8DBU

E. coli ATP synthase imaged in 10mM MgATP State2 "down" Fo classified

• PDB DOI:  https://doi.org/10.2210/pdb8DBU/pdb
• EM Map EMD-27307: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• Deposited: 2022-06-14 Released: 2023-01-25 
• Deposition Author(s): Sobti, M., Stewart, A.G.
• Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.40 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

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

• PubMed: 36631659 
• 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 22-mer - A10B3C3D2E1F1G1H1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 22-mer - A10B6C1D1E1F1G1H1 

Local Symmetry: Cyclic - C10  (Explore in 3D)
Local Stoichiometry: Homo 10-mer - A10 Local Symmetry: Cyclic - C3  (Explore in 3D)
Local Stoichiometry: Homo 3-mer - C3 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 532.91 kDa 
• Atom Count: 36,917 
• Modelled Residue Count: 4,845 
• Deposited Residue Count: 4,895 
• Unique protein chains: 8

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase subunit alpha	A, B, C	513	Escherichia coli	Mutation(s): 0  Gene Names: atpA, ECLG_02126 EC: 7.1.2.2

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase subunit beta	D, E, F	460	Escherichia coli	Mutation(s): 0  Gene Names: atpD, EWT59_16525, WLH_03015 EC: 7.1.2.2 Membrane Entity: Yes
UniProt
Find proteins for A0A192CEZ8 (Escherichia coli O25b:H4) Explore A0A192CEZ8  Go to UniProtKB:  A0A192CEZ8

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase gamma chain	G	287	Escherichia coli	Mutation(s): 0  Gene Names:  atpG, atpG_1, A5U30_003290, A6592_18305, A8499_003851, A8502_003955, A9X72_25275, AAG43_003026, AAG80_004738, AAS29_003449, ACN68_12800, ACU57_03275, AF998_003408, AM464_11940, APX88_23995, AT335_004102, AT845_000768, AW118_21725, AW119_07640, AWP47_06340, B6R12_004264, B6R15_003154, B6R31_004850, B6R48_003395, B6R87_004916, BANRA_00246, BANRA_04799, BEA19_15290, BER14_24310, BF481_004026, BG944_002342, BGM66_001358, BHS81_22280, BJI68_21495, BJJ90_26485, BK292_20080, BK383_23390, BKL28_001431, BMT49_22370, BMT50_09765, BMT91_10625, BO068_002400, BOB65_002788, BON63_19115, BON64_06055, BON66_26890, BON68_19975, BON69_17450, BON72_01100, BON75_22045, BON76_09175, BON80_03550, BON81_25250, BON82_25505, BON83_15575, BON84_00135, BON86_07730, BON87_04115, BON88_19125, BON89_05735, BON90_04545, BON92_06025, BON95_10845, BON96_19380, BON97_15960, BON98_14785, BR158_003957, BR331_09110, BRV02_002572, BRV34_001508, BRV41_002028, BTB68_001535, BTQ06_19330, BUO55_001867, BvCmsHHP019_05385, BvCmsHHP056_00159, BvCmsKSNP073_00088, BVL39_06815, BXT93_21170, BZL69_24175, C0P57_002352, C1Q91_001801, C2121_002372, C2M16_19985, C2R31_003577, C3F40_17015, C5N07_23100, C9114_08795, C9E67_00045, C9Z68_15835, CA593_07325, CCS08_08895, CCV12_002411, CDC27_20215, CDL36_13060, CDL37_07525, CF22_002133, CG831_001092, CHM61_003636, CQ986_004529, CR538_25560, CR628_001673, CSE52_003589, CTR35_001178, CWS33_22510, CX690_003323, CX938_001099, CXJ73_003749, CY655_23810, D0X26_21565, D1H34_003056, D3G36_11035, D3Y67_00135, D4N09_17390, D4U49_15530, D9D43_11335, D9E34_14495, D9E49_10970, D9H94_18005, D9J03_09360, D9J61_13700, DAH18_20330, DAH19_18295, DAH20_24015, DAH21_17730, DAH23_18130, DAH24_17665, DAH25_17920, DAH26_16965, DAH31_22985, DAH33_22055, DAH34_09130, DAH35_20680, DAH37_15345, DAH38_15030, DAH40_17030, DAH42_13480, DAH43_16430, DAH45_16810, DAH46_15650, DAH47_17305, DAH48_15610, DAH49_16690, DD762_08985, DEN86_12400, DEN87_10835, DEN88_13825, DEN89_16010, DEN90_12395, DEN91_23245, DEN92_12230, DEN93_08995, DEN94_10335, DEN95_14210, DEN96_09815, DEN97_10720, DEN98_07830, DEN99_11535, DEO00_06605, DEO02_16550, DEO03_19720, DEO04_18965, DEO05_18835, DEO06_16245, DEO07_15705, DEO08_21675, DEO09_18690, DEO10_18955, DEO11_18845, DEO13_12595, DEO14_23370, DEO15_11230, DEO17_21855, DEO18_15255, DM870_19035, DN627_09970, DNQ45_04245, DNX30_13315, DRW19_13730, DS732_00210, DTL43_15425, DTL90_16110, DTM45_17550, DU321_22555, DXT69_23195, DXT73_04770, E0I42_12495, E2114_21430, E2115_20650, E2116_20405, E2118_21930, E2120_20890, E2123_19280, E2124_19895, E2125_20830, E2127_21235, E2129_07980, E2130_15715, E2131_06535, E2132_10935, E2133_17220, E2134_19690, E2135_06925, E2136_19955, E3N34_08900, E3O05_11760, E4K51_16165, E4T84_16615, E5H86_09085, E5P26_09545, E5P27_22845, E5P28_10570, E5P29_05185, E5P34_15705, E5S45_08700, E5S52_15385, E5S53_08055, E5S54_07225, E5S55_07015, E5S57_15780, E5S59_08710, E6D34_08960, EA239_12120, EA435_07830, EAI46_06700, EAN77_19470, EAX79_08870, EBP16_13390, ECs4675, EHD79_09580, EI021_09280, EIA08_19370, EIZ93_14020, EL79_4688, ELT16_12825, ELT17_19015, ELT24_10100, ELT25_13190, ELT26_19965, ELT28_22380, ELT31_15905, ELT32_22410, ELT35_13110, ELT36_21245, ELT39_13040, ELT44_12720, ELT48_19930, ELT49_15745, ELT52_17185, ELT54_16715, ELT56_20230, ELT58_19250, ELT60_07965, ELT61_16115, ELT63_20665, ELU85_22890, ELU96_15955, ELU98_21830, ELV01_18750, ELV02_15415, ELV03_17520, ELV08_24400, ELV10_16135, ELV11_18690, ELV12_21505, ELV13_15700, ELV15_16125, ELV16_20220, ELV21_12065, ELV26_08405, ELV28_03910, ELV40_12430, ELX68_12700, ELX69_19740, ELX76_22475, ELX79_13910, ELX96_13300, ELY32_23950, ELY36_20675, ELY41_15020, ELY48_10545, EN85_003463, EPS76_13990, ERS085406_02407, ERS085411_04313, ERS139208_02924, EWK56_18705, ExPECSC038_00222, EXX13_13725, F0L67_11220, F2N20_20320, F2N31_18955, F2N31_28850, F3N40_21715, F7F11_14340, F7N46_22015, F9413_21010, F9461_19825, F9B07_23365, F9S83_19915, F9V22_10990, F9V24_15555, FA849_20155, FA868_20675, FDM60_00740, FE584_11630, FE587_10635, FEJ01_08625, FEL34_12330, FFF58_16445, FGG80_19750, FHD44_19380, FHO90_23835, FIJ20_20550, FJQ40_21670, FKO60_16095, FNA08_11610, FOI11_016960, FOI11_06220, FPI65_22945, FPS11_21255, FQF29_14350, FV293_15975, FWK02_01230, FY127_20850, FZC17_20445, FZN31_24340, FZU14_23265, G3565_07700, G3V95_07060, G3W53_09190, G4A38_07015, G4A47_06415, G5603_13560, G7630_003974, G9448_14785, GAI66_12670, GAI89_17315, GAJ12_11620, GAJ26_16130, GF199_10830, GF698_17285, GF699_13340, GFY34_11800, GIB53_15055, GJ11_23845, GJO56_16000, GKF66_17460, GKF89_22125, GNW61_20550, GNZ05_15985, GOP25_14930, GP711_13495, GP944_09560, GP954_05530, GP965_06250, GP979_07110, GQA06_03765, GQM04_04775, GQM13_19780, GQM21_09995, GQN34_13890, GQW07_08580, GQW80_20445, GRC73_07760, GRO95_08210, GRW05_11265, GRW56_03580, GRW57_03875, GSM54_05950, GSY44_20705, GTP88_22615, GUC01_19665, GUI33_04255, H0O37_20080, H0O39_19775, H0O51_25120, H0O53_09535, H0O72_18960, H6Y26_002492, HEP30_003795, HEP34_004326, HHH44_002062, HI055_004373, HIE29_002423, HIN64_000504, HJ942_001824, HJQ60_003303, HJS37_002338, HKA49_003856, HL563_13665, HL601_17825, HLV18_19285, HLX92_16310, HLZ50_19965, HmCms169_04481, HMU06_12205, HMV95_19380, HMW38_12865, HNC59_18730, HNC59_28625, HNC66_19995, HNC99_14745, HNC99_28920, HV109_23890, HV146_24070, HV209_21695, HVV39_11770, HVW04_15255, HVW43_16325, HVZ71_25215, HX136_24885, I6H00_18510, I6H01_13010, I6H02_14200, IA00_003426, IFB95_001500, IH768_12440, IH772_07065, IT029_001525, J0541_001620, J4S20_002457, J5U05_004133, JE86ST02C_42880, JE86ST05C_42960, JFD_02820, JNP96_27800, NCTC10082_02362, NCTC10089_05028, NCTC10090_03059, NCTC10429_00464, NCTC10767_01013, NCTC10974_05706, NCTC11112_01880, NCTC11126_01882, NCTC11181_02284, NCTC13127_06468, NCTC13148_04071, NCTC13216_01840, NCTC4450_02011, NCTC7927_05535, NCTC7928_03201, NCTC8009_08817, NCTC8333_05850, NCTC8450_00026, NCTC8621_05141, NCTC8959_03773, NCTC9001_03646, NCTC9036_04914, NCTC9037_05084, NCTC9044_01989, NCTC9075_06807, NCTC9077_06277, NCTC9111_05230, NCTC9117_06287, NCTC9706_02272, NCTC9775_03454, NCTC9777_01404, ND22_002723, RG28_23970, SAMEA3472044_00553, SAMEA3472056_03690, SAMEA3472147_03711, SAMEA3751407_02374, SAMEA3753106_03210, TUM18780_44090, WP4S18E07_45030, XU56_002945 Membrane Entity: Yes
UniProt
Find proteins for C3SLA2 (Escherichia coli) Explore C3SLA2  Go to UniProtKB:  C3SLA2

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase epsilon chain	H	139	Escherichia coli	Mutation(s): 0  Gene Names: atpC Membrane Entity: Yes
UniProt
Find proteins for A0A4V1DSB5 (Escherichia coli O145:NM) Explore A0A4V1DSB5  Go to UniProtKB:  A0A4V1DSB5

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase subunit c	I, J, K [auth L], L [auth M], M [auth N], N [auth O], O [auth P], P [auth Q], Q [auth R], R [auth S]	79	Escherichia coli	Mutation(s): 0  Gene Names: atpE, ECJG_03465 Membrane Entity: Yes
UniProt
Find proteins for F4TL55 (Escherichia coli M718) Explore F4TL55  Go to UniProtKB:  F4TL55

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase subunit delta	S [auth W]	177	Escherichia coli	Mutation(s): 0  Gene Names: atpH, HMPREF1611_00658 Membrane Entity: Yes
UniProt
Find proteins for V0ZA15 (Escherichia coli 908573) Explore V0ZA15  Go to UniProtKB:  V0ZA15

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase subunit b	T [auth X], U [auth Y]	156	Escherichia coli	Mutation(s): 0  Gene Names: atpF Membrane Entity: Yes
UniProt
Find proteins for D6IFY0 (Escherichia coli B185) Explore D6IFY0  Go to UniProtKB:  D6IFY0

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase subunit a	V [auth a]	271	Escherichia coli	Mutation(s): 0  Gene Names:  atpB, atpB_1, A9X72_25250, AAG43_003021, ACN68_12775, ACN81_06510, ACU57_03300, AM464_11965, AT335_004107, AT845_000773, AW119_07615, BANRA_00251, BF481_004021, BG944_002347, BGM66_001363, BHS81_22305, BJI68_21520, BK292_20055, BLM69_002282, BMT50_09740, BMT91_10650, BN17_36921, BO068_002405, BOH76_10175, BON63_19140, BON64_06080, BON67_02005, BON68_19950, BON69_17475, BON70_16820, BON72_01125, BON76_09200, BON80_03525, BON89_05760, BON95_10870, BON97_15985, BRV02_002577, BTB68_001540, BTQ06_19305, BUO55_001872, BvCmsHHP056_00154, BvCmsKKP036_01773, BvCmsKKP061_01916, BvCmsKSNP073_00093, BVL39_06790, C1Q91_001796, C3F40_16990, C5N07_23075, C9114_08770, C9160_23510, C9E67_00020, CA593_07300, CCS08_08920, CDC27_20240, CF22_002138, CG831_001097, CHM61_003641, CIG67_24440, CO706_18150, CQ986_004524, CR538_25535, CR539_00375, CTR35_001183, CV83915_02325, CWS33_22485, CX938_001104, D0X26_21590, D4M65_17870, DAH19_18320, DAH20_23990, DAH21_17755, DAH22_23595, DAH23_18155, DAH24_17640, DAH25_17895, DAH26_16990, DAH27_18155, DAH28_17805, DAH31_22960, DAH32_19125, DAH33_22080, DAH34_09105, DAH37_15370, DAH38_15005, DAH40_17005, DAH41_14135, DAH42_13455, DAH43_16455, DAH45_16835, DAH46_15675, DAH47_17330, DAH48_15585, DAH49_16665, 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, 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, DXT69_23170, DXT71_06450, E0I42_12470, E2117_22135, E2127_21210, E2129_07955, E2132_10910, E2134_19715, E4K51_16190, E5H86_09110, E5S45_08675, E5S52_15360, E5S53_08080, E5S54_07200, E5S55_07040, E5S57_15755, E6D34_08985, EAI46_06675, EAX79_08895, EBP16_13415, EC95NR1_03180, ECs4680, EHD79_09605, EI021_09305, EIZ93_13995, EKI52_15345, EL79_4683, ELV08_24425, EN85_003468, ERS139208_02919, EXX13_13750, EYX47_15940, F0L67_11195, F2N20_20345, F2N31_18980, F2N31_28875, F9461_19850, F9V24_15580, FDM60_00765, FFF58_16420, FIJ20_20575, FJQ40_21695, FOI11_016935, FOI11_06245, FPJ29_19990, FPS11_21280, FQF29_14375, FV293_15950, FVB16_05450, FWK02_01255, FY127_20825, G3V95_07085, G9448_14760, GAI66_12695, GAI89_17340, GAJ12_11645, GAJ26_16155, GF699_13365, GFY34_11825, GIB53_15080, GJ11_23870, GJO56_16025, GKF89_22150, GNW61_20575, GNZ05_15960, GP944_09535, GP954_05505, GP965_06225, GP979_07135, GQA06_03740, GQM04_04750, GQM21_10020, GRW05_11240, GRW24_05800, GRW56_03605, GRW57_03900, GUC01_19690, H0O72_18985, HEP30_003770, HHH44_002067, HKA49_003861, HLZ50_19940, HMV95_19405, HV109_23865, HV209_21670, 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, NCTC8179_05398, NCTC8333_05845, NCTC8622_01220, NCTC8960_02611, NCTC9036_04909, NCTC9037_05079, NCTC9045_05855, NCTC9073_06659, NCTC9111_05225, NCTC9117_06282, NCTC9706_02267, ND22_002728, RG28_23995, SAMEA3472044_00548, SAMEA3472056_03685, SAMEA3472147_03706, SAMEA3751407_02369, SAMEA3752557_01245, TUM18780_44040, WR15_16550 Membrane Entity: Yes
UniProt
Find proteins for C3SL77 (Escherichia coli) Explore C3SL77  Go to UniProtKB:  C3SL77

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP	AA [auth C], DA [auth D], W [auth A], Y [auth B]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
ADP	EA [auth E], GA [auth F]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG	BA [auth C], CA [auth D], FA [auth E], X [auth A], Z [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.40 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-01-25 
Deposition Author(s): Sobti, M., Stewart, A.G.

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Funding Organization	Location	Grant Number
National Health and Medical Research Council (NHMRC, Australia)	Australia	--

Revision History  

• Version 1.0: 2023-01-25
  Type: Initial release