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- PDB-5fl7: Structure of the F1c10 complex from Yarrowia lipolytica ATP synthase -

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Basic information

Entry
Database: PDB / ID: 5fl7
TitleStructure of the F1c10 complex from Yarrowia lipolytica ATP synthase
Components(ATP SYNTHASE ...) x 6
KeywordsHYDROLASE / ATP SYNTHASE FAMILY / NUCLEOTIDE BINDING / PROTON TRANSPORTING / ROTATIONAL MECHANISM / ATP BIOSYNTHETIC PROCESS / ATP SYNTHESIS/HYDROLYSIS
Function / homology
Function and homology information


mitochondrial proton-transporting ATP synthase complex, coupling factor F(o) / mitochondrial proton-transporting ATP synthase complex / mitochondrial proton-transporting ATP synthase complex, catalytic sector F(1) / 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 ...mitochondrial proton-transporting ATP synthase complex, coupling factor F(o) / mitochondrial proton-transporting ATP synthase complex / mitochondrial proton-transporting ATP synthase complex, catalytic sector F(1) / 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 / mitochondrial inner membrane / membrane => GO:0016020 / lipid binding / ATP binding / plasma membrane
Similarity search - Function
ATP Synthase; domain 1 / F0F1 ATP synthase delta/epsilon subunit, N-terminal / ATP synthase, F1 complex, gamma subunit / ATP synthase alpha/beta chain, C-terminal domain / F1F0 ATP synthase subunit C / F1FO ATP Synthase / Lysin / Thrombin, subunit H - #170 / Elongation Factor Tu (Ef-tu); domain 3 - #20 / Pyruvate Kinase; Chain: A, domain 1 ...ATP Synthase; domain 1 / F0F1 ATP synthase delta/epsilon subunit, N-terminal / ATP synthase, F1 complex, gamma subunit / ATP synthase alpha/beta chain, C-terminal domain / F1F0 ATP synthase subunit C / F1FO ATP Synthase / Lysin / Thrombin, subunit H - #170 / Elongation Factor Tu (Ef-tu); domain 3 - #20 / Pyruvate Kinase; Chain: A, domain 1 / Bovine Mitochondrial F1-ATPase, ATP Synthase Beta Chain; Chain D, domain3 / Bovine Mitochondrial F1-atpase; Atp Synthase Beta Chain; Chain D, domain 3 / ATP synthase, gamma subunit, helix hairpin domain / 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 / Elongation Factor Tu (Ef-tu); domain 3 / Helix Hairpins / Thrombin, subunit H / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Up-down Bundle / Beta Barrel / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / ATP synthase subunit 9, mitochondrial / ATP synthase subunit alpha, mitochondrial / ATP synthase subunit gamma, mitochondrial / ATP synthase subunit delta, mitochondrial / ATP synthase subunit beta, mitochondrial
Similarity search - Component
Biological speciesYARROWIA LIPOLYTICA (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsParey, K. / Bublitz, M. / Meier, T.
CitationJournal: 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
DepositionOct 22, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2016Group: Database references
Revision 1.2Aug 24, 2016Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATP SYNTHASE SUBUNIT ALPHA
B: ATP SYNTHASE SUBUNIT ALPHA
C: ATP SYNTHASE SUBUNIT ALPHA
D: ATP SYNTHASE SUBUNIT BETA
E: ATP SYNTHASE SUBUNIT BETA
F: ATP SYNTHASE SUBUNIT BETA
G: ATP SYNTHASE SUBUNIT GAMMA CHAIN, MITOCHONDRIAL
H: ATP SYNTHASE DELTA CHAIN, MITOCHONDRIAL
I: ATP SYNTHASE EPSILON CHAIN, MITOCHONDRIAL
K: ATP SYNTHASE SUBUNIT 9, MITOCHONDRIAL
L: ATP SYNTHASE SUBUNIT 9, MITOCHONDRIAL
M: ATP SYNTHASE SUBUNIT 9, MITOCHONDRIAL
N: ATP SYNTHASE SUBUNIT 9, MITOCHONDRIAL
O: ATP SYNTHASE SUBUNIT 9, MITOCHONDRIAL
P: ATP SYNTHASE SUBUNIT 9, MITOCHONDRIAL
Q: ATP SYNTHASE SUBUNIT 9, MITOCHONDRIAL
R: ATP SYNTHASE SUBUNIT 9, MITOCHONDRIAL
S: ATP SYNTHASE SUBUNIT 9, MITOCHONDRIAL
T: ATP SYNTHASE SUBUNIT 9, MITOCHONDRIAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)466,47529
Polymers463,97719
Non-polymers2,49710
Water30617
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)169.500, 182.200, 193.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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ATP SYNTHASE ... , 6 types, 19 molecules ABCDEFGHIKLMNOPQRST

#1: Protein ATP SYNTHASE SUBUNIT ALPHA / / ATP SYNTHASE SUBUNIT ALPHA / MITOCHONDRIAL


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 ATP SYNTHASE SUBUNIT BETA / / ATP SYNTHASE SUBUNIT BETA / MITOCHONDRIAL


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 ATP SYNTHASE SUBUNIT GAMMA CHAIN, MITOCHONDRIAL /


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 ATP SYNTHASE DELTA CHAIN, MITOCHONDRIAL


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 ATP SYNTHASE EPSILON CHAIN, MITOCHONDRIAL


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
ATP SYNTHASE SUBUNIT 9, MITOCHONDRIAL / / LIPID-BINDING PROTEIN / OLIGOMYCIN RESISTANCE PROTEIN 1


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 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
#8: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#9: 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
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsCHAIN I NOT ANNOTATED IN THE UNIPROT DATABANK

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 47 % / Description: NONE
Crystal growpH: 8 / Details: 100 MM TRIS-HCL, POLYETHYLENE GLYCOL 400, pH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00774
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 5, 2015 / Details: MIRRORS
RadiationMonochromator: SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00774 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 3.5→3.6 Å / Redundancy: 19.8 % / Mean I/σ(I) obs: 0.61 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XOK

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
RfactorNum. reflection% reflection
Rfree0.3054 1897 2.5 %
Rwork0.2739 --
obs0.2747 75790 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 166.52 Å2
Refinement stepCycle: LAST / Resolution: 3.5→49.366 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29950 0 152 17 30119
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00430573
X-RAY DIFFRACTIONf_angle_d0.44841382
X-RAY DIFFRACTIONf_dihedral_angle_d8.1218311
X-RAY DIFFRACTIONf_chiral_restr0.0394901
X-RAY DIFFRACTIONf_plane_restr0.0035326
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-3.58750.38991470.39565181X-RAY DIFFRACTION100
3.5875-3.68450.39711150.37335233X-RAY DIFFRACTION100
3.6845-3.79290.40181470.35525227X-RAY DIFFRACTION100
3.7929-3.91520.38061240.32325191X-RAY DIFFRACTION100
3.9152-4.05510.37361450.3195223X-RAY DIFFRACTION100
4.0551-4.21740.31831300.29935256X-RAY DIFFRACTION100
4.2174-4.40920.30551270.27055225X-RAY DIFFRACTION100
4.4092-4.64150.33481390.25525263X-RAY DIFFRACTION100
4.6415-4.93210.27921300.25225279X-RAY DIFFRACTION100
4.9321-5.31250.31861390.27715259X-RAY DIFFRACTION100
5.3125-5.84630.35261350.28255310X-RAY DIFFRACTION100
5.8463-6.69050.32831420.28295300X-RAY DIFFRACTION100
6.6905-8.42250.31251350.25065378X-RAY DIFFRACTION100
8.4225-49.37110.24881420.25425568X-RAY DIFFRACTION100

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