8DBW

E. coli ATP synthase imaged in 10mM MgATP State3 "down" Fo classified


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Changes within the central stalk of E. coli F 1 F o ATP synthase observed after addition of ATP.

Sobti, M.Zeng, Y.C.Walshe, J.L.Brown, S.H.J.Ishmukhametov, R.Stewart, A.G.

(2023) Commun Biol 6: 26-26

  • DOI: https://doi.org/10.1038/s42003-023-04414-z
  • Primary Citation of Related Structures:  
    8DBP, 8DBQ, 8DBR, 8DBS, 8DBT, 8DBU, 8DBV, 8DBW

  • PubMed Abstract: 

    F 1 F o ATP synthase functions as a biological generator and makes a major contribution to cellular energy production. Proton flow generates rotation in the F o motor that is transferred to the F 1 motor to catalyze ATP production, with flexible F 1 /F o coupling required for efficient catalysis. F 1 F o 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 F 1 F o 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 ο motor. This highlights the importance of the central rotor for flexible coupling of the F 1 and F o motors and provides further insight into the regulatory mechanism mediated by subunit ε.


  • Organizational Affiliation

    Molecular, Structural and Computational Biology Division, The Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit alpha
A, B, C
512Escherichia coliMutation(s): 0 
Gene Names: atpAECLG_02126
EC: 7.1.2.2
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit beta
D, E, F
460Escherichia coliMutation(s): 0 
Gene Names: atpDEWT59_16525WLH_03015
EC: 7.1.2.2
Membrane Entity: Yes 
UniProt
Find proteins for A0A192CEZ8 (Escherichia coli O25b:H4)
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UniProt GroupA0A192CEZ8
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase gamma chain284Escherichia coliMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for C3SLA2 (Escherichia coli)
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UniProt GroupC3SLA2
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase epsilon chain134Escherichia coliMutation(s): 0 
Gene Names: atpCCCU01_030215
Membrane Entity: Yes 
UniProt
Find proteins for A0A4V1DSB5 (Escherichia coli O145:NM)
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UniProt GroupA0A4V1DSB5
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit c77Escherichia coliMutation(s): 0 
Gene Names: atpEECJG_03465
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit deltaS [auth W]173Escherichia coliMutation(s): 0 
Gene Names: atpHHMPREF1611_00658
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit bT [auth X],
U [auth Y]
155Escherichia coliMutation(s): 0 
Gene Names: atpFECDG_04362
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit aV [auth a]266Escherichia coliMutation(s): 0 
Gene Names: 
atpBatpB_1A9X72_25250AAG43_003021ABE90_000165ACN68_12775ACN81_06510ACU57_03300AM464_11965AT335_004107AT845_000773AW119_07615BANRA_00251BANRA_02401BF481_004021BG944_002347BGZ_02071BGZ_04636BHS81_22305BJI68_21520BK292_20055BMT50_09740BMT91_10650BN17_36921BO068_002405BOH76_10175BON63_19140BON64_06080BON65_14675BON67_02005BON68_19950BON69_17475BON70_16820BON71_24505BON72_01125BON73_15370BON74_23490BON76_09200BON77_19820BON80_03525BON89_05760BON93_25670BON94_01520BON95_10870BON97_15985BTQ06_19305BvCmsF30A_02552BvCmsHHP056_00154BvCmsKKP036_01773BvCmsKKP061_01916BvCmsKSNP073_00093BvCmsNSP072_01187BVL39_06790C2U48_14255C3F40_16990C5N07_23075C5Y87_17890C9114_08770C9160_23510C9E67_00020CA593_07300CCS08_08920CDC27_20240CG692_21460CG831_001097CIG67_24440CO706_18150CR538_25535CR539_00375CV83915_02325CWS33_22485D0X26_21590D9D77_23770DAH17_15930DAH19_18320DAH20_23990DAH21_17755DAH22_23595DAH23_18155DAH24_17640DAH25_17895DAH26_16990DAH27_18155DAH28_17805DAH29_15920DAH31_22960DAH32_19125DAH33_22080DAH34_09105DAH36_07465DAH37_15370DAH38_15005DAH40_17005DAH41_14135DAH42_13455DAH43_16455DAH45_16835DAH46_15675DAH47_17330DAH48_15585DAH49_16665DAH50_22615DEN88_13850DEN89_15985DEN90_12370DEN91_23220DEN92_12205DEN93_09020DEN94_10360DEN95_14235DEN96_09840DEN97_10745DEN98_07855DEN99_11560DEO00_06580DEO01_09365DEO02_16525DEO03_19745DEO04_18940DEO05_18810DEO06_16220DEO07_15680DEO08_21650DEO09_18665DEO10_18930DEO11_18820DEO12_10795DEO13_12620DEO14_23345DEO15_11255DEO17_21830DEO18_15280DEO19_13515DEO20_16610DIV22_14605DN627_09995DNQ45_04220DRW19_13755DS732_00235DTL43_15450DTL90_16085DTM16_24900DXT69_23170DXT70_14015DXT71_06450E0I42_12470E2112_06550E2113_20865E2117_22135E2119_14450E2121_20725E2127_21210E2128_05660E2129_07955E2132_10910E2134_19715E4K51_16190E4T14_07510E5M02_07130E5P22_11935E5P23_15735E5P24_15900E5P25_18200E5P30_22395E5P31_17880E5P32_06360E5P33_18010E5P35_14070E5P36_12975E5P40_10335E5P51_17750E5P52_17720E5S34_11685E5S35_09845E5S36_12285E5S37_13645E5S38_13500E5S39_09575E5S42_10245E5S43_09805E5S44_11620E5S45_08675E5S47_13500E5S48_08510E5S51_11505E5S52_15360E5S53_08080E5S54_07200E5S55_07040E5S56_16355E5S57_15755EAI46_06675EAX79_08895EBP16_13415EC1094V2_4559EC95NR1_03180ECs4680ED648_17305EHD79_09605EI021_09305EIZ93_13995EKI52_15345EL79_4683EL80_4591ELT18_19250ELT20_19840ELT21_07710ELT41_12325ELU87_20420ELV08_24425ELX57_19380ELX65_18890ELX67_20675ELX72_20815ELX82_07860ELX84_11040ELX85_19160ELX87_21655ELY02_10830ELY39_11115ERS139208_02919EXX13_13750EYV17_12540EYV18_08920EYX47_15940F0L67_11195F2N31_18980F2N31_28875F9V24_15580F9X20_04505FDM60_00765FFF58_16420FOI11_016935FOI11_06245FQF29_14375FV293_15950FVB16_05450FWK02_01255FY127_20825G5632_18870G9448_14760GAJ26_16155GF699_13365GFY34_11825GIB53_15080GJ11_23870GKF89_22150GNZ05_15960GP662_07560GP946_02135GP954_05505GP979_07135GQA06_03740GQE64_11005GQF59_16640GQM04_04750GQM09_09025GRW05_11240GRW57_03900GRW81_18100GUC01_19690H0O72_18985HHH44_002067HKA49_003861HLZ50_19940HMV95_19405HV109_23865HV209_21670HVW19_22170HVW43_16300HVY77_25765HVZ71_25190HX136_24860I6H00_18485I6H01_13035I6H02_14225IH772_07040J0541_001625J4S20_002462J5U05_004128JE86ST02C_42930JE86ST05C_43010JFD_02815JNP96_27775NCTC10090_03054NCTC10418_07533NCTC10429_00459NCTC11126_01888NCTC11181_02279NCTC13127_06463NCTC13216_01845NCTC4450_02006NCTC8008_04535NCTC8179_05398NCTC8333_05845NCTC8622_01220NCTC8960_02611NCTC9036_04909NCTC9037_05079NCTC9045_05855NCTC9073_06659NCTC9111_05225NCTC9117_06282NCTC9706_02267ND22_002728PGD_00238RG28_23995SAMEA3472044_00548SAMEA3472056_03685SAMEA3472067_04030SAMEA3472080_03392SAMEA3472147_03706SAMEA3751407_02369SAMEA3752557_01245TUM18780_44040WP2S18E08_47850WR15_16550

Membrane Entity: Yes 
UniProt
Find proteins for C3SL77 (Escherichia coli)
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UniProt GroupC3SL77
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download Ideal Coordinates CCD File 
AA [auth C],
GA [auth F],
W [auth A],
Y [auth B]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
ADP
Query on ADP

Download Ideal Coordinates CCD File 
CA [auth D],
EA [auth E]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
BA [auth C],
DA [auth D],
FA [auth F],
X [auth A],
Z [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)Australia--

Revision History  (Full details and data files)

  • Version 1.0: 2023-01-25
    Type: Initial release
  • Version 1.1: 2024-06-12
    Changes: Data collection