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 8YS5 | pdb_00008ys5

Cryo-EM structure of the Helicobacter pylori OorDABC complex in the apo-form

  • Classification: OXIDOREDUCTASE
  • Organism(s): Helicobacter pylori
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2024-03-22 Released: 2025-07-02 
  • Deposition Author(s): Lan, W., Gao, Y., Bi, H.
  • Funding Organization(s): National Natural Science Foundation of China (NSFC), The National Key Research and Development Program of China, Shanghai Rising-Star Program

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.95 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 8YS5

This is version 1.2 of the entry. See complete history. 

Literature

2-oxoglutarate:acceptor oxidoreductase-catalyzed redox cycling effectively targets coccoid forms of Helicobacter pylori.

Hang, X., Lan, W., Yanqiang, H., Huang, H., Zhang, M., Zeng, L., Shi, T., Bai, Y., Yang, Z., Hu, S., Wang, J., Dong, L., Tong, Q., Jia, J., Bi, S., Xia, Q., Gao, Y., Bi, H.

(2025) Nat Commun 16: 6965-6965

  • DOI: https://doi.org/10.1038/s41467-025-62477-4
  • Primary Citation Related Structures: 
    8YS5, 8YS6

  • PubMed Abstract: 

    Helicobacter pylori, a globally significant pathogen, plays a central etiological role in diverse gastric pathologies ranging from chronic gastritis and peptic ulcers to gastric adenocarcinoma. Although conventional antibiotics effectively inhibit or kill growing helical H. pylori, metabolically dormant coccoid forms of H. pylori exhibit considerable tolerance, posing a persistent and clinically significant challenge. Here, we report napabucasin (2-acetylfuro-1,4-naphthoquinone) as a redox-cycling antibiotic with potent bactericidal activity against both drug-resistant helical and coccoid forms of H. pylori. Notably, napabucasin does not induce acquired resistance in vitro and demonstrates superior efficacy compared to standard triple therapy in murine infection models. Mechanistic studies reveal that napabucasin acts through 2-oxoglutarate:acceptor oxidoreductase (OOR)-catalyzed futile redox cycling, generating bactericidal levels of reactive oxygen species (ROS). Compared to menaquinone 6, a proposed physiological electron acceptor, napabucasin exhibits enhanced oxidative capacity. Structural, biochemical, and microbiological analyses identify Leu44 and Lys46 within the OorD subunit as critical residues for napabucasin recognition and catalysis. These findings establish OOR-mediated redox cycling as a robust antimicrobial strategy that sustains endogenous ROS production to combat refractory H. pylori infections.

    • Organizational Affiliation: 
    • NHC Key Laboratory of Tropical Disease Control, School of Tropical Medicine, Hainan Medical University, Haikou, Hainan, China.

Macromolecule Content 

  • Total Structure Weight: 212.55 kDa 
  • Atom Count: 14,618 
  • Modeled Residue Count: 1,874 
  • Deposited Residue Count: 1,894 
  • Unique protein chains: 4

Macromolecules

Find similar proteins by:
|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
2-oxoglutarate:acceptor oxidoreductaseA [auth D],
E [auth F]		113Helicobacter pyloriMutation(s): 0 
Gene Names: AM496_04450, BB411_07145, C2R64_04560, D8X81_03145, DD775_02535, EC515_04135, EC541_05865, EC589_03065, HPY1198_04840, HPY1846_01345
UniProt
Find proteins for O68227 (Helicobacter pylori)
Explore O68227 
Go to UniProtKB:  O68227
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UniProt GroupO68227
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Reference Sequence
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|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
2-oxoglutarate synthase subunit alphaB [auth A],
F [auth G]		375Helicobacter pyloriMutation(s): 0 
Gene Names: C2R48_00275
UniProt
Find proteins for B5Z6W0 (Helicobacter pylori (strain G27))
Explore B5Z6W0 
Go to UniProtKB:  B5Z6W0
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UniProt GroupB5Z6W0
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Reference Sequence
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|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
2-oxoglutarate ferredoxin oxidoreductase subunit betaC,
G [auth H]		273Helicobacter pyloriMutation(s): 0 
Gene Names: 
oorB, korB, AM497_01150, AM498_01330, B0X30_00560, B0X44_00010, B0X50_03675, B0X54_05595, B0X62_02935, BB411_07135, BB413_05640, BB424_05915, BB459_03745, BB461_04720, BB464_04365, BB477_04855, BB479_06520, BGL55_07715, BGL66_00450, BGL68_05120, BGL69_01465, BGL72_06170, BXP09_03780, C2840_03070, C2R45_06185, C2R60_07105, C2R62_02105, C2R64_04570, C2R66_01600, C2R71_01550, C2R81_00990, C2R85_07970, C2R86_01670, C2R96_02100, C2S01_06600, C2S04_03540, C2S07_06030, C2S08_01675, C2S19_05560, C2S26_01775, C2S41_04370, C2S43_01830, C2S44_08445, CV723_03795, CV726_04550, CV728_03440, CV729_03960, CV730_03830, D2C73_05440, D2C76_08055, D2C79_04285, D2C84_02640, D2C85_05055, D2C87_02355, D8X56_03120, D8X81_03155, DD750_02510, DD754_03015, DD756_02785, DD764_03055, DD775_02545, DD794_03540, DDP37_03580, DDP42_03140, DDP57_02985, EC508_04845, EC515_04145, EC518_06710, EC525_03565, EC532_06000, EC533_02415, EC535_02670, EC538_03525, EC547_02955, EC551_04645, EC553_02910, EC556_02780, EC568_02905, EC569_04000, EC570_04715, EC572_05350, EC574_04050, EC582_05020, EC589_03055, EC595_02590, EC597_01970, EC598_00990, EC600_00880, EC601_02710, ECB88_05740, ECB91_01840, ECC09_04670, ECC11_04890, ECC12_01920, ECC19_03410, ECC24_01145, ECC25_02460, ECC26_02695, ECC33_03050, ECC34_02995, ECC35_03455, ECC43_04085, ECC49_04355, ECE46_02140, EDB75_01155, EDC85_02050, EGW01_04140, EPC67_05165, EPC72_01580, EPC80_01190, F7187_05770, F7198_05900, F7221_03625, F7229_07365, HPPMSS1_c00647, HPY1198_04850, NCTC12823_00718

EC: 1.2.7.3
UniProt
Find proteins for A0A024BZG2 (Helicobacter pylori)
Explore A0A024BZG2 
Go to UniProtKB:  A0A024BZG2
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UniProt GroupA0A024BZG2
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Reference Sequence
Find similar proteins by:
|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
2-oxoglutarate:acceptor oxidoreductaseD [auth B],
H [auth I]		186Helicobacter pyloriMutation(s): 0 
Gene Names: oorC, C2R64_04575, C2S01_06595, EC570_04720, ECC29_01410, ECC33_03045
UniProt
Find proteins for B5Z6W2 (Helicobacter pylori (strain G27))
Explore B5Z6W2 
Go to UniProtKB:  B5Z6W2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB5Z6W2
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TPP
(Subject of Investigation/LOI)

Query on TPP


Download:Ideal Coordinates CCD File
M [auth C],
R [auth H]		THIAMINE DIPHOSPHATE
C12 H19 N4 O7 P2 S
AYEKOFBPNLCAJY-UHFFFAOYSA-O
SF4
(Subject of Investigation/LOI)

Query on SF4


Download:Ideal Coordinates CCD File
I [auth D]
J [auth D]
K [auth C]
N [auth F]
O [auth F]
I [auth D],
J [auth D],
K [auth C],
N [auth F],
O [auth F],
P [auth H]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
MG
(Subject of Investigation/LOI)

Query on MG


Download:Ideal Coordinates CCD File
L [auth C],
Q [auth H]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.95 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History 

& Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China82302542
National Natural Science Foundation of China (NSFC)China82073899
National Natural Science Foundation of China (NSFC)China31570053
National Natural Science Foundation of China (NSFC)China31870029
The National Key Research and Development Program of China2018YFC0311003
The National Key Research and Development Program of China2022YFA1305900
Shanghai Rising-Star Program23QA1406400

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-02
    Type: Initial release
  • Version 1.1: 2026-01-21
    Changes: Data collection, Database references
  • Version 1.2: 2026-08-12
    Type: Remediation
    Reason: Metalloprotein remediation
    Changes: Data collection, Derived calculations, Structure summary