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- PDB-1qo1: Molecular Architecture of the Rotary Motor in ATP Synthase from Y... -

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Basic information

Entry
Database: PDB / ID: 1qo1
TitleMolecular Architecture of the Rotary Motor in ATP Synthase from Yeast Mitochondria
Components
  • ATP SYNTHASE ALPHA CHAIN
  • ATP SYNTHASE BETA CHAIN
  • ATP SYNTHASE DELTA CHAIN
  • ATP SYNTHASE GAMMA CHAIN
  • ATP SYNTHASE PROTEIN 9
KeywordsATP SYNTHASE / LOW RESOLUTION MODEL / C-ALPHA ONLY
Function / homology
Function and homology information


Formation of ATP by chemiosmotic coupling / Cristae formation / mitochondrial proton-transporting ATP synthase, catalytic core / proton-transporting ATP synthase complex / proton motive force-driven plasma membrane ATP synthesis / 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 ...Formation of ATP by chemiosmotic coupling / Cristae formation / mitochondrial proton-transporting ATP synthase, catalytic core / proton-transporting ATP synthase complex / proton motive force-driven plasma membrane ATP synthesis / 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-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 / membrane => GO:0016020 / lipid binding / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
ATP synthase delta/epsilon subunit, C-terminal domain / ATP synthase, Delta/Epsilon chain, long alpha-helix domain / ATP synthase delta/epsilon subunit, C-terminal domain superfamily / ATP synthase, F0 complex, subunit C, bacterial/chloroplast / 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 delta/epsilon subunit, C-terminal domain / ATP synthase, Delta/Epsilon chain, long alpha-helix domain / ATP synthase delta/epsilon subunit, C-terminal domain superfamily / ATP synthase, F0 complex, subunit C, bacterial/chloroplast / 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 / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ATP synthase subunit beta, mitochondrial / ATP synthase epsilon chain / ATP synthase subunit c / ATP synthase subunit gamma, mitochondrial / ATP synthase epsilon chain / ATP synthase subunit alpha, mitochondrial / ATP synthase subunit c
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.9 Å
Model type detailsCA ATOMS ONLY, CHAIN A, B, C, D, E, F, G, J, K, L, M, N, O, P, Q, R, S, T
AuthorsStock, D. / Leslie, A.G.W. / Walker, J.E.
Citation
Journal: Science / Year: 1999
Title: Molecular Architecture of the Rotary Motor in ATP Synthase
Authors: Stock, D. / Leslie, A.G.W. / Walker, J.E.
#1: Journal: Biochemistry / Year: 1998
Title: Solution Structure of the Transmembrane H -Transporting Subunit C of the F1F0 ATP Synthase
Authors: Girvin, M.E. / Rastogi, V.K. / Abildgaard, F. / Markley, J.L. / Fillingame, R.H.
#2: Journal: Structure / Year: 1997
Title: Crystal Structure of the Epsilon Subunit of the Proton-Translocating ATP Synthase from Escherichia Coli
Authors: Uhlin, U. / Cox, G.B. / Guss, J.M.
#3: Journal: Nature / Year: 1994
Title: Structure at 2.8-Angstrom Resolution of F1-ATPase from Bovine Heart Mitochondria
Authors: Abrahams, J.P. / Leslie, A.G.W. / Lutter, R. / Walker, J.E.
History
DepositionNov 1, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 4, 1999Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.2Dec 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATP SYNTHASE ALPHA CHAIN
B: ATP SYNTHASE ALPHA CHAIN
C: ATP SYNTHASE ALPHA CHAIN
D: ATP SYNTHASE BETA CHAIN
E: ATP SYNTHASE BETA CHAIN
F: ATP SYNTHASE BETA CHAIN
G: ATP SYNTHASE GAMMA CHAIN
J: ATP SYNTHASE DELTA CHAIN
K: ATP SYNTHASE PROTEIN 9
L: ATP SYNTHASE PROTEIN 9
M: ATP SYNTHASE PROTEIN 9
N: ATP SYNTHASE PROTEIN 9
O: ATP SYNTHASE PROTEIN 9
P: ATP SYNTHASE PROTEIN 9
Q: ATP SYNTHASE PROTEIN 9
R: ATP SYNTHASE PROTEIN 9
S: ATP SYNTHASE PROTEIN 9
T: ATP SYNTHASE PROTEIN 9


Theoretical massNumber of molelcules
Total (without water)448,85118
Polymers448,85118
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)135.900, 175.300, 139.200
Angle α, β, γ (deg.)90.00, 91.60, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ATP SYNTHASE ALPHA CHAIN / ATP1 / YBL099W / YBL0827 / Coordinate model: Cα atoms only


Mass: 55301.207 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Details: THE BOS TAURUS (BOVINE) ATP SYNTHASE ALPHA CHAIN HEART ISOFORM SEQUENCE (SWISSPROT P19483) AND MODEL (PDB ENTRY 1BMF) ARE GIVEN IN THE COORDINATES OF THIS ENTRY
Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / Organelle: MITOCHONDRIALMitochondrion / References: UniProt: P19483, EC: 3.6.1.34
#2: Protein ATP SYNTHASE BETA CHAIN / ATP2 / YJR121W / J204 / Coordinate model: Cα atoms only


Mass: 51757.836 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Details: THE BOS TAURUS (BOVINE) ATP SYNTHASE BETA CHAIN SEQUENCE (SWISSPROT P00829) AND MODEL (PDB ENTRY 1BMF) ARE GIVEN IN THE COORDINATES OF THIS ENTRY
Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / Organelle: MITOCHONDRIALMitochondrion / References: UniProt: P00829, EC: 3.6.1.34
#3: Protein ATP SYNTHASE GAMMA CHAIN / ATP3 / YBR039W / YBR0408 / Coordinate model: Cα atoms only


Mass: 30185.674 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: THE BOS TAURUS (BOVINE) ATP SYNTHASE GAMMA CHAIN SEQUENCE (SWISSPROT P05631) AND MODEL (PDB ENTRY 1BMF) ARE GIVEN IN THE COORDINATES OF THIS ENTRY
Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / Organelle: MITOCHONDRIALMitochondrion / References: UniProt: P05631, EC: 3.6.1.34
#4: Protein ATP SYNTHASE DELTA CHAIN / ATP16 / YDL004W / YD8119.03 / D2935 / Coordinate model: Cα atoms only


Mass: 14897.904 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: THE ESCHERICHIA COLI ATP SYNTHASE EPSILON CHAIN SEQUENCE (SWISSPROT P00832) AND MODEL (PDB ENTRY 1AQT) ARE GIVEN IN THE COORDINATES OF THIS ENTRY
Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / Organelle: MITOCHONDRIALMitochondrion
References: UniProt: P00832, UniProt: P0A6E6*PLUS, EC: 3.6.1.34
#5: Protein
ATP SYNTHASE PROTEIN 9 / / LIPID-BINDING PROTEIN / ATP9 / OLI1 / PHO2 / Coordinate model: Cα atoms only


Mass: 8259.064 Da / Num. of mol.: 10 / Source method: isolated from a natural source
Details: THE ESCHERICHIA COLI ATP SYNTHASE C CHAIN SEQUENCE (SWISSPROT P00844) AND MODEL (PDB ENTRY 1A91) ARE GIVEN IN THE COORDINATES OF THIS ENTRY
Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / Cellular location: MEMBRANEBiological membrane / Organelle: MITOCHONDRIALMitochondrion
References: UniProt: P00844, UniProt: P68699*PLUS, EC: 3.6.1.34
Compound detailsTHE F-TYPE ATPASES HAVE 2 COMPONENTS, F1 - THE CATALYTIC CORE AND F0 - THE MEMBRANE PROTON CHANNEL. ...THE F-TYPE ATPASES HAVE 2 COMPONENTS, F1 - THE CATALYTIC CORE AND F0 - THE MEMBRANE PROTON CHANNEL. F1 HAS FIVE SUBUNITS: ALPHA(3), BETA(3), GAMMA(1), DELTA(1), EPSILON(1). F0 HAS THREE MAIN SUBUNITS: A, B AND C. THE DBREF, SEQRES AND ATOM RECORDS GIVE THE BOVINE AND E.COLI MODEL COORDINATES AND SEQUENCE AS: THE TRUE YEAST PROTEINS ARE: WHILE THE MODELS USED ARE: CHAIN SWS-AC RESIDUES SWS-AC SEQUENCE PDB-1QO1 A P07251 36 545 P19483 67 553 24 510 B P07251 36 545 P19483 67 553 24 510 C P07251 36 545 P19483 62 553 19 510 D P00830 34 511 P00829 59 525 9 475 E P00830 34 511 P00829 59 524 9 474 F P00830 34 511 P00829 59 524 9 474 G P38077 34 311 P05631 26 297 1 272 CHAIN G FOUND IN 3 FRAGMENTS J Q12165 23 160 P00832 3 121 2 136 K P00841 1 76 P00844 1 79 1 79 L P00841 1 76 P00844 1 79 1 79 M P00841 1 76 P00844 1 79 1 79 N P00841 1 76 P00844 1 79 1 79 O P00841 1 76 P00844 1 79 1 79 P P00841 1 76 P00844 1 79 1 79 Q P00841 1 76 P00844 1 79 1 79 R P00841 1 76 P00844 1 79 1 79 S P00841 1 76 P00844 1 79 1 79 T P00841 1 76 P00844 1 79 1 79

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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: 3.66 Å3/Da / Density % sol: 66 %
Crystal growMethod: microbatch / pH: 8
Details: 0.1 M TRIS/CL PH8.0, 12% PEG 6000, 150 MM NACL, 1 MM AMP-PNP, 40 MICROM ADP, 1 MM DTT, 0.02% NAN3, MIXED 1:1 WITH PROTEIN SOLUTION UNDER PARAFFIN OIL IN MICROBATCH PLATE., pH 8.00
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein11
20.1 MTris11
312 %PEG600011
4150 mM11NaCl
51 mMAMP-PNP11
60.040 mMADP11
71 mMdithiothreitol11
80.02 %sodium azide11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID2 / Wavelength: 0.99
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 15, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 3.9→15 Å / Num. obs: 55593 / % possible obs: 93.3 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 4
Reflection shellResolution: 3.9→4.11 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 1.3 / % possible all: 95.5
Reflection
*PLUS
Rmerge(I) obs: 0.1
Reflection shell
*PLUS
% possible obs: 95.5 % / Num. unique obs: 8288 / Rmerge(I) obs: 0.372

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Processing

Software
NameClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BMF

1bmf


Highest resolution: 3.9 Å
Details: THE MODEL CONSISTS OF C ALPHA COORDINATES OF PDB ENTRIES 1BMF, 1AQT, AND 1A91, WHICH WERE FITTED INTO THE DENSITY AS RIGID BODIES. NO REFINEMENT WAS CARRIED OUT ON THIS MODEL. THE ELECTRON ...Details: THE MODEL CONSISTS OF C ALPHA COORDINATES OF PDB ENTRIES 1BMF, 1AQT, AND 1A91, WHICH WERE FITTED INTO THE DENSITY AS RIGID BODIES. NO REFINEMENT WAS CARRIED OUT ON THIS MODEL. THE ELECTRON DENSITY AT 3.9 ANGSTROM RESOLUTION DOES NOT PROVIDE THE INFORMATION REQUIRED TO DERIVE AN ATOMIC MODEL. THE COORDINATES ARE BASED ON COORDINATES OF MODELS OF SUBUNITS OR DOMAINS DERIVED FROM HIGHER RESOLUTION X-RAY EXPERIMENTS (1BMF, 1AQT) OR NMR- EXPERIMENTS (1A91). THESE MODELS WERE FITTED INTO THE DENSITY AS RIGID BODIES. THEREFORE THE RESIDUE NAMES OF THE C ALPHA ATOMS HAVE NO MEANING.
Refinement stepCycle: LAST / Highest resolution: 3.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3912 0 0 0 3912
Refinement
*PLUS
Lowest resolution: 15 Å / Num. reflection obs: 55593 / Rfactor obs: 0.467
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor obs: 0.506

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