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- PDB-8dbw: E. coli ATP synthase imaged in 10mM MgATP State3 "down" Fo classified -

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Basic information

Entry
Database: PDB / ID: 8dbw
TitleE. coli ATP synthase imaged in 10mM MgATP State3 "down" Fo classified
Components(ATP synthase ...) x 8
KeywordsMEMBRANE PROTEIN / Energy / ATP hyrolysis / ATP synthesis / Motor / cryoEM
Function / homology
Function and homology information


proton motive force-driven plasma membrane ATP synthesis / proton-transporting ATP synthase complex, coupling factor F(o) / 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 / hydrolase activity / 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, F0 complex, subunit b, bacterial / F-type ATP synthase subunit B-like, membrane domain superfamily / ATP synthase, F0 complex, subunit A, bacterial/chloroplast / ATP synthase, F0 complex, subunit b/b', bacterial/chloroplast / ATP synthase B/B' CF(0) / ATP synthase delta/epsilon subunit, C-terminal domain superfamily / ATP synthase, F0 complex, subunit C, bacterial/chloroplast / ATPase, OSCP/delta subunit, conserved site ...ATP synthase delta/epsilon subunit, C-terminal domain / ATP synthase, Delta/Epsilon chain, long alpha-helix domain / ATP synthase, F0 complex, subunit b, bacterial / F-type ATP synthase subunit B-like, membrane domain superfamily / ATP synthase, F0 complex, subunit A, bacterial/chloroplast / ATP synthase, F0 complex, subunit b/b', bacterial/chloroplast / ATP synthase B/B' CF(0) / ATP synthase delta/epsilon subunit, C-terminal domain superfamily / ATP synthase, F0 complex, subunit C, bacterial/chloroplast / ATPase, OSCP/delta subunit, conserved site / ATP synthase delta (OSCP) subunit signature. / F1F0 ATP synthase OSCP/delta subunit, N-terminal domain superfamily / ATP synthase, F0 complex, subunit A / ATP synthase, F0 complex, subunit A, active site / ATP synthase, F0 complex, subunit A superfamily / ATP synthase A chain / ATP synthase a subunit signature. / ATPase, OSCP/delta subunit / ATP synthase delta (OSCP) subunit / 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 / C-terminal domain of V and A type ATP synthase / 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
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / ATP synthase subunit beta / ATP synthase epsilon chain / ATP synthase subunit alpha / ATP synthase subunit a / ATP synthase gamma chain / ATP synthase subunit b / ATP synthase subunit c / ATP synthase subunit delta
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsSobti, M. / Stewart, A.G.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia) Australia
CitationJournal: Commun Biol / Year: 2023
Title: Changes within the central stalk of E. coli FF ATP synthase observed after addition of ATP.
Authors: Meghna Sobti / Yi C Zeng / James L Walshe / Simon H J Brown / Robert Ishmukhametov / Alastair G Stewart /
Abstract: FF ATP synthase functions as a biological generator and makes a major contribution to cellular energy production. Proton flow generates rotation in the F motor that is transferred to the F motor to ...FF ATP synthase functions as a biological generator and makes a major contribution to cellular energy production. Proton flow generates rotation in the F motor that is transferred to the F motor to catalyze ATP production, with flexible F/F coupling required for efficient catalysis. FF ATP synthase can also operate in reverse, hydrolyzing ATP and pumping protons, and in bacteria this function can be regulated by an inhibitory ε subunit. Here we present cryo-EM data showing E. coli FF ATP synthase in different rotational and inhibited sub-states, observed following incubation with 10 mM MgATP. Our structures demonstrate how structural transitions within the inhibitory ε subunit induce torsional movement in the central stalk, thereby enabling its rotation within the F motor. This highlights the importance of the central rotor for flexible coupling of the F and F motors and provides further insight into the regulatory mechanism mediated by subunit ε.
History
DepositionJun 14, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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 gamma chain
H: ATP synthase epsilon chain
I: ATP synthase subunit c
J: ATP synthase subunit c
L: ATP synthase subunit c
M: ATP synthase subunit c
N: ATP synthase subunit c
O: ATP synthase subunit c
P: ATP synthase subunit c
Q: ATP synthase subunit c
R: ATP synthase subunit c
S: ATP synthase subunit c
W: ATP synthase subunit delta
X: ATP synthase subunit b
Y: ATP synthase subunit b
a: ATP synthase subunit a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)527,74033
Polymers524,73622
Non-polymers3,00511
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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ATP synthase ... , 8 types, 22 molecules ABCDEFGHIJLMNOPQRSWXYa

#1: Protein ATP synthase subunit alpha / ATP synthase F1 sector subunit alpha / F-ATPase subunit alpha


Mass: 55007.336 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: atpA, ECLG_02126 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A7U9G3U3, H+-transporting two-sector ATPase
#2: Protein ATP synthase subunit beta / ATP synthase F1 sector subunit beta / F-ATPase subunit beta


Mass: 50346.129 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: atpD, EWT59_16525, WLH_03015 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A192CEZ8, H+-transporting two-sector ATPase
#3: Protein ATP synthase gamma chain / ATP synthase F1 sector gamma subunit / F-ATPase gamma subunit


Mass: 31237.883 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: C3SLA2
#4: Protein ATP synthase epsilon chain / ATP synthase F1 sector epsilon subunit / F-ATPase epsilon subunit


Mass: 14551.498 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: atpC, CCU01_030215 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A4V1DSB5
#5: Protein
ATP synthase subunit c / ATP synthase F(0) sector subunit c / F-type ATPase subunit c / F-ATPase subunit c / Lipid-binding protein


Mass: 7998.754 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: atpE, ECJG_03465 / Production host: Escherichia coli (E. coli) / References: UniProt: F4TL55
#6: Protein ATP synthase subunit delta / ATP synthase F(1) sector subunit delta / F-type ATPase subunit delta / F-ATPase subunit delta


Mass: 18855.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: atpH, HMPREF1611_00658 / Production host: Escherichia coli (E. coli) / References: UniProt: V0ZA15
#7: Protein ATP synthase subunit b / ATP synthase F(0) sector subunit b / ATPase subunit I / F-type ATPase subunit b / F-ATPase subunit b


Mass: 17144.730 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: atpF, ECDG_04362 / Production host: Escherichia coli (E. coli) / References: UniProt: D6IFY0
#8: Protein ATP synthase subunit a / ATP synthase F0 sector subunit a / F-ATPase subunit 6


Mass: 29753.461 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: atpB, atpB_1, A9X72_25250, AAG43_003021, ABE90_000165, ACN68_12775, ACN81_06510, ACU57_03300, AM464_11965, AT335_004107, AT845_000773, AW119_07615, BANRA_00251, BANRA_02401, BF481_004021, BG944_ ...Gene: atpB, atpB_1, A9X72_25250, AAG43_003021, ABE90_000165, ACN68_12775, ACN81_06510, ACU57_03300, AM464_11965, AT335_004107, AT845_000773, AW119_07615, BANRA_00251, BANRA_02401, BF481_004021, BG944_002347, BGZ_02071, BGZ_04636, BHS81_22305, BJI68_21520, BK292_20055, BMT50_09740, BMT91_10650, BN17_36921, BO068_002405, BOH76_10175, BON63_19140, BON64_06080, BON65_14675, BON67_02005, BON68_19950, BON69_17475, BON70_16820, BON71_24505, BON72_01125, BON73_15370, BON74_23490, BON76_09200, BON77_19820, BON80_03525, BON89_05760, BON93_25670, BON94_01520, BON95_10870, BON97_15985, BTQ06_19305, BvCmsF30A_02552, BvCmsHHP056_00154, BvCmsKKP036_01773, BvCmsKKP061_01916, BvCmsKSNP073_00093, BvCmsNSP072_01187, BVL39_06790, C2U48_14255, C3F40_16990, C5N07_23075, C5Y87_17890, C9114_08770, C9160_23510, C9E67_00020, CA593_07300, CCS08_08920, CDC27_20240, CG692_21460, CG831_001097, CIG67_24440, CO706_18150, CR538_25535, CR539_00375, CV83915_02325, CWS33_22485, D0X26_21590, D9D77_23770, DAH17_15930, DAH19_18320, DAH20_23990, DAH21_17755, DAH22_23595, DAH23_18155, DAH24_17640, DAH25_17895, DAH26_16990, DAH27_18155, DAH28_17805, DAH29_15920, DAH31_22960, DAH32_19125, DAH33_22080, DAH34_09105, DAH36_07465, DAH37_15370, DAH38_15005, DAH40_17005, DAH41_14135, DAH42_13455, DAH43_16455, DAH45_16835, DAH46_15675, DAH47_17330, DAH48_15585, DAH49_16665, DAH50_22615, DEN88_13850, DEN89_15985, DEN90_12370, DEN91_23220, DEN92_12205, DEN93_09020, DEN94_10360, DEN95_14235, DEN96_09840, DEN97_10745, DEN98_07855, DEN99_11560, DEO00_06580, DEO01_09365, DEO02_16525, DEO03_19745, DEO04_18940, DEO05_18810, DEO06_16220, DEO07_15680, DEO08_21650, DEO09_18665, DEO10_18930, DEO11_18820, DEO12_10795, DEO13_12620, DEO14_23345, DEO15_11255, DEO17_21830, DEO18_15280, DEO19_13515, DEO20_16610, DIV22_14605, DN627_09995, DNQ45_04220, DRW19_13755, DS732_00235, DTL43_15450, DTL90_16085, DTM16_24900, DXT69_23170, DXT70_14015, DXT71_06450, E0I42_12470, E2112_06550, E2113_20865, E2117_22135, E2119_14450, E2121_20725, E2127_21210, E2128_05660, E2129_07955, E2132_10910, E2134_19715, E4K51_16190, E4T14_07510, E5M02_07130, E5P22_11935, E5P23_15735, E5P24_15900, E5P25_18200, E5P30_22395, E5P31_17880, E5P32_06360, E5P33_18010, E5P35_14070, E5P36_12975, E5P40_10335, E5P51_17750, E5P52_17720, E5S34_11685, E5S35_09845, E5S36_12285, E5S37_13645, E5S38_13500, E5S39_09575, E5S42_10245, E5S43_09805, E5S44_11620, E5S45_08675, E5S47_13500, E5S48_08510, E5S51_11505, E5S52_15360, E5S53_08080, E5S54_07200, E5S55_07040, E5S56_16355, E5S57_15755, EAI46_06675, EAX79_08895, EBP16_13415, EC1094V2_4559, EC95NR1_03180, ECs4680, ED648_17305, EHD79_09605, EI021_09305, EIZ93_13995, EKI52_15345, EL79_4683, EL80_4591, ELT18_19250, ELT20_19840, ELT21_07710, ELT41_12325, ELU87_20420, ELV08_24425, ELX57_19380, ELX65_18890, ELX67_20675, ELX72_20815, ELX82_07860, ELX84_11040, ELX85_19160, ELX87_21655, ELY02_10830, ELY39_11115, ERS139208_02919, EXX13_13750, EYV17_12540, EYV18_08920, EYX47_15940, F0L67_11195, F2N31_18980, F2N31_28875, F9V24_15580, F9X20_04505, FDM60_00765, FFF58_16420, FOI11_016935, FOI11_06245, FQF29_14375, FV293_15950, FVB16_05450, FWK02_01255, FY127_20825, G5632_18870, G9448_14760, GAJ26_16155, GF699_13365, GFY34_11825, GIB53_15080, GJ11_23870, GKF89_22150, GNZ05_15960, GP662_07560, GP946_02135, GP954_05505, GP979_07135, GQA06_03740, GQE64_11005, GQF59_16640, GQM04_04750, GQM09_09025, GRW05_11240, GRW57_03900, GRW81_18100, GUC01_19690, H0O72_18985, HHH44_002067, HKA49_003861, HLZ50_19940, HMV95_19405, HV109_23865, HV209_21670, HVW19_22170, HVW43_16300, HVY77_25765, HVZ71_25190, HX136_24860, I6H00_18485, I6H01_13035, I6H02_14225, IH772_07040, J0541_001625, J4S20_002462, J5U05_004128, JE86ST02C_42930, JE86ST05C_43010, JFD_02815, JNP96_27775, NCTC10090_03054, NCTC10418_07533, NCTC10429_00459, NCTC11126_01888, NCTC11181_02279, NCTC13127_06463, NCTC13216_01845, NCTC4450_02006, NCTC8008_04535, NCTC8179_05398, NCTC8333_05845, NCTC8622_01220, NCTC8960_02611, NCTC9036_04909, NCTC9037_05079, NCTC9045_05855, NCTC9073_06659, NCTC9111_05225, NCTC9117_06282, NCTC9706_02267, ND22_002728, PGD_00238, RG28_23995, SAMEA3472044_00548, SAMEA3472056_03685, SAMEA3472067_04030, SAMEA3472080_03392, SAMEA3472147_03706, SAMEA3751407_02369, SAMEA3752557_01245, TUM18780_44040, WP2S18E08_47850, WR15_16550
Production host: Escherichia coli (E. coli) / References: UniProt: C3SL77

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Non-polymers , 3 types, 11 molecules

#9: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#10: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#11: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM

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Details

Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: ATP synthase / Type: COMPLEX / Entity ID: #1-#8 / Source: RECOMBINANT
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1500 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 48 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 8757 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00437396
ELECTRON MICROSCOPYf_angle_d0.79150645
ELECTRON MICROSCOPYf_dihedral_angle_d14.24913814
ELECTRON MICROSCOPYf_chiral_restr0.0485901
ELECTRON MICROSCOPYf_plane_restr0.0116550

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