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 6WNR | pdb_00006wnr

E. coli ATP synthase State 3b


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report

Validation slider image for 6WNR

This is version 1.4 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: https://doi.org/10.1038/s41467-020-16387-2
  • Primary Citation Related Structures: 
    6OQR, 6OQS, 6OQT, 6OQU, 6OQV, 6OQW, 6PQV, 6VWK, 6WNQ, 6WNR

  • 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. 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: 
    • Molecular, Structural and Computational Biology Division, The Victor Chang Cardiac Research Institute, Darlinghurst, NSW, 2010, Australia.

Macromolecule Content 

  • Total Structure Weight: 536.82 kDa 
  • Atom Count: 36,934 
  • Modeled Residue Count: 4,851 
  • Deposited Residue Count: 4,928 
  • Unique protein chains: 8

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ATP synthase subunit deltaA [auth W]177Escherichia coliMutation(s): 0 
Gene Names: atpH, AB67_4411
Membrane Entity: Yes 
UniProt
Find proteins for P0ABA4 (Escherichia coli (strain K12))
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Go to UniProtKB:  P0ABA4
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UniProt GroupP0ABA4
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
ATP synthase subunit alphaB [auth C],
C [auth B],
D [auth A]
513Escherichia coliMutation(s): 0 
Gene Names: atpA
EC: 7.1.2.2
Membrane Entity: Yes 
UniProt
Find proteins for P0ABB0 (Escherichia coli (strain K12))
Explore P0ABB0 
Go to UniProtKB:  P0ABB0
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UniProt GroupP0ABB0
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
ATP synthase subunit bE [auth X],
U [auth Y]
156Escherichia coliMutation(s): 0 
Gene Names: atpF
Membrane Entity: Yes 
UniProt
Find proteins for P0ABA0 (Escherichia coli (strain K12))
Explore P0ABA0 
Go to UniProtKB:  P0ABA0
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UniProt GroupP0ABA0
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
ATP synthase epsilon chainF [auth H]139Escherichia coliMutation(s): 0 
Gene Names: atpC, A1WS_04460
Membrane Entity: Yes 
UniProt
Find proteins for P0A6E6 (Escherichia coli (strain K12))
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UniProt GroupP0A6E6
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
ATP synthase gamma chain287Escherichia coliMutation(s): 0 
Gene Names: atpG, BN16_43751
Membrane Entity: Yes 
UniProt
Find proteins for P0ABA6 (Escherichia coli (strain K12))
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UniProt GroupP0ABA6
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
ATP synthase subunit betaH [auth F],
I [auth E],
J [auth D]
471Escherichia coliMutation(s): 0 
Gene Names: atpD, WLH_03015
EC: 7.1.2.2
Membrane Entity: Yes 
UniProt
Find proteins for P0ABB4 (Escherichia coli (strain K12))
Explore P0ABB4 
Go to UniProtKB:  P0ABB4
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UniProt GroupP0ABB4
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
ATP synthase subunit c79Escherichia coliMutation(s): 0 
Gene Names: atpE, ECJG_03465
Membrane Entity: Yes 
UniProt
Find proteins for P68699 (Escherichia coli (strain K12))
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UniProt GroupP68699
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
ATP synthase subunit aV [auth a]271Escherichia coliMutation(s): 0 
Gene Names: 
atpB, A6581_09625, A8C65_04635, A8G17_13205, A9819_21465, AC789_1c41260, ACN002_3840, ACN77_20010, ACN81_06510, ACU57_03300, ACU90_00315, AKG99_01200, AM464_11965, AMK83_17435, AML07_02005, AML35_23925, APZ14_19970, AU473_02230, AUQ13_19445, AUS26_01135, AW059_18665, AW106_23235, B1K96_28785, B7C53_19560, BANRA_02401, BANRA_03128, BANRA_03214, BANRA_04536, BANRA_04611, BB545_21600, BHF46_03220, BHS81_22305, BIZ41_19310, BK292_20055, BK400_00980, BMT53_14990, BMT91_10650, BN17_36921, BTQ04_25560, BTQ06_19305, BUE81_18230, BVL39_06790, BW690_12705, BWP17_17405, BZL31_21415, C2U48_14255, C4J69_12205, C5N07_23075, C5P01_14375, C5P43_18495, C5P44_14015, C6669_08960, C7235_25075, C7B02_15545, C7B06_18115, C7B07_18555, CA593_07300, CG691_14695, CG692_21460, CG705_13230, CG706_05505, COD30_14545, COD46_05110, CR538_25535, CR539_00375, CRD98_06365, CRE06_22220, CRM83_19985, CV83915_02325, CVH05_22810, CWS33_22485, D0X26_21590, D2F89_18645, D3821_26125, D3I61_22220, D6Z21_17295, D7K63_14130, D8K42_12760, D9D20_15080, D9D23_18435, D9D65_17115, D9D69_04800, D9D77_23770, D9E35_19420, D9F57_04785, D9G42_23250, D9H12_19550, D9H53_20710, D9H66_14770, D9H68_12120, D9H70_07975, D9H84_13135, D9I18_08055, D9I52_22315, D9I93_11990, D9J11_15870, D9J44_15620, D9J48_14640, D9K10_12565, DIV22_14605, DL800_26315, DL925_10465, DLU27_05670, DM262_10125, DMI41_02740, DNQ45_04220, DOT75_06920, DP258_23940, DP277_10610, DQF57_16240, DS732_00235, DTL43_15450, DTL90_16085, DV750_19840, E2855_04743, EAI42_11905, EAI44_10320, EAI52_06435, EB510_22250, EB553_22600, EB569_11805, EB595_21530, EC1094V2_4559, EC3234A_68c00800, EC95NR1_03180, ECs4680, ED060_20795, ED098_20360, ED124_20405, ED133_14365, ED287_08070, ED600_20035, ED648_17305, ED653_18700, ED658_09750, ED944_14625, EEP03_14120, EEP23_14845, EF364_23525, EFV06_19295, EIA21_14165, EL75_4432, EL79_4683, EL80_4591, ERS085374_04660, ERS085379_02386, ERS085383_02615, ERS085386_04244, ERS085404_04407, ERS150876_04315, FORC28_6046, GJ11_23870, HW43_00205, JD73_04915, NCTC10090_03054, NCTC10418_07533, NCTC10429_00459, NCTC10444_05020, NCTC11022_03985, NCTC11126_01888, NCTC11181_02279, NCTC13125_03147, NCTC13127_06463, NCTC13462_03577, NCTC7152_05030, NCTC8179_05398, NCTC8622_01220, NCTC8960_02611, NCTC9036_04909, NCTC9037_05079, NCTC9045_05855, NCTC9054_05546, NCTC9055_01929, NCTC9058_01885, NCTC9062_03146, NCTC9073_06659, NCTC9111_05225, NCTC9117_06282, NCTC9119_05322, NCTC9701_05266, NCTC9703_04488, NCTC9706_02267, NCTC9969_05235, PU06_21025, RG28_23995, RK56_018685, RX35_03591, SAMEA3472044_00548, SAMEA3472047_02992, SAMEA3472055_04839, SAMEA3472056_03685, SAMEA3472067_04030, SAMEA3472070_05212, SAMEA3472080_03392, SAMEA3472108_02423, SAMEA3472114_05011, SAMEA3472147_03706, SAMEA3484427_03569, SAMEA3484429_03570, SAMEA3484433_04143, SAMEA3485101_04107, SAMEA3752557_01245, SAMEA3752559_04742, SAMEA3753064_05400, SAMEA3753097_00985, SAMEA3753290_05396, SAMEA3753300_04372, SAMEA3753397_02464, SK85_04068, UN86_05680, UN91_09915, WQ89_11300, WR15_16550

Membrane Entity: Yes 
UniProt
Find proteins for P0AB98 (Escherichia coli (strain K12))
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UniProt GroupP0AB98
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP

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
ADP

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
PO4

Query on PO4



Download:Ideal Coordinates CCD File
GA [auth D]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
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

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



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: Structure summary
  • Version 1.3: 2024-03-06
    Changes: Data collection, Database references, Derived calculations
  • Version 1.4: 2025-05-28
    Changes: Data collection, Structure summary