6OQV

E. coli ATP Synthase State 2b


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Cryo-EM structures provide insight into how E. coli F1FoATP synthase accommodates symmetry mismatch.

Sobti, M.Walshe, J.L.Wu, D.Ishmukhametov, R.Zeng, Y.C.Robinson, C.V.Berry, R.M.Stewart, A.G.

(2020) Nat Commun 11: 2615-2615

  • DOI: 10.1038/s41467-020-16387-2
  • Primary Citation of Related Structures:  
    6VWK, 6WNR, 6WNQ, 6OQS, 6OQR, 6OQU, 6OQT, 6OQW, 6OQV, 6PQV

  • PubMed Abstract: 
  • F 1 F o ATP synthase functions as a biological rotary generator that makes a major contribution to cellular energy production. It comprises two molecular motors coupled together by a central and a peripheral stalk. Proton flow through the F o motor generates rotation of the central stalk, inducing conformational changes in the F 1 motor that catalyzes ATP production ...

    F 1 F o ATP synthase functions as a biological rotary generator that makes a major contribution to cellular energy production. It comprises two molecular motors coupled together by a central and a peripheral stalk. Proton flow through the F o motor generates rotation of the central stalk, inducing conformational changes in the F 1 motor that catalyzes ATP production. Here we present nine cryo-EM structures of E. coli ATP synthase to 3.1-3.4 Å resolution, in four discrete rotational sub-states, which provide a comprehensive structural model for this widely studied bacterial molecular machine. We observe torsional flexing of the entire complex and a rotational sub-step of F o associated with long-range conformational changes that indicates how this flexibility accommodates the mismatch between the 3- and 10-fold symmetries of the F 1 and F o motors. We also identify density likely corresponding to lipid molecules that may contribute to the rotor/stator interaction within the F o motor.


    Organizational Affiliation

    Faculty of Medicine, St Vincent's Clinical School, UNSW Sydney, Kensington, NSW, 2052, Australia. a.stewart@victorchang.edu.au.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ATP synthase subunit deltaA [auth W]177Escherichia coliMutation(s): 0 
Gene Names: atpHHMPREF1611_00658
Membrane Entity: Yes 
UniProt
Find proteins for P0ABA4 (Escherichia coli (strain K12))
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
ATP synthase subunit alphaD [auth A], C [auth B], B [auth C]513Escherichia coliMutation(s): 0 
Gene Names: atpAAD31_4476
EC: 7.1.2.2
Membrane Entity: Yes 
UniProt
Find proteins for P0ABB0 (Escherichia coli (strain K12))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
ATP synthase subunit bE [auth X], U [auth Y]156Escherichia coliMutation(s): 0 
Gene Names: atpFAD31_4478
Membrane Entity: Yes 
UniProt
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
ATP synthase epsilon chainF [auth H]139Escherichia coliMutation(s): 0 
Gene Names: atpCCCU01_030215
Membrane Entity: Yes 
UniProt
Find proteins for P0A6E6 (Escherichia coli (strain K12))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
ATP synthase gamma chainG287Escherichia coliMutation(s): 0 
Gene Names: atpGBN16_43751
Membrane Entity: Yes 
UniProt
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
ATP synthase subunit betaJ [auth D], I [auth E], H [auth F]471Escherichia coliMutation(s): 0 
Gene Names: atpDCDCO157_4410
EC: 7.1.2.2
Membrane Entity: Yes 
UniProt
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
ATP synthase subunit c79Escherichia coliMutation(s): 0 
Gene Names: atpEECJG_03465
Membrane Entity: Yes 
UniProt
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
ATP synthase subunit aV [auth a]271Escherichia coliMutation(s): 0 
Gene Names: 
atpBA6581_09625A8C65_04635A8G17_13205A9819_21465AC789_1c41260ACN002_3840ACN77_20010ACN81_06510ACU57_03300ACU90_00315AKG99_01200AM464_11965AMK83_17435AML07_02005AML35_23925APZ14_19970AU473_02230AUQ13_19445AUS26_01135AW059_18665AW106_23235B1K96_28785B7C53_19560BANRA_02401BANRA_03128BANRA_03214BANRA_04536BANRA_04611BB545_21600BHF46_03220BHS81_22305BIZ41_19310BK292_20055BK400_00980BMT53_14990BMT91_10650BN17_36921BTQ04_25560BTQ06_19305BUE81_18230BVL39_06790BW690_12705BWP17_17405BZL31_21415C2U48_14255C4J69_12205C5N07_23075C5P01_14375C5P43_18495C5P44_14015C6669_08960C7235_25075C7B02_15545C7B06_18115C7B07_18555CA593_07300CG691_14695CG692_21460CG705_13230CG706_05505COD30_14545COD46_05110CR538_25535CR539_00375CRD98_06365CRE06_22220CRM83_19985CV83915_02325CVH05_22810CWS33_22485D0X26_21590D2F89_18645D3821_26125D3I61_22220D6Z21_17295D7K63_14130D8K42_12760D9D20_15080D9D23_18435D9D65_17115D9D69_04800D9D77_23770D9E35_19420D9F57_04785D9G42_23250D9H12_19550D9H53_20710D9H66_14770D9H68_12120D9H70_07975D9H84_13135D9I18_08055D9I52_22315D9I93_11990D9J11_15870D9J44_15620D9J48_14640D9K10_12565DIV22_14605DL800_26315DL925_10465DLU27_05670DM262_10125DMI41_02740DNQ45_04220DOT75_06920DP258_23940DP277_10610DQF57_16240DS732_00235DTL43_15450DTL90_16085DV750_19840E2855_04743EAI42_11905EAI44_10320EAI52_06435EB510_22250EB553_22600EB569_11805EB595_21530EC1094V2_4559EC3234A_68c00800EC95NR1_03180ECs4680ED060_20795ED098_20360ED124_20405ED133_14365ED287_08070ED600_20035ED648_17305ED653_18700ED658_09750ED944_14625EEP03_14120EEP23_14845EF364_23525EFV06_19295EIA21_14165EL75_4432EL79_4683EL80_4591ERS085374_04660ERS085379_02386ERS085383_02615ERS085386_04244ERS085404_04407ERS150876_04315FORC28_6046GJ11_23870HW43_00205JD73_04915NCTC10090_03054NCTC10418_07533NCTC10429_00459NCTC10444_05020NCTC11022_03985NCTC11126_01888NCTC11181_02279NCTC13125_03147NCTC13127_06463NCTC13462_03577NCTC7152_05030NCTC8179_05398NCTC8622_01220NCTC8960_02611NCTC9036_04909NCTC9037_05079NCTC9045_05855NCTC9054_05546NCTC9055_01929NCTC9058_01885NCTC9062_03146NCTC9073_06659NCTC9111_05225NCTC9117_06282NCTC9119_05322NCTC9701_05266NCTC9703_04488NCTC9706_02267NCTC9969_05235PU06_21025RG28_23995RK56_018685RX35_03591SAMEA3472044_00548SAMEA3472047_02992SAMEA3472055_04839SAMEA3472056_03685SAMEA3472067_04030SAMEA3472070_05212SAMEA3472080_03392SAMEA3472108_02423SAMEA3472114_05011SAMEA3472147_03706SAMEA3484427_03569SAMEA3484429_03570SAMEA3484433_04143SAMEA3485101_04107SAMEA3752557_01245SAMEA3752559_04742SAMEA3753064_05400SAMEA3753097_00985SAMEA3753290_05396SAMEA3753300_04372SAMEA3753397_02464SK85_04068UN86_05680UN91_09915WQ89_11300WR15_16550

Membrane Entity: Yes 
UniProt
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP (Subject of Investigation/LOI)
Query on ATP

Download Ideal Coordinates CCD File 
AA [auth A], W [auth C], Y [auth B]ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
ADP (Subject of Investigation/LOI)
Query on ADP

Download Ideal Coordinates CCD File 
CA [auth F], EA [auth E], FA [auth D]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
PO4
Query on PO4

Download Ideal Coordinates CCD File 
GA [auth D]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
MG
Query on MG

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

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 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: 2020-06-03
    Type: Initial release
  • Version 1.1: 2020-06-10
    Changes: Database references
  • Version 1.2: 2020-06-24
    Changes: Data processing, Structure summary