacteria. To date, a comprehensively structural study on chloroplast FF-ATP synthase is very limited compared with their counterparts in mitochondria and bacteria. In this study, we in-situ extracted and purified chloroplast FF-ATP synthase from the photosynthetic unicellular green algae Chlamydomonas reinhardtii. The ATPase activity of the holoenzyme was validated by a combination of BN-PAGE separation and in-gel detection. We determined the structure of Chlamydomonas reinhardtii FF-ATP synthase at 3.2 Å resolution using single particle cryo-electron microscopy (cryo-EM). The structure is in an oxidized state with a disulfide bond formation in the γ subunit. More acidic residues were found to be involved in the proton translocation across the F segment compared with their counterparts of the higher plants. Overall, the structure presented here provides novel structural information, giving us comprehensive understanding of the photosynthetic chloroplast FF-ATP synthase from lower unicellular algae to higher plants.
History
DepositionJan 25, 2026Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 17, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)547,33734
Polymers544,72826
Non-polymers2,6098
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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ATP synthase ... , 10 types, 26 molecules apDdbeMFGHIJKLNOPQRSAVBETU

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


Mass: 24538.498 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: O63075
#2: Protein ATP synthase subunit b', chloroplastic / ATP synthase F(0) sector subunit b' / ATPase subunit II


Mass: 14161.326 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8J785
#3: Protein ATP synthase gamma chain, chloroplastic / F-ATPase gamma subunit


Mass: 35283.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P12113
#4: Protein ATP synthase delta chain, chloroplastic / F-ATPase delta chain


Mass: 19165.072 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q42687
#5: Protein ATP synthase subunit b, chloroplastic / ATP synthase F(0) sector subunit b / ATPase subunit I


Mass: 17584.096 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q8HTL5
#6: Protein ATP synthase epsilon chain, chloroplastic / ATP synthase F1 sector epsilon subunit / F-ATPase epsilon subunit


Mass: 14807.804 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P07891
#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: 7793.086 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q37304
#8: Protein ATP synthase subunit alpha, chloroplastic / ATP synthase F1 sector subunit alpha / F-ATPase subunit alpha


Mass: 51999.223 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant)
References: UniProt: P26526, H+-transporting two-sector ATPase
#9: Protein ATP synthase subunit alpha, chloroplastic / ATP synthase F1 sector subunit alpha / F-ATPase subunit alpha


Mass: 51798.965 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant)
References: UniProt: P26526, H+-transporting two-sector ATPase
#10: Protein ATP synthase subunit beta, chloroplastic / ATP synthase F1 sector subunit beta / F-ATPase subunit beta


Mass: 51428.941 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant)
References: UniProt: P06541, H+-transporting two-sector ATPase

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Non-polymers , 2 types, 8 molecules

#11: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#12: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM

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Details

Has ligand of interestN
Has protein modificationN

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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: F1Fo-ATP synthase / Type: COMPLEX / Entity ID: #8, #1-#3, #10, #4-#7 / Source: NATURAL
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Buffer solutionpH: 8
SpecimenConc.: 8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: TFS TALOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 53.68 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
11cryoSPARC3.1final Euler assignment
13cryoSPARC3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 64764 / Symmetry type: POINT
RefinementHighest resolution: 3.2 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00338973
ELECTRON MICROSCOPYf_angle_d0.59652837
ELECTRON MICROSCOPYf_dihedral_angle_d7.0985649
ELECTRON MICROSCOPYf_chiral_restr0.0426248
ELECTRON MICROSCOPYf_plane_restr0.0056787

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