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- PDB-8ad4: X-ray structure of NqrF(129-408)of Vibrio cholerae in complex wit... -

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Basic information

Entry
Database: PDB / ID: 8ad4
TitleX-ray structure of NqrF(129-408)of Vibrio cholerae in complex with NADH
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 / 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: 1.5 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)69,73315
Polymers64,5512
Non-polymers5,18213
Water8,989499
1
A: Na(+)-translocating NADH-quinone reductase subunit F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5347
Polymers32,2751
Non-polymers2,2586
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)35,1998
Polymers32,2751
Non-polymers2,9247
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.200, 89.380, 95.210
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 32275.482 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Residues 129-408 of subunit NqrF. Residues GSH are residual after cleavage of N-terminal His-tag.
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)

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Non-polymers , 5 types, 512 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 499 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.38 Å3/Da / Density % sol: 48.31 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 0.1 M Citrate, 0.2 M MgAcetate, 35% 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: Jun 13, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→48.38 Å / Num. obs: 93788 / % possible obs: 94.6 % / Redundancy: 4.161 % / Biso Wilson estimate: 20.02 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.063 / Rrim(I) all: 0.071 / Χ2: 0.916 / Net I/σ(I): 15.05 / Num. measured all: 390283 / Scaling rejects: 71
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
1.5-1.62.340.9391.143093517247132190.4551.16376.6
1.6-1.73.3740.6312.584301513447127500.740.73794.8
1.7-1.84.770.4195.415064910638106180.9240.46799.8
1.8-24.6210.2239.877081515428153260.9760.2599.3
2-34.6930.07222.2513738729497292750.9970.08199.2
3-44.6660.03338.2233602730172020.9990.03798.6
4-104.4350.02942.1822227514750120.9980.03397.4
10-124.4970.02944.867151621590.9990.03398.1
12-48.384.1320.03241.139382372270.9980.03695.8

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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: 1.5→48.38 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 22.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2049 4690 5 %
Rwork0.1789 89091 -
obs0.1802 93781 94.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 107.65 Å2 / Biso mean: 26.3868 Å2 / Biso min: 10.76 Å2
Refinement stepCycle: final / Resolution: 1.5→48.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4498 0 484 499 5481
Biso mean--34.65 30.08 -
Num. residues----559
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5-1.520.55561060.58722013211965
1.52-1.530.52881200.51222271239172
1.53-1.550.52981250.46672389251477
1.55-1.570.40971330.4432510264381
1.57-1.590.42261390.37792650278985
1.59-1.620.36721450.33342760290589
1.62-1.640.35381520.31562876302893
1.64-1.660.31371560.26712974313096
1.66-1.690.27111600.243027318798
1.69-1.720.24411630.213430983261100
1.72-1.750.22551620.208830853247100
1.75-1.780.2291640.197331193283100
1.78-1.810.23181630.198531023265100
1.81-1.850.23851630.201530943257100
1.85-1.890.22721650.2063128329399
1.89-1.930.22721610.20333052321399
1.93-1.980.23681640.19063116328099
1.98-2.040.19441630.166630963259100
2.04-2.10.20621650.162831393304100
2.1-2.160.2021640.15723117328199
2.16-2.240.19891630.15443107327099
2.24-2.330.19341640.15693118328299
2.33-2.440.17961640.15573101326599
2.44-2.560.19531650.16633143330899
2.57-2.730.19921650.16353125329099
2.73-2.940.19281650.17623140330599
2.94-3.230.20951630.16533105326898
3.23-3.70.15951680.14653181334999
3.7-4.660.13731660.12863157332398
4.66-48.380.18841740.17353298347298
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.71310.0684-0.00061.09330.34851.06620.15730.25070.1328-0.1503-0.0321-0.1204-0.02720.0803-0.12880.18690.03180.01910.1930.02680.153114.23465.968213.4625
21.52850.08020.27961.22410.17490.96180.22430.2474-0.0582-0.0709-0.0279-0.12070.08970.0273-0.18670.16910.0385-0.00530.1634-0.00370.14713.7431-3.356714.8562
31.35070.96850.06612.01380.41950.57610.1518-0.02610.1448-0.0504-0.0585-0.3147-0.09280.0593-0.07380.1467-0.00450.04370.1240.00410.222320.56613.248420.1594
41.0766-0.3393-0.25270.98040.57840.85820.08270.04420.014-0.0053-0.11920.0579-0.0031-0.14990.03610.1405-0.0056-0.00570.15870.00980.09920.40615.928423.6652
51.54940.3666-0.09342.7887-0.07960.64520.1929-0.16850.16160.4692-0.23740.2723-0.063-0.17040.03960.1972-0.0320.0390.1957-0.04570.1541-2.841718.148136.3724
62.07871.0039-0.53931.23030.05531.21410.0422-0.5088-0.34910.3321-0.1953-0.28860.11460.13950.150.247-0.0394-0.03260.26620.05530.17793.05942.963439.3421
71.59910.4211-0.18471.1458-0.05730.94410.13910.19030.0773-0.17240.0229-0.0733-0.05650.1798-0.16880.19150.02150.00470.1591-0.01590.13624.592818.352-20.5835
81.71730.4354-0.22291.6086-0.15821.19030.02940.4025-0.0091-0.33720.07360.0508-0.21380.0396-0.09030.24280.00970.00830.2258-0.05250.15713.836111.1197-26.6168
91.12180.19810.59131.16170.30561.14210.0429-0.36520.25610.0452-0.011-0.1301-0.33330.1744-0.06020.2512-0.07520.02480.2466-0.07490.217614.837525.9448-6.7157
102.2560.68290.43731.78780.34171.41150.07890.0013-0.126-0.00330.0754-0.2825-0.14310.1719-0.15580.1744-0.01120.01320.1649-0.03370.14511.864314.8179-15.8481
111.05920.268-0.06630.1582-0.24931.00630.0570.1846-0.08580.04040.013-0.07750.0286-0.0214-0.05690.18050.0194-0.00030.1603-0.02860.14171.06467.1103-20.7006
120.53750.2421-0.37660.9849-0.00611.3030.01520.05430.0556-0.06530.05810.033-0.0106-0.1225-0.07970.1549-0.0082-0.01440.14250.00640.1273-8.07665.182-10.907
132.26011.03130.45082.13560.34861.9979-0.0151-0.05470.3308-0.0055-0.07290.2667-0.14750.01010.0880.16350.02390.01390.1482-0.02050.1686-6.259116.2122-4.9673
140.95460.10.11751.07650.03861.81420.0073-0.14570.06060.1460.0370.04280.032-0.0516-0.03890.15410.0059-0.00680.1498-0.00540.1168-5.98484.59021.821
151.80360.1028-0.55061.5323-0.8662.6263-0.0583-0.3089-0.1871-0.0537-0.0023-0.130.30160.38450.05830.24190.06620.02180.27620.01950.2012.7855-5.0189-4.2236
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 129 through 153 )A129 - 153
2X-RAY DIFFRACTION2chain 'A' and (resid 154 through 174 )A154 - 174
3X-RAY DIFFRACTION3chain 'A' and (resid 175 through 251 )A175 - 251
4X-RAY DIFFRACTION4chain 'A' and (resid 252 through 339 )A252 - 339
5X-RAY DIFFRACTION5chain 'A' and (resid 340 through 369 )A340 - 369
6X-RAY DIFFRACTION6chain 'A' and (resid 370 through 407 )A370 - 407
7X-RAY DIFFRACTION7chain 'B' and (resid 129 through 153 )B129 - 153
8X-RAY DIFFRACTION8chain 'B' and (resid 154 through 174 )B154 - 174
9X-RAY DIFFRACTION9chain 'B' and (resid 175 through 200 )B175 - 200
10X-RAY DIFFRACTION10chain 'B' and (resid 201 through 251 )B201 - 251
11X-RAY DIFFRACTION11chain 'B' and (resid 252 through 275 )B252 - 275
12X-RAY DIFFRACTION12chain 'B' and (resid 276 through 311 )B276 - 311
13X-RAY DIFFRACTION13chain 'B' and (resid 312 through 329 )B312 - 329
14X-RAY DIFFRACTION14chain 'B' and (resid 330 through 380 )B330 - 380
15X-RAY DIFFRACTION15chain 'B' and (resid 381 through 407 )B381 - 407

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