8QBY

Respiratory complex I from Paracoccus denitrificans in MSP2N2 nanodiscs


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Respiratory complex I from Paracoccus denitrificans

Ivanov, B.S.Bridges, H.R.Hirst, J.Jarman, O.D.

To be published.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit KA [auth K]101Paracoccus denitrificans PD1222Mutation(s): 0 
EC: 7.1.1
Membrane Entity: Yes 
UniProt
Find proteins for A1B482 (Paracoccus denitrificans (strain Pd 1222))
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UniProt GroupA1B482
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductaseB [auth G]674Paracoccus denitrificans PD1222Mutation(s): 0 
EC: 7.1.1
UniProt
Find proteins for A1B489 (Paracoccus denitrificans (strain Pd 1222))
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UniProt GroupA1B489
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Protein-L-isoaspartate O-methyltransferaseC [auth t]217Paracoccus denitrificans PD1222Mutation(s): 0 
UniProt
Find proteins for A1B5L6 (Paracoccus denitrificans (strain Pd 1222))
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UniProt GroupA1B5L6
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit ID [auth I]163Paracoccus denitrificans PD1222Mutation(s): 0 
EC: 7.1.1
Membrane Entity: Yes 
UniProt
Find proteins for A1B486 (Paracoccus denitrificans (strain Pd 1222))
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UniProt GroupA1B486
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase subunit E239Paracoccus denitrificans PD1222Mutation(s): 0 
EC: 1.6.5.3
UniProt
Find proteins for A1B494 (Paracoccus denitrificans (strain Pd 1222))
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UniProt GroupA1B494
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit NF [auth N]499Paracoccus denitrificans PD1222Mutation(s): 0 
EC: 7.1.1
Membrane Entity: Yes 
UniProt
Find proteins for A1B479 (Paracoccus denitrificans (strain Pd 1222))
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UniProt GroupA1B479
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit HG [auth H]345Paracoccus denitrificans PD1222Mutation(s): 0 
EC: 7.1.1
Membrane Entity: Yes 
UniProt
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UniProt GroupA1B487
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit FH [auth F]431Paracoccus denitrificans PD1222Mutation(s): 0 
EC: 7.1.1
UniProt
Find proteins for A1B491 (Paracoccus denitrificans (strain Pd 1222))
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UniProt GroupA1B491
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit DI [auth D]412Paracoccus denitrificans PD1222Mutation(s): 0 
EC: 7.1.1
Membrane Entity: Yes 
UniProt
Find proteins for A1B495 (Paracoccus denitrificans (strain Pd 1222))
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UniProt GroupA1B495
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
NADH:ubiquinone oxidoreductase 17.2 kD subunitJ [auth q]124Paracoccus denitrificans PD1222Mutation(s): 0 
UniProt
Find proteins for A1B1H8 (Paracoccus denitrificans (strain Pd 1222))
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UniProt GroupA1B1H8
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit AK [auth A]121Paracoccus denitrificans PD1222Mutation(s): 0 
EC: 7.1.1
Membrane Entity: Yes 
UniProt
Find proteins for A1B498 (Paracoccus denitrificans (strain Pd 1222))
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UniProt GroupA1B498
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase chain 10L [auth J]200Paracoccus denitrificans PD1222Mutation(s): 0 
EC: 7.1.1
Membrane Entity: Yes 
UniProt
Find proteins for A1B483 (Paracoccus denitrificans (strain Pd 1222))
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UniProt GroupA1B483
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Zinc finger CHCC-type domain-containing proteinM [auth R]62Paracoccus denitrificans PD1222Mutation(s): 0 
UniProt
Find proteins for A1B357 (Paracoccus denitrificans (strain Pd 1222))
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UniProt GroupA1B357
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
ETC complex I subunit conserved regionN [auth Q]103Paracoccus denitrificans PD1222Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A1B1M0 (Paracoccus denitrificans (strain Pd 1222))
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UniProt GroupA1B1M0
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit CO [auth C]208Paracoccus denitrificans PD1222Mutation(s): 0 
EC: 7.1.1
Membrane Entity: Yes 
UniProt
Find proteins for A1B496 (Paracoccus denitrificans (strain Pd 1222))
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UniProt GroupA1B496
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit BP [auth B]175Paracoccus denitrificans PD1222Mutation(s): 0 
EC: 7.1.1
Membrane Entity: Yes 
UniProt
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UniProt GroupA1B497
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase subunit LQ [auth L]703Paracoccus denitrificans PD1222Mutation(s): 0 
EC: 1.6.5.3
Membrane Entity: Yes 
UniProt
Find proteins for A1B481 (Paracoccus denitrificans (strain Pd 1222))
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase subunit MR [auth M]513Paracoccus denitrificans PD1222Mutation(s): 0 
EC: 1.6.5.3
Membrane Entity: Yes 
UniProt
Find proteins for A1B480 (Paracoccus denitrificans (strain Pd 1222))
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UniProt GroupA1B480
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Small Molecules
Ligands 12 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL

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JA [auth H],
LB [auth M]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
U10
Query on U10

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YA [auth B]UBIQUINONE-10
C59 H90 O4
ACTIUHUUMQJHFO-UPTCCGCDSA-N
P5S
Query on P5S

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CB [auth L],
Z [auth I]
O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine
C42 H82 N O10 P
TZCPCKNHXULUIY-RGULYWFUSA-N
PC1
Query on PC1

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QA [auth D],
UA [auth J]
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C44 H88 N O8 P
NRJAVPSFFCBXDT-HUESYALOSA-N
3PE
Query on 3PE

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CA [auth N]
DB [auth L]
EA [auth N]
FA [auth N]
HB [auth M]
CA [auth N],
DB [auth L],
EA [auth N],
FA [auth N],
HB [auth M],
IA [auth H],
JB [auth M],
KB [auth M],
MA [auth H],
SA [auth q]
1,2-Distearoyl-sn-glycerophosphoethanolamine
C41 H82 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-N
3PH
Query on 3PH

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AB [auth L]
BB [auth L]
DA [auth N]
EB [auth L]
FB [auth L]
AB [auth L],
BB [auth L],
DA [auth N],
EB [auth L],
FB [auth L],
GA [auth N],
GB [auth M],
IB [auth M],
KA [auth H],
LA [auth H],
MB [auth M],
NA [auth H],
NB [auth M],
TA [auth A],
VA [auth J],
WA [auth J],
Y [auth I]
1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE
C39 H77 O8 P
YFWHNAWEOZTIPI-DIPNUNPCSA-N
FMN
Query on FMN

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OA [auth F]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
SF4
Query on SF4

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PA [auth F]
S [auth G]
T [auth G]
W [auth I]
X [auth I]
PA [auth F],
S [auth G],
T [auth G],
W [auth I],
X [auth I],
ZA [auth B]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
FES
Query on FES

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BA [auth E],
U [auth G]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
ZN
Query on ZN

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XA [auth R]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA
Query on CA

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AA [auth I],
HA [auth N],
OB [auth M],
RA [auth D]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
NA
Query on NA

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V [auth G]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
2MR
Query on 2MR
I [auth D]L-PEPTIDE LINKINGC8 H18 N4 O2ARG
FME
Query on FME
K [auth A]L-PEPTIDE LINKINGC6 H11 N O3 SMET
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1.0
MODEL REFINEMENTPHENIX1.2

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (MRC, United Kingdom)United KingdomMC_UU_00015/2
Medical Research Council (MRC, United Kingdom)United KingdomMC_UU_00028/1

Revision History  (Full details and data files)

  • Version 1.0: 2024-09-11
    Type: Initial release
  • Version 1.1: 2024-11-06
    Changes: Data collection, Structure summary