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


This is version 1.0 of the entry. See complete history. 


Literature

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

Lan, W., Gao, Y., Bi, H.

To be published.

Macromolecules
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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
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
2-oxoglutarate synthase subunit alphaB [auth A],
F [auth G]		375Helicobacter pyloriMutation(s): 0 
Gene Names: C2R48_00275
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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
Entity Groups  
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UniProt GroupA0A024BZG2
Sequence Annotations
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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
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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