6OQW

E. coli ATP synthase State 3a


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report



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
  • Structures With Same Primary Citation

  • 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 ...

    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 LengthOrganismDetails
ATP synthase subunit deltaW177Escherichia coliMutation(s): 0 
Gene Names: atpHHMPREF1611_00658
Find proteins for V0ZA15 (Escherichia coli 908573)
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ATP synthase subunit alphaA, B, C513Escherichia coli 2-427-07_S4_C3Mutation(s): 0 
Gene Names: atpAAD31_4476
EC: 7.1.2.2
Find proteins for A0A073FQ32 (Escherichia coli 2-427-07_S4_C3)
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
ATP synthase subunit bX, Y156Escherichia coli 2-427-07_S4_C3Mutation(s): 0 
Gene Names: atpFAD31_4478
Find proteins for A0A073FPT7 (Escherichia coli 2-427-07_S4_C3)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
ATP synthase epsilon chainH139Escherichia coli O145:NMMutation(s): 0 
Gene Names: atpCCCU01_030215
Find proteins for A0A4V1DSB5 (Escherichia coli O145:NM)
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
ATP synthase gamma chainG287Escherichia coli chi7122Mutation(s): 0 
Gene Names: atpGBN16_43751
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
ATP synthase subunit betaD, E, F471Escherichia coli Xuzhou21Mutation(s): 0 
Gene Names: atpDCDCO157_4410
EC: 7.1.2.2
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
ATP synthase subunit cI, J, L, M, N, O, P, Q, R, S79Escherichia coliMutation(s): 0 
Gene Names: atpEECJG_03465
Find proteins for F4TL55 (Escherichia coli M718)
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  • Reference Sequence

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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
ATP synthase subunit aa271Escherichia 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_16550A6V01_13905A9X72_25250ACN68_12775AWB10_26310BHF03_11720BHJ80_00225BK296_18055BMA87_22930BOH76_10175BON63_19140BON65_14675BON69_17475BON71_24505BON72_01125BON76_09200BON94_01520BON95_10870BvCms2454_00281BvCms28BK_02489BvCms35BK_04117BvCmsC61A_04415BvCmsHHP001_00453BvCmsHHP056_00154BvCmsKKP036_01773BvCmsKKP061_01916BvCmsKSNP073_00093BvCmsKSNP081_05071BvCmsKSNP120_03395BvCmsKSP011_01371BvCmsKSP024_04404BvCmsKSP026_00181BvCmsKSP045_03908BvCmsKSP058_02760BvCmsKSP067_00562BvCmsKSP076_00424BvCmsNSNP036_04867BvCmsNSP006_02080BvCmsNSP007_04528BvCmsNSP047_02777BvCmsNSP072_01187BvCmsOUP014_03362BvCmsSINP011_01257BvCmsSINP022_02724BvCmsSIP019_01743BvCmsSIP044_00499C9098_18860C9114_08770C9160_23510C9162_15620C9201_16960C9306_10215C9E67_00020C9Z03_01220C9Z23_09490C9Z28_20370C9Z29_14640C9Z37_12720C9Z39_22645C9Z69_09245C9Z70_17985C9Z89_23245CDC27_20240CF006_11055CI641_012050CI693_04745CI694_10005CIG45_22185CJU63_22185CJU64_22320CMR93_11185CO706_18150D2184_12985D2185_10375D4011_10175D4023_13855D4074_11080D4628_10500D4636_13715D4638_14030D4660_11590D4718_17720D4L91_08515D4M06_08335D4U85_12055D5H35_02975D5I97_20230D6004_02875D6C36_11220D6D43_12450D6T60_12750D6T98_06775D6W00_24075D6X36_14360D6X63_19260D6X76_15770D7K33_13710D7K66_10765D7W70_03850D7Z75_18930D8Y65_22425D9610_01775D9D44_13565D9E19_19095D9E73_18625D9F87_23820D9G29_11550D9G69_19305D9G95_12740D9I87_07940D9I97_18935D9J52_19590D9J63_09365D9K48_05990D9K54_02710D9L89_14160D9S45_18285D9X77_10480D9X97_21615DAH26_16990DAH32_19125DAH34_09105DAH37_15370DAH43_16455DBQ99_25830DEN89_15985DEN97_10745DEO04_18940DEO19_13515DJ503_21285DK132_06520DL292_08945DL326_21700DL455_13635DL479_19395DL530_06530DL705_04390DLT82_05575DLU50_05805DLU67_18915DLU82_11225DLW60_08435DLX40_10810DLY41_02290DLY44_15035DM155_02910DM267_18590DM296_19990DM382_01995DM820_16020DM962_09605DM973_13335DMI04_10190DMI53_10480DMO02_11775DMY83_12215DN627_09995DN660_14530DN700_15395DN703_10755DN808_15535DNB37_12895DND79_13835DNI21_17685DNJ62_13625DNK12_11325DNR35_18440DNW42_09920DNX19_19905DOE35_09675DOS18_10255DOT81_11345DOU81_08765DOY22_15010DOY56_10725DOY61_15040DOY67_09070DP265_03290DQE91_13520DQF71_08105DQF72_05820DQG35_23905DQO13_14620DQP61_06090DRP48_11690DRW19_13755DS143_08340DS721_08790DT034_13820DVB38_01845DXT69_23170DXT71_06450DXX80_012780E0I42_12470E0K84_08760E2112_06550E2119_14450E2127_21210E2128_05660E2129_07955E2134_19715E2863_04339E4K55_18930E4K60_17185E5P22_11935E5S42_10245E5S47_13500EA213_15905EA223_15900EAI46_06675EAM59_19015EAN70_12780EAX79_08895EB476_21525EB509_20085EB515_14180EBA46_18920EBA84_13295EBJ06_18130EBM08_01735EC3426_00041EC382_16060ECTO6_04776ED225_21160ED307_04675ED607_18830ED611_15550ED903_15875EEA45_20970EF173_14695EG075_17095EG599_08845EG796_07205EGC26_18240EGU87_10010EH412_16410EHD63_20970EHD79_09605EHJ36_17270EHJ66_15250EHV81_10455EHV90_11205EHW09_18920EHX09_10245EI021_09305EI028_20515EI032_05105EI041_19815EIZ86_18085EIZ93_13995EJ366_23160EJC75_18335EKI52_15345ELT20_19840ELV08_24425EO241_24385EPT01_04130EQ825_04780EXM29_08385EXX06_15355EXX13_13750EXX23_21120EXX24_15045EXX53_13875EXX55_17050EXX71_21770EXX78_08825EXX87_24120EYD11_23075EYY78_20435F1E13_14495F1E19_19440F7F00_12795F7F18_09175F7F23_11700F7F26_17820F7F29_10290F7G01_11555F7G03_21945F9Z74_13490FE846_11995FQ022_10645FQ915_15565FQR64_23085FQZ46_08310FRV13_17455FV293_15950FV438_15615FVB16_05450FWK02_01255FY127_20825FZ043_25135GHR40_04795GII67_11535GIY19_17515GJD97_27285GKF74_18975GKF86_20550GKF89_22150GKG12_12770GN312_09740GNZ03_19905GP654_17460GP661_13410GP664_09215GP666_22490GP689_17865GP700_17560GP720_16435GP727_19735GP912_19340GP935_23765GP946_02135GP950_06840GQA06_03740GQE22_20175GQE30_11445GQE34_04175GQE42_18115GQE51_13765GQE64_11005GQE93_08335GQM06_02630GQM09_09025GQM17_19285GQN16_14355GRW42_15600GRW80_05440HmCms184_00443HmCmsJML079_01077NCTC10963_05094NCTC13216_01845PGD_00238SAMEA3472043_04155SAMEA3752553_02696

Find proteins for C3SL77 (Escherichia coli)
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

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A, B, C
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
ADP
Query on ADP

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D, E, F
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
PO4
Query on PO4

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D
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
MG
Query on MG

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A, B, C, D, F
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 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 

  • Version 1.0: 2020-06-24
    Type: Initial release