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- PDB-8ad5: X-ray structure of NqrF(129-408)of Vibrio cholerae variant F406A -

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Basic information

Entry
Database: PDB / ID: 8ad5
TitleX-ray structure of NqrF(129-408)of Vibrio cholerae variant F406A
ComponentsNa(+)-translocating NADH-quinone reductase subunit F
KeywordsFLAVOPROTEIN / NADH / FAD / Na+-NQR / NADH ubiquinone oxido reducatase
Function / homology
Function and homology information


NADH:ubiquinone reductase (Na+-transporting) / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / sodium ion transport / 2 iron, 2 sulfur cluster binding / metal ion binding / plasma membrane
Similarity search - Function
Na(+)-translocating NADH-quinone reductase subunit F / Flavoprotein pyridine nucleotide cytochrome reductase-like, FAD-binding domain / Oxidoreductase FAD-binding domain / 2Fe-2S iron-sulfur cluster binding domain / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / Oxidoreductase FAD/NAD(P)-binding / Oxidoreductase NAD-binding domain ...Na(+)-translocating NADH-quinone reductase subunit F / Flavoprotein pyridine nucleotide cytochrome reductase-like, FAD-binding domain / Oxidoreductase FAD-binding domain / 2Fe-2S iron-sulfur cluster binding domain / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / Oxidoreductase FAD/NAD(P)-binding / Oxidoreductase NAD-binding domain / FAD-binding domain, ferredoxin reductase-type / Ferredoxin-NADP reductase (FNR), nucleotide-binding domain / Ferredoxin reductase-type FAD binding domain profile. / Riboflavin synthase-like beta-barrel
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Na(+)-translocating NADH-quinone reductase subunit F
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsFritz, G.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)311211092 Germany
CitationJournal: Nat Struct Mol Biol / Year: 2023
Title: Conformational coupling of redox-driven Na-translocation in Vibrio cholerae NADH:quinone oxidoreductase.
Authors: Jann-Louis Hau / Susann Kaltwasser / Valentin Muras / Marco S Casutt / Georg Vohl / Björn Claußen / Wojtek Steffen / Alexander Leitner / Eckhard Bill / George E Cutsail / Serena DeBeer / ...Authors: Jann-Louis Hau / Susann Kaltwasser / Valentin Muras / Marco S Casutt / Georg Vohl / Björn Claußen / Wojtek Steffen / Alexander Leitner / Eckhard Bill / George E Cutsail / Serena DeBeer / Janet Vonck / Julia Steuber / Günter Fritz /
Abstract: In the respiratory chain, NADH oxidation is coupled to ion translocation across the membrane to build up an electrochemical gradient. In the human pathogen Vibrio cholerae, the sodium-pumping NADH: ...In the respiratory chain, NADH oxidation is coupled to ion translocation across the membrane to build up an electrochemical gradient. In the human pathogen Vibrio cholerae, the sodium-pumping NADH:quinone oxidoreductase (Na-NQR) generates a sodium gradient by a so far unknown mechanism. Here we show that ion pumping in Na-NQR is driven by large conformational changes coupling electron transfer to ion translocation. We have determined a series of cryo-EM and X-ray structures of the Na-NQR that represent snapshots of the catalytic cycle. The six subunits NqrA, B, C, D, E, and F of Na-NQR harbor a unique set of cofactors that shuttle the electrons from NADH twice across the membrane to quinone. The redox state of a unique intramembranous [2Fe-2S] cluster orchestrates the movements of subunit NqrC, which acts as an electron transfer switch. We propose that this switching movement controls the release of Na from a binding site localized in subunit NqrB.
History
DepositionJul 7, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 12, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.title
Revision 1.2Sep 27, 2023Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Nov 22, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.4Feb 7, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Na(+)-translocating NADH-quinone reductase subunit F
B: Na(+)-translocating NADH-quinone reductase subunit F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,8288
Polymers63,8802
Non-polymers2,9486
Water8,665481
1
A: Na(+)-translocating NADH-quinone reductase subunit F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4144
Polymers31,9401
Non-polymers1,4743
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Na(+)-translocating NADH-quinone reductase subunit F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4144
Polymers31,9401
Non-polymers1,4743
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.880, 90.470, 94.500
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Na(+)-translocating NADH-quinone reductase subunit F / NQR complex subunit F / NQR-1 subunit F


Mass: 31940.084 Da / Num. of mol.: 2 / Mutation: F406A
Source method: isolated from a genetically manipulated source
Details: Subunit NqrF, variant F406A residues 129-408; residues after cleavage of N-terminal His-tag residual residues after are GP
Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: nqrF, ERS013200_03807
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A656ARB0, NADH:ubiquinone reductase (Na+-transporting)
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH / Nicotinamide adenine dinucleotide


Mass: 665.441 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 481 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.56 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.1 M citrate, 0.2 M MgAcetate, 20-27 % PEG5000 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 14, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→48.65 Å / Num. obs: 74065 / % possible obs: 97.7 % / Redundancy: 10.561 % / Biso Wilson estimate: 23.46 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.153 / Rrim(I) all: 0.161 / Χ2: 0.812 / Net I/σ(I): 12.87 / Num. measured all: 782172 / Scaling rejects: 127
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.65-1.7510.8192.541.2612495712133115500.5782.66495.2
1.75-210.691.0993.3921558520728201670.891.15397.3
2-2.510.5920.39410.0321498120674202970.980.41498.2
2.5-310.3730.14719.594577922491180.9960.15598.9
3-410.4250.06532.9276502739873380.9980.06999.2
4-610.1410.04543.2239267389238720.9990.04899.5
6-109.4190.03945.2912499133113270.9990.04299.7
10-48.659.6060.03751.0338044033960.9990.03998.3

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.20.1_4487refinement
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4U9U

4u9u


Resolution: 1.65→48.65 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2142 3704 5 %
Rwork0.1809 70358 -
obs0.1826 74062 97.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 85.75 Å2 / Biso mean: 27.8995 Å2 / Biso min: 13.29 Å2
Refinement stepCycle: final / Resolution: 1.65→48.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4456 0 196 481 5133
Biso mean--26.78 36.55 -
Num. residues----555
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.65-1.670.35621390.31782633277297
1.67-1.70.3271380.30592622276096
1.7-1.720.31041400.28942655279597
1.72-1.750.3621390.28952638277797
1.75-1.770.31711400.27972660280097
1.77-1.80.25741380.26582635277397
1.8-1.830.31161400.27792666280697
1.83-1.870.33381400.28232648278897
1.87-1.90.37011400.26362666280697
1.9-1.940.2671390.23562646278597
1.94-1.980.27711410.20792679282098
1.98-2.030.24961410.1982671281298
2.03-2.080.21551420.19392702284498
2.08-2.140.22951420.19042693283598
2.14-2.20.21681420.18762699284198
2.2-2.270.21531420.19752707284999
2.27-2.350.22641430.192699284298
2.35-2.450.22411420.18832716285899
2.45-2.560.21161440.18562723286798
2.56-2.690.23091440.18792736288099
2.69-2.860.25181440.19022737288199
2.86-3.080.19771450.18122761290699
3.08-3.390.17481460.16452772291899
3.39-3.880.19241480.14182801294999
3.88-4.890.14821480.12052830297899
4.89-48.650.17851570.15552963312099

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