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- PDB-3u2f: ATP synthase c10 ring in proton-unlocked conformation at PH 8.3 -

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Basic information

Entry
Database: PDB / ID: 3u2f
TitleATP synthase c10 ring in proton-unlocked conformation at PH 8.3
ComponentsATP synthase subunit C, mitochondrial
KeywordsMEMBRANE PROTEIN / F1FO ATP synthase / proton pore / c10 ring
Function / homology
Function and homology information


mitochondrial 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 / 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
ATP synthase subunit 9, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSymersky, J. / Pagadala, V. / Osowski, D. / Krah, A. / Meier, T. / Faraldo-Gomez, J. / Mueller, D.M.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2012
Title: Structure of the c(10) ring of the yeast mitochondrial ATP synthase in the open conformation.
Authors: Symersky, J. / Pagadala, V. / Osowski, D. / Krah, A. / Meier, T. / Faraldo-Gomez, J.D. / Mueller, D.M.
History
DepositionOct 3, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2012Group: Database references
Revision 1.2Jun 13, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
K: ATP synthase subunit C, mitochondrial
L: ATP synthase subunit C, mitochondrial
M: ATP synthase subunit C, mitochondrial
N: ATP synthase subunit C, mitochondrial
O: ATP synthase subunit C, mitochondrial


Theoretical massNumber of molelcules
Total (without water)38,9525
Polymers38,9525
Non-polymers00
Water1,20767
1
K: ATP synthase subunit C, mitochondrial
L: ATP synthase subunit C, mitochondrial
M: ATP synthase subunit C, mitochondrial
N: ATP synthase subunit C, mitochondrial
O: ATP synthase subunit C, mitochondrial

K: ATP synthase subunit C, mitochondrial
L: ATP synthase subunit C, mitochondrial
M: ATP synthase subunit C, mitochondrial
N: ATP synthase subunit C, mitochondrial
O: ATP synthase subunit C, mitochondrial


Theoretical massNumber of molelcules
Total (without water)77,90410
Polymers77,90410
Non-polymers00
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area31050 Å2
ΔGint-410 kcal/mol
Surface area22700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.184, 54.184, 245.977
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number93
Space group name H-MP4222

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Components

#1: Protein
ATP synthase subunit C, mitochondrial / / Lipid-binding protein


Mass: 7790.385 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P61829
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O

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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: 46.92 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8.3
Details: 68% MPD, 8% PROPYLENE GLYCOL, 0.3M NACL, 0.1M MALONATE PH 7.0, 2MM MGSO4, 50MM BICINE, PH 8.3, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 20, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 25587 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.6 % / Biso Wilson estimate: 20 Å2 / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): 13.8
Reflection shellResolution: 2→2.07 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.276 / Mean I/σ(I) obs: 3.2 / Num. unique all: 2438 / Rsym value: 0.276 / % possible all: 96.4

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Processing

Software
NameVersionClassification
Blu-Icedata collection
MOLREPphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XOK, CHAINS K,L,M,N,O

2xok


Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.95 / SU B: 6.522 / SU ML: 0.085 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.183 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21618 1296 5.1 %RANDOM
Rwork0.19192 ---
all0.19316 24159 --
obs0.19316 24159 97.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 25.728 Å2
Baniso -1Baniso -2Baniso -3
1-0.7 Å20 Å20 Å2
2--0.7 Å20 Å2
3----1.4 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2643 0 0 67 2710
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222792
X-RAY DIFFRACTIONr_angle_refined_deg1.0422.0023822
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.5215416
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.95323.23165
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.20215447
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.197155
X-RAY DIFFRACTIONr_chiral_restr0.070.2495
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211976
X-RAY DIFFRACTIONr_mcbond_it0.4131.51894
X-RAY DIFFRACTIONr_mcangle_it0.76123034
X-RAY DIFFRACTIONr_scbond_it1.683898
X-RAY DIFFRACTIONr_scangle_it2.7734.5763
LS refinement shellResolution: 1.999→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.24 99 -
Rwork0.197 1666 -
obs-1666 95.46 %
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)
10.63560.0215-2.15730.3874-1.478117.620.0411-0.11830.02150.11450.0233-0.0285-0.09390.1308-0.06440.075-0.0153-0.01370.0466-0.01060.117934.902910.928932.5729
20.40620.1169-1.83470.683-1.559721.26460.0962-0.17040.03110.2174-0.06940.0296-0.78090.7658-0.02680.1243-0.0322-0.01370.1141-0.01940.168735.118219.215727.2296
30.56560.1643-0.75040.7152-2.699417.57990.1258-0.08320.07130.14680.05780.0224-0.248-0.185-0.18360.0615-0.00550.00390.0284-0.00750.095626.976113.285931.6498
40.0822-0.1608-0.13590.8358-2.031719.4315-0.0272-0.05860.02620.2633-0.019-0.0225-0.92660.14670.04610.1351-0.01980.00130.1152-0.01640.15522.467720.327127.7969
50.44480.05150.98451.0197-3.103417.52690.085-0.1010.02440.17420.0460.0626-0.1789-0.3367-0.1310.0478-0.00510.0150.0544-0.00950.099219.187910.625531.6234
60.50430.08261.27160.5568-2.041323.193-0.0244-0.17410.07880.206-0.01120.0969-0.938-0.60970.03560.12280.03590.02340.1474-0.03330.168711.400613.797928.3351
70.4182-0.09912.51080.734-1.601419.47510.0755-0.0979-0.00740.17150.11130.0751-0.0456-0.3548-0.18670.0744-0.01770.02110.0754-0.0090.110814.44683.999232.3733
80.8645-0.12632.80920.4968-1.316221.2986-0.0524-0.26520.04460.19150.08160.0536-0.553-1.1502-0.02910.09010.02340.03460.1808-0.00970.17736.38482.009227.9717
90.6765-0.12682.64820.4480.017419.38930.1015-0.136-0.0630.12720.10480.04090.26-0.3093-0.20630.0813-0.00890.01480.06640.00120.095514.4236-4.286632.0474
100.9210.19443.2320.29720.651124.01950.0279-0.2822-0.02260.1446-0.08250.12520.1749-1.23120.05460.0968-0.02840.0290.16730.00370.1819.11-10.719327.9546
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1K1 - 41
2X-RAY DIFFRACTION2K42 - 74
3X-RAY DIFFRACTION3L1 - 41
4X-RAY DIFFRACTION4L42 - 74
5X-RAY DIFFRACTION5M1 - 41
6X-RAY DIFFRACTION6M42 - 75
7X-RAY DIFFRACTION7N1 - 41
8X-RAY DIFFRACTION8N42 - 74
9X-RAY DIFFRACTION9O1 - 41
10X-RAY DIFFRACTION10O42 - 74

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