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- PDB-3m9c: Crystal structure of the membrane domain of respiratory complex I... -

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Basic information

Entry
Database: PDB / ID: 3m9c
TitleCrystal structure of the membrane domain of respiratory complex I from Escherichia coli
Components
  • NADH-quinone oxidoreductase subunit NuoL
  • NADH-quinone oxidoreductase subunit NuoM
  • NADH-quinone oxidoreductase subunit NuoN
  • NADH-quinone oxidoreductase subunits NuoA,J and K
KeywordsOXIDOREDUCTASE / MEMBRANE PROTEIN / COMPLEX I / ELECTRON TRANSPORT / RESPIRATORY CHAIN
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 3.9 Å
AuthorsEfremov, R.G. / Baradaran, R. / Sazanov, L.A.
CitationJournal: Nature / Year: 2010
Title: The architecture of respiratory complex I
Authors: Efremov, R.G. / Baradaran, R. / Sazanov, L.A.
History
DepositionMar 22, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 21, 2015Group: Database references
Revision 1.3Feb 21, 2024Group: Database references / Category: database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: NADH-quinone oxidoreductase subunit NuoL
M: NADH-quinone oxidoreductase subunit NuoM
N: NADH-quinone oxidoreductase subunit NuoN
R: NADH-quinone oxidoreductase subunits NuoA,J and K


Theoretical massNumber of molelcules
Total (without water)129,7724
Polymers129,7724
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)114.060, 182.170, 185.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein NADH-quinone oxidoreductase subunit NuoL


Mass: 40357.742 Da / Num. of mol.: 1 / Fragment: Membrane domain / Mutation: Subunit NuoH is missing / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: BL21 / References: NADH:ubiquinone reductase (H+-translocating)
#2: Protein NADH-quinone oxidoreductase subunit NuoM


Mass: 33293.949 Da / Num. of mol.: 1 / Fragment: Membrane domain / Mutation: Subunit NuoH is missing / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: BL21 / References: NADH:ubiquinone reductase (H+-translocating)
#3: Protein NADH-quinone oxidoreductase subunit NuoN


Mass: 32187.574 Da / Num. of mol.: 1 / Fragment: Membrane domain / Mutation: Subunit NuoH is missing / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: BL21 / References: NADH:ubiquinone reductase (H+-translocating)
#4: Protein NADH-quinone oxidoreductase subunits NuoA,J and K


Mass: 23932.375 Da / Num. of mol.: 1 / Fragment: Membrane domain / Mutation: Subunit NuoH is missing / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: BL21 / References: NADH:ubiquinone reductase (H+-translocating)
Compound detailsTHE LONG C-N BONDS ARE BECAUSE OF THE LOOPS NOT BEING MODELED.
Sequence detailsTHE ACTUAL SEQUENCE FOR CHAIN L: MNMLALTIILPLIGFVLLAFSRGRWSENVSAIVGVGSVGLAALVTAFIGVDFFANGEQTYSQPLW ...THE ACTUAL SEQUENCE FOR CHAIN L: MNMLALTIILPLIGFVLLAFSRGRWSENVSAIVGVGSVGLAALVTAFIGVDFFANGEQTYSQPLW TWMSVGDFNIGFNLVLDGLSLTMLSVVTGVGFLIHMYASWYMRGEEGYSRFFAYTNLFIASMVV LVLADNLLLMYLGWEGVGLCSYLLIGFYYTDPKNGAAAMKAFVVTRVGDVFLAFALFILYNELG TLNFREMVELAPAHFADGNNMLMWATLMLLGGAVGKSAQLPLQTWLADAMAGPTPVSALIHAAT MVTAGVYLIARTHGLFLMTPEVLHLVGIVGAVTLLLAGFAALVQTDIKRVLAYSTMSQIGYMFL ALGVQAWDAAIFHLMTHAFFKALLFLASGSVILACHHEQNIFKMGGLRKSIPLVYLCFLVGGAA LSALPLVTAGFFSKDEILAGAMANGHINLMVAGLVGAFMTSLYTFRMIFIVFHGKEQIHAHAVK GVTHSLPLIVLLILSTFVGALIVPPLQGVLPQTTELAHGSMLTLEITSGVVAVVGILLAAWLWL GKRTLVTSIANSAPGRLLGTWWYNAWGFDWLYDKVFVKPFLGIAWLLKRDPLNSMMNIPAVLSR FAGKGLLLSENGYLRWYVASMSIGAVVVLALLMVLR THE ACTUAL SEQUENCE FOR CHAIN M: MLLPWLILIPFIGGFLCWQTERFGVKVPRWIALITMGLTLALSLQLWLQGGYSLTQSAGIPQWQ SEFDMPWIPRFGISIHLAIDGLSLLMVVLTGLLGVLAVLCSWKEIEKYQGFFHLNLMWILGGVI GVFLAIDMFLFFFFWEMMLVPMYFLIALWGHKASDGKTRITAATKFFIYTQASGLVMLIAILAL VFVHYNATGVWTFNYEELLNTPMSSGVEYLLMLGFFIAFAVKMPVVPLHGWLPDAHSQAPTAGS VDLAGILLKTAAYGLLRFSLPLFPNASAEFAPIAMWLGVIGIFYGAWMAFAQTDIKRLIAYTSV SHMGFVLIAIYTGSQLAYQGAVIQMIAHGLSAAGLFILCGQLYERIHTRDMRMMGGLWSKMKWL PALSLFFAVATLGMPGTGNFVGEFMILFGSFQVVPVITVISTFGLVFASVYSLAMLHRAYFGKA KSQIASQELPGMSLRELFMILLLVVLLVLLGFYPQPILDTSHSAIGNIQQWFVNSVTTTR THE ACTUAL SEQUENCE FOR CHAIN N: MTITPQNLIALLPLLIVGLTVVVVMLSIAWRRNHFLNATLSVIGLNAALVSLWFVGQAGAMDVTP LMRVDGFAMLYTGLVLLASLATCTFAYPWLEGYNDNKDEFYLLVLIAALGGILLANANHLASLFL GIELISLPLFGLVGYAFRQKRSLEASIKYTILSAAASSFLLFGMALVYAQSGDLSFVALGKNLGD GMLNEPLLLAGFGLMIVGLGFKLSLVPFHLWTPDVYQGAPAPVSTFLATASKIAIFGVVMRLFLY APVGDSEAIRVVLAIIAFASIIFGNLMALSQTNIKRLLGYSSISHLGYLLVALIALQTGEMSMEA VGVYLAGYLFSSLGAFGVVSLMSSPYRGPDADSLFSYRGLFWHRPILAAVMTVMMLSLAGIPMTL GFIGKFYVLAVGVQAHLWWLVGAVVVGSAIGLYYYLRVAVSLYLHAPEQPGRDAPSNWQYSAGGI VVLISALLVLVLGVWPQPLISIVRLAMPLM THE ACTUAL SEQUENCE FOR CHAIN R: MSMSTSTEVIAHHWAFAIFLIVAIGLCCLMLVGGWFLGGRARARSKNVPFESGIDSVGSARLRLS AKFYLVAMFFVIFDVEALYLFAWSTSIRESGWVGFVEAAIFIFVLLAGLVYLVRIGALDWTPARS RRERMNPETNSIANRQRMEFAFYICGLIAILATLRVITHTNPVHALLYLIISLLAISGVFFSLGA YFAGALEIIVYAGAIMVLFVFVVMMLNLGGSEIEQERQWLKPQVWIGPAILSAIMLVVIVYAILG VNDQGIDGTPISAKAVGITLFGPYVLAVELASMLLLAGLVVAFHVGREERAGEVLSNRKDDSAKR KTEEHAMIPLQHGLILAAILFVLGLTGLVIRRNLLFMLIGLEIMINASALAFVVAGSYWGQTDGQ VMYILAISLAAAEASIGLALLLQLHRRRQNLNIDSVSEMRG

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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: 7.42 Å3/Da / Density % sol: 73 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 4.8
Details: 9% PEG4000, 0.1 M sodium acetate, 1.0 M sodium formate, pH 4.8, VAPOR DIFFUSION, SITTING DROP, temperature 283K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 21, 2009 / Details: Mirrors
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 3.9→30 Å / Num. all: 34983 / Num. obs: 34983 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 82.3 Å2 / Rmerge(I) obs: 0.205 / Net I/σ(I): 4
Reflection shellResolution: 3.9→4.11 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.846 / Mean I/σ(I) obs: 1.5 / Num. unique all: 5022 / % possible all: 97.4

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Processing

Software
NameClassification
MOSFLMdata reduction
PHENIXmodel building
Omodel building
Cootmodel building
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MIRAS / Resolution: 3.9→30 Å / Num. reflection all: 34983 / Num. reflection obs: 34983
Details: This is not refined backbone model. The directionality of alpha-helices is not known. For the optimal calculation of electron density the data should be anisotropically scaled.
Refinement stepCycle: LAST / Resolution: 3.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4572 0 0 0 4572

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