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- PDB-4f4s: Structure of the yeast F1Fo ATPase c10 ring with bound oligomycin -

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Basic information

Entry
Database: PDB / ID: 4f4s
TitleStructure of the yeast F1Fo ATPase c10 ring with bound oligomycin
ComponentsATP synthase subunit 9, mitochondrial
KeywordsMEMBRANE PROTEIN/ANTIBIOTIC / c10 ring / F1Fo ATP synthase / Oligomycin / mitochondria / MEMBRANE PROTEIN-ANTIBIOTIC complex
Function / homology
Function and homology information


proton transmembrane transporter activity / proton motive force-driven ATP synthesis / proton-transporting two-sector ATPase complex, proton-transporting domain / proton-transporting ATP synthase complex / mitochondrial intermembrane space / mitochondrial inner membrane / lipid binding / mitochondrion / identical protein binding / cytosol
Similarity search - Function
F1F0 ATP synthase subunit C / F1FO ATP Synthase / 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. / V-ATPase proteolipid subunit C-like domain / F/V-ATP synthase subunit C superfamily / ATP synthase subunit C / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Oligomycin A / ATP synthase subunit 9, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.9 Å
AuthorsSymersky, J. / Mueller, D.M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Oligomycin frames a common drug-binding site in the ATP synthase.
Authors: Symersky, J. / Osowski, D. / Walters, D.E. / Mueller, D.M.
History
DepositionMay 11, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 15, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 22, 2012Group: Database references
Revision 1.2Sep 26, 2012Group: Database references
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Mar 13, 2024Group: Source and taxonomy / Category: pdbx_entity_src_syn
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATP synthase subunit 9, mitochondrial
B: ATP synthase subunit 9, mitochondrial
C: ATP synthase subunit 9, mitochondrial
D: ATP synthase subunit 9, mitochondrial
E: ATP synthase subunit 9, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,44117
Polymers77,90410
Non-polymers5,5377
Water2,702150
1
A: ATP synthase subunit 9, mitochondrial
B: ATP synthase subunit 9, mitochondrial
C: ATP synthase subunit 9, mitochondrial
D: ATP synthase subunit 9, mitochondrial
E: ATP synthase subunit 9, mitochondrial
hetero molecules

A: ATP synthase subunit 9, mitochondrial
B: ATP synthase subunit 9, mitochondrial
C: ATP synthase subunit 9, mitochondrial
D: ATP synthase subunit 9, mitochondrial
E: ATP synthase subunit 9, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,65016
Polymers77,90410
Non-polymers4,7466
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_655-x+1,-y,z1
Buried area32590 Å2
ΔGint-416 kcal/mol
Surface area23510 Å2
MethodPISA
2
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
hetero molecules

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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,23218
Polymers77,90410
Non-polymers6,3288
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_565-x,-y+1,z1
Buried area33230 Å2
ΔGint-419 kcal/mol
Surface area23650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.674, 75.674, 488.205
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein
ATP synthase subunit 9, mitochondrial / Lipid-binding protein / Oligomycin resistance protein 1


Mass: 7790.385 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: OLI1, ATP9, OLI3, PHO2, Q0130 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P61829
#2: Chemical
ChemComp-EFO / Oligomycin A / (1R,4E,5'S,6S,6'S,7R,8S,10R,11R,12S,14R,15S,16R,18E,20E,22R,25S,27R,28S,29R)-22-ethyl-7,11,14,15-tetrahydroxy-6'-[(2R)-2-hydroxypropyl]-5',6,8,10,12,14,16,28,29-nonamethyl-3',4',5',6'-tetrahydro-3H,9H,13H-spiro[2,26-dioxabicyclo[23.3.1]nonacosa-4,18,20-triene-27,2'-pyran]-3,9,13-trione


Mass: 791.062 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C45H74O11
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.11 Å3/Da / Density % sol: 41.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 68% MPD, 8% PROPYLENE GLYCOL, 0.3M NACL, 2MM MGSO4, 50MM MES PH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 14, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. all: 56957 / Num. obs: 55875 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Biso Wilson estimate: 26.8 Å2 / Rmerge(I) obs: 0.084 / Rsym value: 0.084 / Net I/σ(I): 20.8
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 6 % / Rmerge(I) obs: 0.652 / Mean I/σ(I) obs: 1.8 / Num. unique all: 5052 / Rsym value: 0.652 / % possible all: 98.1

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Processing

Software
NameVersionClassification
MD2data collection
MOLREPphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 3UD0

3ud0


Resolution: 1.9→30 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.939 / SU B: 6.211 / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.179 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.22771 2828 5.1 %RANDOM
Rwork0.20178 ---
obs0.20309 53035 98.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 26.787 Å2
Baniso -1Baniso -2Baniso -3
1-0.97 Å20 Å20 Å2
2--0.97 Å20 Å2
3----1.94 Å2
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5301 0 392 150 5843
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.026034
X-RAY DIFFRACTIONr_angle_refined_deg1.1812.0668273
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.8615837
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.55823.077130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.31515895
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.821510
X-RAY DIFFRACTIONr_chiral_restr0.0690.21119
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214102
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 164 -
Rwork0.247 3219 -
obs-3219 88.49 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.82190.0584-1.40880.6048-0.881312.10490.0048-0.15280.07330.08910.0385-0.0344-0.17630.2207-0.04330.01440.0057-0.01230.0329-0.01240.056648.17318.442831.9563
20.55150.226-1.26950.7242-1.50315.4055-0.0108-0.1650.02090.1228-0.0486-0.0668-0.16580.66220.05940.0615-0.0174-0.00920.0758-0.01510.1250.637816.272928.028
30.8240.0914-1.29610.7042-1.911415.07960.0893-0.14990.0780.09630.08220.0303-0.1680.0335-0.17150.0259-0.00260.00180.0412-0.01250.065241.209512.869831.9539
40.6854-0.0157-0.44240.7935-1.850713.60080.0025-0.17010.12120.15610.00110.0164-0.72320.1819-0.00360.0791-0.0103-0.00080.0439-0.02940.116938.589320.757228.4743
50.6750.04890.19420.6393-1.658415.09170.0553-0.1350.03220.11510.0480.0701-0.15480.0099-0.10330.02670.00280.00520.0371-0.00860.074433.007312.352332.0651
60.7009-0.0030.78120.5189-1.80115.1225-0.018-0.15190.06620.17020.04080.041-0.6939-0.0897-0.02280.07450.0280.00070.0523-0.02370.118926.397217.186428.4715
70.7744-0.05450.74270.7095-1.437814.48430.0932-0.13070.01540.12190.10970.0658-0.0677-0.0114-0.20290.03510.00560.01030.0454-0.0040.075126.68637.115131.9921
80.580.00151.30640.4191-0.864413.3215-0.0065-0.18070.0350.1099-0.00550.0778-0.396-0.53250.0120.04330.02190.01280.09-0.01230.118418.4297.193128.8376
90.796-0.15071.63450.6979-0.270915.51280.0447-0.1643-0.02390.12790.12570.0931-0.0473-0.128-0.17050.03170.00760.0180.05290.00310.070424.5122-0.828432.1383
100.4103-0.04522.08710.65110.256714.54880.0073-0.1936-0.01690.1373-0.05580.08050.0151-0.80860.04850.0342-0.02810.01690.11610.0070.125317.7678-5.612328.5088
110.92550.28720.68380.73891.10618.93040.159-0.2307-0.06710.1861-0.03970.02470.2891-0.1016-0.11930.0579-0.03460.00830.06050.00960.0653-8.486427.60431.9374
120.2668-0.07320.10430.65021.544513.4193-0.0097-0.1614-0.02330.1961-0.11710.02150.4837-0.56140.12680.1161-0.07490.0090.15740.02050.1191-9.468919.373728.7293
130.70990.28471.0010.72731.868713.93660.1572-0.212-0.05290.1855-0.0162-0.05820.281-0.0928-0.14110.0652-0.0337-0.01620.07250.02240.0825-0.923724.578131.8681
140.7338-0.03350.06520.50672.650115.5946-0.0143-0.2282-0.11340.2129-0.0516-0.02750.8879-0.13910.06590.1581-0.0411-0.01750.10130.0620.14523.037717.245328.8045
150.61320.0791-0.47280.82591.603414.12510.1898-0.2081-0.06820.1940.0146-0.05380.1490.1944-0.20440.0933-0.0547-0.02650.07610.03730.08467.044626.546632.2231
161.27110.1899-1.02051.1272.522919.13460.0454-0.2958-0.10930.2723-0.0515-0.07570.76280.29810.00620.0783-0.0012-0.03290.0890.0430.13514.558623.197728.1522
170.86590.0697-1.30760.65751.260411.08280.1293-0.2295-0.00130.1843-0.0199-0.05790.27670.133-0.10940.0673-0.0383-0.01580.07660.02630.082512.405732.856532.6788
181.3026-0.0254-1.32040.65890.808214.96660.0574-0.2805-0.08860.1867-0.0133-0.05730.54840.5544-0.04420.0706-0.0141-0.04050.07960.0470.127520.421634.344628.8159
191.0167-0.0225-1.78960.75190.50410.66830.1134-0.22520.00410.1713-0.0482-0.06930.04530.1517-0.06520.0559-0.0423-0.02160.06140.01450.072712.969641.190732.343
201.04850.1764-2.46940.7492-0.572515.02480.0179-0.2761-0.00590.1932-0.1301-0.05420.01540.6110.11220.0718-0.0495-0.02540.10780.01080.115618.513547.110628.7013
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 41
2X-RAY DIFFRACTION2A42 - 74
3X-RAY DIFFRACTION3B1 - 41
4X-RAY DIFFRACTION4B42 - 75
5X-RAY DIFFRACTION5C1 - 41
6X-RAY DIFFRACTION6C42 - 75
7X-RAY DIFFRACTION7D1 - 41
8X-RAY DIFFRACTION8D42 - 75
9X-RAY DIFFRACTION9E1 - 41
10X-RAY DIFFRACTION10E42 - 75
11X-RAY DIFFRACTION11K1 - 41
12X-RAY DIFFRACTION12K42 - 75
13X-RAY DIFFRACTION13L1 - 41
14X-RAY DIFFRACTION14L42 - 75
15X-RAY DIFFRACTION15M1 - 41
16X-RAY DIFFRACTION16M42 - 75
17X-RAY DIFFRACTION17N1 - 41
18X-RAY DIFFRACTION18N42 - 75
19X-RAY DIFFRACTION19O1 - 41
20X-RAY DIFFRACTION20O42 - 75

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