8EW3 | pdb_00008ew3

Cryo EM structure of Vibrio cholerae NQR

PDB DOI: https://doi.org/10.2210/pdb8EW3/pdb
EM Map EMD-28641: EMDB EMDataResource

Classification: ELECTRON TRANSPORT, TRANSLOCASE
Organism(s): Vibrio cholerae O395
Expression System: Vibrio cholerae O395
Mutation(s): No
Membrane Protein: Yes OPM PDBTM MemProtMD

Deposited: 2022-10-21 Released: 2022-11-16
Deposition Author(s): Fuller, J.R., Juarez, O.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.65 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Novel cofactor binding motifs, electron transfer and ion pumping mechanisms of the respiratory complex NQR

Juarez, O., Fuller, J.R.

To be published.

Macromolecule Content

Total Structure Weight: 212.89 kDa
Atom Count: 11,902
Modeled Residue Count: 1,540
Deposited Residue Count: 1,934
Unique protein chains: 6

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Na(+)-translocating NADH-quinone reductase subunit A	A	446	Vibrio cholerae O395	Mutation(s): 0 Gene Names: nqrA, D6U24_04460, EYB64_17955, FLM02_04825 EC: 7.2.1.1
UniProt
Find proteins for A5F5X1 (Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395)) Explore A5F5X1 Go to UniProtKB: A5F5X1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A5F5X1
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Na(+)-translocating NADH-quinone reductase subunit B	B	415	Vibrio cholerae O395	Mutation(s): 0 Gene Names: nqrB, D6U24_04465, ERS013186_02082, ERS013198_02508, ERS013199_02395, ERS013200_04117, ERS013202_01883, ERS013206_02987, ERS013207_01958, EYB64_17950... nqrB, D6U24_04465, ERS013186_02082, ERS013198_02508, ERS013199_02395, ERS013200_04117, ERS013202_01883, ERS013206_02987, ERS013207_01958, EYB64_17950, F0H40_10090, FLM02_04820, FLM12_12920, FXE67_12105 EC: 7.2.1.1 Membrane Entity: Yes
UniProt
Find proteins for A5F5X0 (Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395)) Explore A5F5X0 Go to UniProtKB: A5F5X0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A5F5X0
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Na(+)-translocating NADH-quinone reductase subunit C	C	257	Vibrio cholerae O395	Mutation(s): 0 Gene Names: nqrC, BC353_01370, D6U24_04470, ERS013165_00616, ERS013186_02083, ERS013198_02507, ERS013199_02396, ERS013200_04118, ERS013201_01110, ERS013202_01884... nqrC, BC353_01370, D6U24_04470, ERS013165_00616, ERS013186_02083, ERS013198_02507, ERS013199_02396, ERS013200_04118, ERS013201_01110, ERS013202_01884, ERS013206_02988, ERS013207_01959, F0H40_10095, FLM02_04815, FLM12_12915 EC: 7.2.1.1 Membrane Entity: Yes
UniProt
Find proteins for A5F5Y7 (Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395)) Explore A5F5Y7 Go to UniProtKB: A5F5Y7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A5F5Y7
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Na(+)-translocating NADH-quinone reductase subunit D	D	210	Vibrio cholerae O395	Mutation(s): 0 Gene Names: nqrD, VC0395_A1881, VC395_2408 EC: 7.2.1.1 Membrane Entity: Yes
UniProt
Find proteins for A5F5Y6 (Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395)) Explore A5F5Y6 Go to UniProtKB: A5F5Y6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A5F5Y6
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Na(+)-translocating NADH-quinone reductase subunit E	E	198	Vibrio cholerae O395	Mutation(s): 0 Gene Names: nqrE, BC353_01360, D6U24_04480, ERS013165_00614, ERS013186_02085, ERS013198_02505, ERS013199_02398, ERS013200_04120, ERS013201_01112, ERS013202_01886... nqrE, BC353_01360, D6U24_04480, ERS013165_00614, ERS013186_02085, ERS013198_02505, ERS013199_02398, ERS013200_04120, ERS013201_01112, ERS013202_01886, ERS013206_02990, ERS013207_01961, EYB64_17935, F0315_08350, F0H40_10105, F0M16_14025, FLM02_04805, FLM12_12905 EC: 7.2.1.1 Membrane Entity: Yes
UniProt
Find proteins for A5F5Y5 (Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395)) Explore A5F5Y5 Go to UniProtKB: A5F5Y5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A5F5Y5
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Na(+)-translocating NADH-quinone reductase subunit F	F	408	Vibrio cholerae O395	Mutation(s): 0 Gene Names: nqrF, D6U24_04485, ERS013198_02504, ERS013199_02399, ERS013201_01113, ERS013202_01887, ERS013206_02991, EYB64_17930, FLM12_12900 EC: 7.2.1.1 Membrane Entity: Yes
UniProt
Find proteins for A5F5Y4 (Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395)) Explore A5F5Y4 Go to UniProtKB: A5F5Y4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A5F5Y4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FMN (Subject of Investigation/LOI) Query on FMN Download:Ideal Coordinates CCD File SDF format, chain J [auth C] SDF format, chain G [auth B] MOL2 format, chain J [auth C] MOL2 format, chain G [auth B] mmCIF format, chain J [auth C] mmCIF format, chain G [auth B]	G [auth B], J [auth C]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain G [auth B] Focus chain J [auth C] Interactions & Density Focus chain G [auth B] Focus chain J [auth C]
RBF (Subject of Investigation/LOI) Query on RBF Download:Ideal Coordinates CCD File SDF format, chain H [auth B] MOL2 format, chain H [auth B] mmCIF format, chain H [auth B]	H [auth B]	RIBOFLAVIN C₁₇ H₂₀ N₄ O₆ AUNGANRZJHBGPY-SCRDCRAPSA-N		Interactions Focus chain H [auth B] Interactions & Density Focus chain H [auth B]
UQ1 (Subject of Investigation/LOI) Query on UQ1 Download:Ideal Coordinates CCD File SDF format, chain I [auth B] MOL2 format, chain I [auth B] mmCIF format, chain I [auth B]	I [auth B]	UBIQUINONE-1 C₁₄ H₁₈ O₄ SOECUQMRSRVZQQ-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Interactions & Density Focus chain I [auth B]
FES (Subject of Investigation/LOI) Query on FES Download:Ideal Coordinates CCD File SDF format, chain K [auth E] MOL2 format, chain K [auth E] mmCIF format, chain K [auth E]	K [auth E]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain K [auth E] Interactions & Density Focus chain K [auth E]