6FKF

Chloroplast F1Fo conformation 1


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.15 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure, mechanism, and regulation of the chloroplast ATP synthase.

Hahn, A.Vonck, J.Mills, D.J.Meier, T.Kuhlbrandt, W.

(2018) Science 360: --

  • DOI: 10.1126/science.aat4318
  • Primary Citation of Related Structures:  

  • PubMed 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 membrane-embedded F <sub>o </sub> motor drive A ...

    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 o motor drive ATP synthesis in the F 1 head by rotary catalysis. We determined the high-resolution structure of the complete cF 1 F o complex by cryo-electron microscopy, resolving side chains of all 26 protein subunits, the five nucleotides in the F 1 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.


    Organizational Affiliation

    School of Biological Sciences, The University of Auckland, Auckland, New Zealand.,RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan.,Department of Chemical Engineering and Applied Chemistry, Chungnam National University, Daejeon, 34134, Republic of Korea.,Department of Molecular Medicine and Pathology, The University of Auckland, Auckland, New Zealand.,Department of Medicine, Division of Infectious Diseases, Albert Einstein College of Medicine, Bronx, NY 10461; johanna.daily@einstein.yu.edu vern.schramm@einstein.yu.edu.,Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology, Daejeon, 34113, Republic of Korea. sglee@kribb.re.kr.,Department of Microbiology, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, Netherlands.,Experimental Therapeutics Centre, Agency for Science, Technology and Research (A(∗)STAR), 31 Biopolis way, Nanos, #03-01, Singapore 138669, Singapore; Lee Kong Chian School of Medicine, Nanyang Technological University, EMB 03-07, 59 Nanyang Drive, Singapore 636921, Singapore. Electronic address: knacro@etc.a-star.edu.sg.,Vollum Institute, Oregon Health and Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA.,Lee Kong Chian School of Medicine, Nanyang Technological University, EMB 03-07, 59 Nanyang Drive, Singapore 636921, Singapore; NTU Institute of Structural Biology, Nanyang Technological University, EMB 06-01, 59 Nanyang Drive, Singapore 636921, Singapore. Electronic address: luodahai@ntu.edu.sg.,Brigham and Women's Hospital Division of Rheumatology, Immunology and Allergy and Harvard Medical School, Boston, MA, 02115, USA. I.vanRhijn@uu.nl.,Ipsen Bioinnovation, 102 Park Drive, Milton Park, Abingdon OX14 4RY, UK.,Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool L69 7ZB, UK.,Lee Kong Chian School of Medicine, Nanyang Technological University, EMB 03-07, 59 Nanyang Drive, Singapore 636921, Singapore; NTU Institute of Structural Biology, Nanyang Technological University, EMB 06-01, 59 Nanyang Drive, Singapore 636921, Singapore.,Experimental Therapeutics Centre, Agency for Science, Technology and Research (A(∗)STAR), 31 Biopolis way, Nanos, #03-01, Singapore 138669, Singapore. Electronic address: cbkang@etc.a-star.edu.sg.,Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori, Ako, Hyogo 678-1297, Japan. yshiro@sci.u-hyogo.ac.jp sawai@sci.u-hyogo.ac.jp.,Vollum Institute, Oregon Health and Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA. gouauxe@ohsu.edu.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, VIC, 3800, Australia. Jamie.rossjohn@monash.edu.,Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany.,Department of Urology, Boston Children's Hospital, Department of Microbiology and Immunobiology and Department of Surgery, Harvard Medical School, Boston, MA 02115, USA.,Department of Microbiology and Immunology, Emory University School of Medicine, 1510 Clifton Road, Atlanta, GA, 30322, USA.,Integrative Omics, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA.,Faculty of Chemistry, Philipps-University Marburg, Hans-Meerwein-Straße 4, 35032, Marburg, Germany.,National Institute of Child Health and Human Development, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD, 20892, USA.,Department of Early Discovery Biochemistry, Genentech, South San Francisco, CA, USA.,Institute of Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, 35032, Marburg, Germany.,Department of Biochemistry and Biophysics, Stockholm University, Stockholm SE-106 91, Sweden.,Experimental Therapeutics Centre, Agency for Science, Technology and Research (A(∗)STAR), 31 Biopolis way, Nanos, #03-01, Singapore 138669, Singapore.,Department of Biophysics, Ruhr University Bochum, 44801 Bochum, Germany.,Ipsen Innovation, 5 Avenue du Canada, 91940 Les Ulis, France.,Institute of Infection and Immunity, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK. Jamie.rossjohn@monash.edu.,Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461.,Synthetic Biology and Bioengineering Research Center, KRIBB, Daejeon, 34141, Republic of Korea.,Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany; baumeist@biochem.mpg.de.,School of Biological Sciences, The University of Auckland, Auckland, New Zealand p.young@auckland.ac.nz n.moreland@auckland.ac.nz.,Department of Pathology, Genentech, South San Francisco, CA, USA.,Department of Pathology and Laboratory Medicine, University of Kansas School of Medicine, Kansas City, KS, USA.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, VIC, 3800, Australia.,Department of Molecular Biology, Genentech, South San Francisco, CA, USA.,Department of Biomolecular Resources, Genentech, South San Francisco, CA, USA.,Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology, Daejeon, 34113, Republic of Korea.,Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584CL, Utrecht, The Netherlands. I.vanRhijn@uu.nl.,Maurice Wilkins Centre, The University of Auckland, Auckland, New Zealand p.young@auckland.ac.nz n.moreland@auckland.ac.nz.,Maurice Wilkins Centre, The University of Auckland, Auckland, New Zealand.,Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia. Jamie.rossjohn@monash.edu.,Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany.,Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461; johanna.daily@einstein.yu.edu vern.schramm@einstein.yu.edu.,Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, USA. sylviegtsodikova@uky.edu.,Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, USA. oleg.tsodikov@uky.edu.,Institute of Organic Chemistry, Justus-Liebig University, Heinrich-Buff-Ring 17, 35392, Giessen, Germany.,Department of Early Discovery Biochemistry, Genentech, South San Francisco, CA, USA. hannoush.rami@gene.com.,Department of Molecular Oncology, Genentech, South San Francisco, CA, USA.,Department of Bioinformatics and Computational Biology, Genentech, South San Francisco, CA, USA.,Department of Experimental Medical Science, Lund University, 221 00 Lund, Sweden.,MRC Laboratory of Molecular Biology, Cambridge, UK. mg@mrc-lmb.cam.ac.uk.,Howard Hughes Medical Institute, Oregon Health and Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA.,Brigham and Women's Hospital Division of Rheumatology, Immunology and Allergy and Harvard Medical School, Boston, MA, 02115, USA.,Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA.,Department of Pharmaceutical Sciences, University of Toronto, Toronto, Ontario, Canada.,Department of Structural Biology, Max Planck Institute of Biophysics, Max-von-Laue-Strasse 3, 60438 Frankfurt am Main, Germany. werner.kuehlbrandt@biophys.mpg.de t.meier@imperial.ac.uk.,Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia.,Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, NY 10461.,Department of Structural Biology, Max Planck Institute of Biophysics, Max-von-Laue-Strasse 3, 60438 Frankfurt am Main, Germany.,Department of Structural Biology, Genentech, South San Francisco, CA, USA.,Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori, Ako, Hyogo 678-1297, Japan.,Synthetic Biology and Bioengineering Research Center, KRIBB, Daejeon, 34141, Republic of Korea. sglee@kribb.re.kr.,MRC Laboratory of Molecular Biology, Cambridge, UK.,Lee Kong Chian School of Medicine, Nanyang Technological University, EMB 03-07, 59 Nanyang Drive, Singapore 636921, Singapore; NTU Institute of Structural Biology, Nanyang Technological University, EMB 06-01, 59 Nanyang Drive, Singapore 636921, Singapore; School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 636921, Singapore.,Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, USA.,Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, Université Paul Sabatier, 31077, Toulouse, France.,Stratingh Institute for Chemistry, University of Groningen, 9747AG, Groningen, The Netherlands.,Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584CL, Utrecht, The Netherlands.,MRC Laboratory of Molecular Biology, Cambridge, UK. scheres@mrc-lmb.cam.ac.uk.,Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ATP synthase subunit alpha, chloroplastic
A, C, E
507Spinacia oleraceaMutation(s): 0 
Gene Names: atpA
EC: 7.1.2.2
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
F-type ATPase
Protein: 
Rotor (c14) of H+-dependent F-ATP Synthase of spinach chloroplasts
Find proteins for P06450 (Spinacia oleracea)
Go to UniProtKB:  P06450
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ATP synthase subunit beta, chloroplastic
B, D, F
498Spinacia oleraceaMutation(s): 0 
Gene Names: atpB
EC: 7.1.2.2
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
F-type ATPase
Protein: 
Rotor (c14) of H+-dependent F-ATP Synthase of spinach chloroplasts
Find proteins for P00825 (Spinacia oleracea)
Go to UniProtKB:  P00825
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
ATP synthase gamma chain, chloroplastic
g
364Spinacia oleraceaMutation(s): 0 
Gene Names: ATPC
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
F-type ATPase
Protein: 
Rotor (c14) of H+-dependent F-ATP Synthase of spinach chloroplasts
Find proteins for P05435 (Spinacia oleracea)
Go to UniProtKB:  P05435
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
ATP synthase delta chain, chloroplastic
d
257Spinacia oleraceaMutation(s): 0 
Gene Names: ATPD
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
F-type ATPase
Protein: 
Rotor (c14) of H+-dependent F-ATP Synthase of spinach chloroplasts
Find proteins for P11402 (Spinacia oleracea)
Go to UniProtKB:  P11402
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
ATP synthase subunit b', chloroplastic
p
222Spinacia oleraceaMutation(s): 0 
Gene Names: ATPG
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
F-type ATPase
Protein: 
Rotor (c14) of H+-dependent F-ATP Synthase of spinach chloroplasts
Find proteins for P31853 (Spinacia oleracea)
Go to UniProtKB:  P31853
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
ATP synthase subunit b, chloroplastic
b
184Spinacia oleraceaMutation(s): 0 
Gene Names: atpF
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
F-type ATPase
Protein: 
Rotor (c14) of H+-dependent F-ATP Synthase of spinach chloroplasts
Find proteins for P06453 (Spinacia oleracea)
Go to UniProtKB:  P06453
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
ATP synthase subunit a, chloroplastic
a
247Spinacia oleraceaMutation(s): 0 
Gene Names: atpI
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
F-type ATPase
Protein: 
Rotor (c14) of H+-dependent F-ATP Synthase of spinach chloroplasts
Find proteins for P06451 (Spinacia oleracea)
Go to UniProtKB:  P06451
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
ATP synthase subunit c, chloroplastic
S, N, O, P, Q, R, M, T, G, H, L, K, J, I
81Spinacia oleraceaMutation(s): 0 
Gene Names: atpH
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
F-type ATPase
Protein: 
Rotor (c14) of H+-dependent F-ATP Synthase of spinach chloroplasts
Find proteins for P69447 (Spinacia oleracea)
Go to UniProtKB:  P69447
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
ATP synthase epsilon chain, chloroplastic
e
134Spinacia oleraceaMutation(s): 0 
Gene Names: atpE
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
F-type ATPase
Protein: 
Rotor (c14) of H+-dependent F-ATP Synthase of spinach chloroplasts
Find proteins for P00833 (Spinacia oleracea)
Go to UniProtKB:  P00833
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download SDF File 
Download CCD File 
A, C, E
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
ADP
Query on ADP

Download SDF File 
Download CCD File 
D, F
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, C, D, E, F
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.15 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-05-23
    Type: Initial release
  • Version 1.1: 2018-06-06
    Type: Advisory, Data collection, Derived calculations
  • Version 1.2: 2018-10-17
    Type: Data collection, Refinement description