8QC1

Respiratory complex I from Paracoccus denitrificans in MSP2N2 nanodiscs (ND4 & ND5 focus refinement)

PDB DOI: https://doi.org/10.2210/pdb8QC1/pdb
EM Map EMD-18325: EMDB EMDataResource

Classification: OXIDOREDUCTASE
Organism(s): Paracoccus denitrificans PD1222
Mutation(s): No
Membrane Protein: Yes PDBTM

Deposited: 2023-08-25 Released: 2024-09-11
Deposition Author(s): Ivanov, B.S., Bridges, H.R., Hirst, J.
Funding Organization(s): Medical Research Council (MRC, United Kingdom)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.50 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 1.0 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.

Macromolecule Content

Total Structure Weight: 145.26 kDa
Atom Count: 9,431
Modelled Residue Count: 1,118
Deposited Residue Count: 1,216
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase subunit M	A [auth M]	513	Paracoccus denitrificans PD1222	Mutation(s): 0 EC: 1.6.5.3 Membrane Entity: Yes
UniProt
Find proteins for A1B480 (Paracoccus denitrificans (strain Pd 1222)) Explore A1B480 Go to UniProtKB: A1B480
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A1B480
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH dehydrogenase subunit L	B [auth L]	703	Paracoccus denitrificans PD1222	Mutation(s): 0 EC: 1.6.5.3 Membrane Entity: Yes
UniProt
Find proteins for A1B481 (Paracoccus denitrificans (strain Pd 1222)) Explore A1B481 Go to UniProtKB: A1B481
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A1B481
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CDL Query on CDL Download Ideal Coordinates CCD File SDF format, chain J [auth M] MOL2 format, chain J [auth M] mmCIF format, chain J [auth M]	J [auth M]	CARDIOLIPIN C₈₁ H₁₅₆ O₁₇ P₂ XVTUQDWPJJBEHJ-KZCWQMDCSA-L		Interactions Focus chain J [auth M] Interactions & Density Focus chain J [auth M]
P5S Query on P5S Download Ideal Coordinates CCD File SDF format, chain O [auth L] MOL2 format, chain O [auth L] mmCIF format, chain O [auth L]	O [auth L]	O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine C₄₂ H₈₂ N O₁₀ P TZCPCKNHXULUIY-RGULYWFUSA-N		Interactions Focus chain O [auth L] Interactions & Density Focus chain O [auth L]
3PE Query on 3PE Download Ideal Coordinates CCD File SDF format, chain F [auth M] SDF format, chain H [auth M] SDF format, chain I [auth M] SDF format, chain P [auth L] MOL2 format, chain F [auth M] MOL2 format, chain H [auth M] MOL2 format, chain I [auth M] MOL2 format, chain P [auth L] mmCIF format, chain F [auth M] mmCIF format, chain H [auth M] mmCIF format, chain I [auth M] mmCIF format, chain P [auth L]	F [auth M], H [auth M], I [auth M], P [auth L]	1,2-Distearoyl-sn-glycerophosphoethanolamine C₄₁ H₈₂ N O₈ P LVNGJLRDBYCPGB-LDLOPFEMSA-N		Interactions Focus chain F [auth M] Focus chain H [auth M] Focus chain I [auth M] Focus chain P [auth L] Interactions & Density Focus chain F [auth M] Focus chain H [auth M] Focus chain I [auth M] Focus chain P [auth L]
3PH Query on 3PH Download Ideal Coordinates CCD File SDF format, chain C [auth M] SDF format, chain D [auth M] SDF format, chain E [auth M] SDF format, chain G [auth M] SDF format, chain K [auth M] SDF format, chain L [auth M] SDF format, chain N [auth L] SDF format, chain Q [auth L] MOL2 format, chain C [auth M] MOL2 format, chain D [auth M] MOL2 format, chain E [auth M] MOL2 format, chain G [auth M] MOL2 format, chain K [auth M] MOL2 format, chain L [auth M] MOL2 format, chain N [auth L] MOL2 format, chain Q [auth L] mmCIF format, chain C [auth M] mmCIF format, chain D [auth M] mmCIF format, chain E [auth M] mmCIF format, chain G [auth M] mmCIF format, chain K [auth M] mmCIF format, chain L [auth M] mmCIF format, chain N [auth L] mmCIF format, chain Q [auth L]	C [auth M] D [auth M] E [auth M] G [auth M] K [auth M] C [auth M], D [auth M], E [auth M], G [auth M], K [auth M], L [auth M], N [auth L], Q [auth L]	1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE C₃₉ H₇₇ O₈ P YFWHNAWEOZTIPI-DIPNUNPCSA-N		Interactions Focus chain C [auth M] Focus chain D [auth M] Focus chain E [auth M] Focus chain G [auth M] Focus chain K [auth M] Focus chain L [auth M] Focus chain N [auth L] Focus chain Q [auth L] Interactions & Density Focus chain C [auth M] Focus chain D [auth M] Focus chain E [auth M] Focus chain G [auth M] Focus chain K [auth M] Focus chain L [auth M] Focus chain N [auth L] Focus chain Q [auth L]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain M MOL2 format, chain M mmCIF format, chain M	M	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain M Interactions & Density Focus chain M