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- PDB-6j5a: Cryo-EM structure of the mammalian DP-state ATP synthase FO section -
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Basic information
Entry | Database: PDB / ID: 6j5a | ||||||||||||
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Title | Cryo-EM structure of the mammalian DP-state ATP synthase FO section | ||||||||||||
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Function / homology | ![]() Formation of ATP by chemiosmotic coupling / Cristae formation / mitochondrial proton-transporting ATP synthase complex, coupling factor F(o) / proton-transporting ATP synthase complex, coupling factor F(o) / mitochondrial proton-transporting ATP synthase complex / proton motive force-driven ATP synthesis / proton transmembrane transporter activity / proton motive force-driven mitochondrial ATP synthesis / proton transmembrane transport / proton-transporting ATP synthase activity, rotational mechanism ...Formation of ATP by chemiosmotic coupling / Cristae formation / mitochondrial proton-transporting ATP synthase complex, coupling factor F(o) / proton-transporting ATP synthase complex, coupling factor F(o) / mitochondrial proton-transporting ATP synthase complex / proton motive force-driven ATP synthesis / proton transmembrane transporter activity / proton motive force-driven mitochondrial ATP synthesis / proton transmembrane transport / proton-transporting ATP synthase activity, rotational mechanism / ![]() ![]() Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Gu, J. / Zhang, L. / Yi, J. / Yang, M. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Cryo-EM structure of the mammalian ATP synthase tetramer bound with inhibitory protein IF1. Authors: Jinke Gu / Laixing Zhang / Shuai Zong / Runyu Guo / Tianya Liu / Jingbo Yi / Peiyi Wang / Wei Zhuo / Maojun Yang / ![]() Abstract: The mitochondrial adenosine triphosphate (ATP) synthase produces most of the ATP required by mammalian cells. We isolated porcine tetrameric ATP synthase and solved its structure at 6.2-angstrom ...The mitochondrial adenosine triphosphate (ATP) synthase produces most of the ATP required by mammalian cells. We isolated porcine tetrameric ATP synthase and solved its structure at 6.2-angstrom resolution using a single-particle cryo-electron microscopy method. Two classical V-shaped ATP synthase dimers lie antiparallel to each other to form an H-shaped ATP synthase tetramer, as viewed from the matrix. ATP synthase inhibitory factor subunit 1 (IF1) is a well-known in vivo inhibitor of mammalian ATP synthase at low pH. Two IF1 dimers link two ATP synthase dimers, which is consistent with the ATP synthase tetramer adopting an inhibited state. Within the tetramer, we refined structures of intact ATP synthase in two different rotational conformations at 3.34- and 3.45-Å resolution. | ||||||||||||
History |
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Structure visualization
Movie |
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 202 KB | Display | ![]() |
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PDB format | ![]() | 161 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 0670MC ![]() 0667C ![]() 0668C ![]() 0669C ![]() 0677C ![]() 6j54C ![]() 6j5iC ![]() 6j5jC ![]() 6j5kC M: map data used to model this data C: citing same article ( |
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Similar structure data | |
EM raw data | ![]() Data size: 141.3 Data #1: Averaged micrographs of mammalian ATP synthase tetramer [micrographs - single frame]) |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Components
-ATP synthase ... , 9 types, 9 molecules bdefgi8au
#1: Protein | Mass: 8886.416 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() |
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#2: Protein/peptide | ![]() Mass: 2933.330 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() |
#3: Protein | ![]() Mass: 5379.623 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() |
#4: Protein | ![]() Mass: 10197.959 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() |
#5: Protein | ![]() Mass: 7166.825 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() |
#6: Protein/peptide | Mass: 4861.770 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() |
#8: Protein/peptide | ![]() Mass: 3577.193 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() |
#9: Protein | ![]() Mass: 25054.143 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() |
#11: Protein/peptide | Mass: 3592.419 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() |
-Protein/peptide / Protein , 2 types, 9 molecules kKLMNOPQR
#10: Protein | Mass: 7311.631 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() #7: Protein/peptide | | Mass: 2486.056 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() |
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-Details
Sequence details | The sequence of the chain e corresponds to Q03654 in the UniProt database. The sequence of the ...The sequence of the chain e corresponds to Q03654 in the UniProt database. The sequence of the chain g corresponds to A0A480XS10 in the UniProt database. The sequence of the chain u corresponds to F1S9V7 in the UniProt database. However, there are UNK (unknown residues) in these chains, as the authors do not know how the coordinates align with the sequences. Therefore the residues numbers are meaningless. As for k chain, the authors don’t know the reference sequence in the UniProt database. |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: ![]() |
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Sample preparation
Component | Name: Cryo-EM structure of the mammalian DP-state ATP synthase FO section Type: COMPLEX / Entity ID: all / Source: NATURAL |
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Source (natural) | Organism: ![]() ![]() ![]() |
Buffer solution | pH: 7 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied![]() ![]() |
Vitrification![]() | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source![]() ![]() |
Electron lens | Mode: BRIGHT FIELD![]() |
Image recording | Electron dose: 1.56 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
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Processing
CTF correction![]() | Type: NONE |
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3D reconstruction![]() | Resolution: 4.35 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 114103 / Symmetry type: POINT |