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Yorodumi- PDB-5fl7: Structure of the F1c10 complex from Yarrowia lipolytica ATP synthase -
+Open data
-Basic information
Entry | Database: PDB / ID: 5fl7 | ||||||
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Title | Structure of the F1c10 complex from Yarrowia lipolytica ATP synthase | ||||||
Components | (ATP SYNTHASE ...) x 6 | ||||||
Keywords | HYDROLASE / ATP SYNTHASE FAMILY / NUCLEOTIDE BINDING / PROTON TRANSPORTING / ROTATIONAL MECHANISM / ATP BIOSYNTHETIC PROCESS / ATP SYNTHESIS/HYDROLYSIS | ||||||
Function / homology | Function and homology information : / : / proton-transporting ATP synthase complex, coupling factor F(o) / : / proton transmembrane transporter activity / proton motive force-driven ATP synthesis / 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 ...: / : / proton-transporting ATP synthase complex, coupling factor F(o) / : / proton transmembrane transporter activity / proton motive force-driven ATP synthesis / 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 / proton motive force-driven mitochondrial ATP synthesis / ADP binding / membrane => GO:0016020 / mitochondrial inner membrane / lipid binding / ATP binding / plasma membrane Similarity search - Function | ||||||
Biological species | YARROWIA LIPOLYTICA (yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å | ||||||
Authors | Parey, K. / Bublitz, M. / Meier, T. | ||||||
Citation | Journal: Mol Cell / Year: 2016 Title: Structure of a Complete ATP Synthase Dimer Reveals the Molecular Basis of Inner Mitochondrial Membrane Morphology. Authors: Alexander Hahn / Kristian Parey / Maike Bublitz / Deryck J Mills / Volker Zickermann / Janet Vonck / Werner Kühlbrandt / Thomas Meier / Abstract: We determined the structure of a complete, dimeric F1Fo-ATP synthase from yeast Yarrowia lipolytica mitochondria by a combination of cryo-EM and X-ray crystallography. The final structure resolves 58 ...We determined the structure of a complete, dimeric F1Fo-ATP synthase from yeast Yarrowia lipolytica mitochondria by a combination of cryo-EM and X-ray crystallography. The final structure resolves 58 of the 60 dimer subunits. Horizontal helices of subunit a in Fo wrap around the c-ring rotor, and a total of six vertical helices assigned to subunits a, b, f, i, and 8 span the membrane. Subunit 8 (A6L in human) is an evolutionary derivative of the bacterial b subunit. On the lumenal membrane surface, subunit f establishes direct contact between the two monomers. Comparison with a cryo-EM map of the F1Fo monomer identifies subunits e and g at the lateral dimer interface. They do not form dimer contacts but enable dimer formation by inducing a strong membrane curvature of ∼100°. Our structure explains the structural basis of cristae formation in mitochondria, a landmark signature of eukaryotic cell morphology. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 10-STRANDED BARREL THIS IS REPRESENTED BY A 11-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "DA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "EA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5fl7.cif.gz | 748.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fl7.ent.gz | 609.9 KB | Display | PDB format |
PDBx/mmJSON format | 5fl7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5fl7_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 5fl7_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 5fl7_validation.xml.gz | 131.4 KB | Display | |
Data in CIF | 5fl7_validation.cif.gz | 177.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fl/5fl7 ftp://data.pdbj.org/pub/pdb/validation_reports/fl/5fl7 | HTTPS FTP |
-Related structure data
Related structure data | 8151C 8152C 8153C 8154C 8155C 2xokS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-ATP SYNTHASE ... , 6 types, 19 molecules ABCDEFGHIKLMNOPQRST
#1: Protein | Mass: 58147.430 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) YARROWIA LIPOLYTICA (yeast) / References: UniProt: Q6C326 #2: Protein | Mass: 54590.828 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) YARROWIA LIPOLYTICA (yeast) References: UniProt: Q6CFT7, H+-transporting two-sector ATPase #3: Protein | | Mass: 32378.797 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) YARROWIA LIPOLYTICA (yeast) / References: UniProt: Q6C338, EC: 3.6.1.34 #4: Protein | | Mass: 14811.274 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) YARROWIA LIPOLYTICA (yeast) / References: UniProt: Q6C877, EC: 3.6.1.34 #5: Protein/peptide | | Mass: 1379.692 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) YARROWIA LIPOLYTICA (yeast) / References: EC: 3.6.1.34 #6: Protein | Mass: 7719.265 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Source: (natural) YARROWIA LIPOLYTICA (yeast) References: UniProt: Q37695, H+-transporting two-sector ATPase |
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-Non-polymers , 4 types, 27 molecules
#7: Chemical | #8: Chemical | ChemComp-MG / #9: Chemical | #10: Water | ChemComp-HOH / | |
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-Details
Sequence details | CHAIN I NOT ANNOTATED IN THE UNIPROT DATABANK |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47 % / Description: NONE |
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Crystal grow | pH: 8 / Details: 100 MM TRIS-HCL, POLYETHYLENE GLYCOL 400, pH 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00774 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 5, 2015 / Details: MIRRORS |
Radiation | Monochromator: SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00774 Å / Relative weight: 1 |
Reflection | Resolution: 3.5→49.19 Å / Num. obs: 75882 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 19.47 % / Biso Wilson estimate: 157.51 Å2 / Rmerge(I) obs: 0.18 / Net I/σ(I): 9.84 |
Reflection shell | Resolution: 3.5→3.6 Å / Redundancy: 19.8 % / Mean I/σ(I) obs: 0.61 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2XOK Resolution: 3.5→49.366 Å / SU ML: 0.64 / σ(F): 1.34 / Phase error: 38.06 / Stereochemistry target values: ML Details: THE FOLLOWING RESIDUES ARE DISORDERED AND HAVE NOT BEEN MODELLED CHAIN A 1-48 534- -536 CHAIN B 1-48 429-434 534-536 CHAIN C 1-48 534-536 CHAIN D 1-36 507-510 CHAIN E 1-38 507-510 CHAIN F 1- ...Details: THE FOLLOWING RESIDUES ARE DISORDERED AND HAVE NOT BEEN MODELLED CHAIN A 1-48 534- -536 CHAIN B 1-48 429-434 534-536 CHAIN C 1-48 534-536 CHAIN D 1-36 507-510 CHAIN E 1-38 507-510 CHAIN F 1-36 507-510 CHAIN G 1-22 117-119 293 CHAIN H 1-14 95-100 134- -136 CHAIN I WAS MODELLED AND REFINED AS POLY-ALANINE CHAIN K 1 75-76 CHAIN L 1 74-76 CHAIN M 1 CHAIN N 76 CHAIN O 1 CHAIN P 76 CHAIN R 1 76 CHAIN S 1 76 CHAIN T 1 76
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 166.52 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.5→49.366 Å
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Refine LS restraints |
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LS refinement shell |
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