7P63

Complex I from E. coli, DDM/LMNG-purified, under Turnover at pH 6, Closed state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 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

A universal coupling mechanism of respiratory complex I

Kravchuk, V.Petrova, O.Kampjut, D.Wojciechowska-Bason, A.Breese, Z.Sazanov, L.

(2022) Nature 


Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit FA [auth F]445Escherichia coli BL21(DE3)Mutation(s): 0 
Gene Names: ECBD_1377
EC: 7.1.1
UniProt
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UniProt GroupA0A140N9Z7
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase I subunit EB [auth E]166Escherichia coli BL21(DE3)Mutation(s): 0 
Gene Names: ECBD_1376
UniProt
Find proteins for A0A140N9K4 (Escherichia coli (strain B / BL21-DE3))
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UniProt GroupA0A140N9K4
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductaseC [auth G]908Escherichia coli BL21(DE3)Mutation(s): 0 
Gene Names: ECBD_1378
EC: 7.1.1
UniProt
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UniProt GroupA0A140N9P3
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit C/DD [auth C]600Escherichia coli BL21(DE3)Mutation(s): 0 
Gene Names: nuoCnuoCDnuoDECBD_1375
EC: 7.1.1
UniProt
Find proteins for A0A140N745 (Escherichia coli (strain B / BL21-DE3))
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UniProt GroupA0A140N745
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit BE [auth B]220Escherichia coli BL21(DE3)Mutation(s): 0 
Gene Names: nuoBECBD_1374
EC: 7.1.1
UniProt
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UniProt GroupA0A140N560
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit IF [auth I]180Escherichia coli BL21(DE3)Mutation(s): 0 
Gene Names: nuoIECBD_1380
EC: 7.1.1
UniProt
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit HG [auth H]325Escherichia coli BL21(DE3)Mutation(s): 0 
Gene Names: nuoHECBD_1379
EC: 7.1.1
UniProt
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit AH [auth A]147Escherichia coli BL21(DE3)Mutation(s): 0 
Gene Names: nuoAECBD_1373
EC: 7.1.1
UniProt
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Proton-translocating NADH-quinone oxidoreductase, chain LI [auth L]613Escherichia coli BL21(DE3)Mutation(s): 0 
Gene Names: ECBD_1383
UniProt
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase I subunit MJ [auth M]509Escherichia coli BL21(DE3)Mutation(s): 0 
Gene Names: ECBD_1384
UniProt
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit NK [auth N]485Escherichia coli BL21(DE3)Mutation(s): 0 
Gene Names: nuoNECBD_1385
EC: 7.1.1
UniProt
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit KL [auth K]100Escherichia coli BL21(DE3)Mutation(s): 0 
Gene Names: nuoKB21_02164ECBD_1382ECD_02204
EC: 7.1.1
UniProt
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit JM [auth J]184Escherichia coli BL21(DE3)Mutation(s): 0 
Gene Names: ECBD_1381
EC: 7.1.1
UniProt
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Small Molecules
Ligands 8 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3PE
Query on 3PE

Download Ideal Coordinates CCD File 
BA [auth A],
CA [auth L],
EA [auth L],
FA [auth L],
GA [auth M],
BA [auth A],
CA [auth L],
EA [auth L],
FA [auth L],
GA [auth M],
HA [auth M],
KA [auth J],
LA [auth J]
1,2-Distearoyl-sn-glycerophosphoethanolamine
C41 H82 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-N
 Ligand Interaction
NAI
Query on NAI

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P [auth F]1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
C21 H29 N7 O14 P2
BOPGDPNILDQYTO-NNYOXOHSSA-N
 Ligand Interaction
FMN
Query on FMN

Download Ideal Coordinates CCD File 
O [auth F]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
SF4
Query on SF4

Download Ideal Coordinates CCD File 
N [auth F],
R [auth G],
S [auth G],
T [auth G],
X [auth B],
N [auth F],
R [auth G],
S [auth G],
T [auth G],
X [auth B],
Y [auth I],
Z [auth I]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
DCQ (Subject of Investigation/LOI)
Query on DCQ

Download Ideal Coordinates CCD File 
W [auth C]2-decyl-5,6-dimethoxy-3-methylcyclohexa-2,5-diene-1,4-dione
C19 H30 O4
VMEGFMNVSYVVOM-UHFFFAOYSA-N
 Ligand Interaction
LFA
Query on LFA

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AA [auth H],
DA [auth L],
IA [auth N],
JA [auth N]
EICOSANE
C20 H42
CBFCDTFDPHXCNY-UHFFFAOYSA-N
 Ligand Interaction
FES
Query on FES

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Q [auth E],
U [auth G]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
V [auth G]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

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

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not fundedAustria25541

Revision History  (Full details and data files)

  • Version 1.0: 2022-09-21
    Type: Initial release