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- EMDB-53583: Complex I from Paracoccus denitrificans in cMSP26 nanodiscs -

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Basic information

Entry
Database: EMDB / ID: EMD-53583
TitleComplex I from Paracoccus denitrificans in cMSP26 nanodiscs
Map data
Sample
  • Complex: Respiratory complex I, NADH:ubiquinone oxidoreductase
    • Protein or peptide: Respiratory complex I, NADH:ubiquinone oxidoreductase
KeywordsRespiratory complex I / NADH:ubiquinone oxidoreductase / Nanodiscs / Circularised nanodiscs / OXIDOREDUCTASE
Biological speciesParacoccus denitrificans PD1222 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsIvanov BS / Hirst J
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC_UU_00015/2 United Kingdom
Medical Research Council (MRC, United Kingdom)MC_UU_00028/1 United Kingdom
CitationJournal: Sci Rep / Year: 2025
Title: Oversized nanodiscs for combined structural and functional investigation of multicomponent membrane protein systems.
Authors: Bozhidar S Ivanov / Judy Hirst /
Abstract: Membrane proteins are fundamental to many crucial cellular processes but removing them from their native environment for structural and functional studies creates experimental challenges. Numerous ...Membrane proteins are fundamental to many crucial cellular processes but removing them from their native environment for structural and functional studies creates experimental challenges. Numerous strategies have been developed to replicate native-like membrane environments in vitro for membrane protein research, however, most studies have focused on systems for either structural or functional characterisation, not both together. Here, we apply an in-vivo split intein strategy to produce stable circularised nanodiscs for combined structural and functional analysis of respiratory complex I, using its highly hydrophobic native ubiquinone-10 substrate and an auxiliary ubiquinol oxidase from Trypanosoma brucei brucei. We successfully reconstituted Paracoccus denitrificans complex I into circularised nanodiscs, determined its cryo-EM structure at 3.1 Å resolution and conducted biophysical and biochemical analyses to demonstrate how the 'oversized' nanodiscs have space to accommodate both enzymes and substrates to sustain steady-state catalysis. Our work establishes a proof-of-principle for using oversized nanodiscs as an integrated platform for structural and functional interrogation of complex membrane proteins in near-native membrane environments.
History
DepositionMay 8, 2025-
Header (metadata) releaseAug 20, 2025-
Map releaseAug 20, 2025-
UpdateAug 20, 2025-
Current statusAug 20, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53583.png

Downloads & links

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Map

FileDownload / File: emd_53583.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.34 Å/pix.
x 450 pix.
= 603. Å		1.34 Å/pix.
x 450 pix.
= 603. Å		1.34 Å/pix.
x 450 pix.
= 603. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.34 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.12258152 - 0.35401818
Average (Standard dev.)-0.00006757525 (±0.0067625535)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions450450450
Spacing450450450
CellA=B=C: 603.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_53583_msk_1.map
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Half map: #1

Fileemd_53583_half_map_1.map
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Half map: #2

Fileemd_53583_half_map_2.map
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Sample components

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Entire : Respiratory complex I, NADH:ubiquinone oxidoreductase

EntireName: Respiratory complex I, NADH:ubiquinone oxidoreductase
Components
  • Complex: Respiratory complex I, NADH:ubiquinone oxidoreductase
    • Protein or peptide: Respiratory complex I, NADH:ubiquinone oxidoreductase

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Supramolecule #1: Respiratory complex I, NADH:ubiquinone oxidoreductase

SupramoleculeName: Respiratory complex I, NADH:ubiquinone oxidoreductase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Paracoccus denitrificans PD1222 (bacteria)
Molecular weightTheoretical: 560 KDa

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Macromolecule #1: Respiratory complex I, NADH:ubiquinone oxidoreductase

MacromoleculeName: Respiratory complex I, NADH:ubiquinone oxidoreductase / type: protein_or_peptide / ID: 1 / Details: OXIDOREDUCTASE / Enantiomer: LEVO
Source (natural)Organism: Paracoccus denitrificans PD1222 (bacteria)
SequenceString: MLNDQDRIFT NLYGMGDRSL AGAKKRGHWD GTAAIIQRGR DKIIDEMKAS GLRGRGGAGF PTGMKWSFM PKESDGRPSY LVINADESEP ATCKDREIMR HDPHTLIEGA LIASFAMGAH A AYIYIRGE FIREREALQA AIDECYDAGL LGRNAAGSGW DFDLYLHHGA ...String:
MLNDQDRIFT NLYGMGDRSL AGAKKRGHWD GTAAIIQRGR DKIIDEMKAS GLRGRGGAGF PTGMKWSFM PKESDGRPSY LVINADESEP ATCKDREIMR HDPHTLIEGA LIASFAMGAH A AYIYIRGE FIREREALQA AIDECYDAGL LGRNAAGSGW DFDLYLHHGA GAYICGEETA LL ESLEGKK GMPRMKPPFP AGAGLYGCPT TVNNVESIAV VPTILRRGAE WFASFGRPNN AGV KLFGLT GHVNTPCVVE EAMSIPMREL IEKHGGGIRG GWKNLKAVIP GGASCPVLTA EQCE NAIMD YDGMRELRSS FGTACMIVMD QSTDVVKAIW RLSKFFKHES CGQCTPCREG TGWMM RVME RLVRGDAEVE EIDMLFDVTK QVEGHTICAL GDAAAWPIQG LIRNFREEIE DRIKAK RTG RMGAMAAE M LRRLSPIQPD SFEFTPANLE WARAQMTKYP EGRQQSAIIP VLWRAQEQEG WLSRPAIEY CADLLGMPYI RALEVATFYF MFQLQPVGSV AHIQICGTTT CMICGAEDLI RVCKEKIAPE PHALSADGR FSWEEVECLG ACTNAPMAQI GKDFYEDLTV EKLAALIDRF AAGEVPVPGP Q NGRFSAEA LGGPTALADL KGGEAHNASV ARALRLGDSI KRIDGTEVPI TTPWLATQNG V MADLRKIK IDDTIIEVDP NMTLIQACEM AGIEVPRFCY HERLSIAGNC RMCLVEVVGG PP KPAASCA MQVKDLRPGP EGAPSEIRTN SPMVKKAREG VMEFLLINHP LDCPICDQGG ECD LQDQAM AYGVDFSRYR EPKRATEDLN LGPLVETHMT RCISCTRCVR FTTEVAGITQ MGQT GRGED SEITSYLNQT LESNMQGNII DLCPVGALVS KPYAFTARPW ELTKTESIDV MDALG SSIR IDTKGREVMR ILPRNHDGVN EEWISDKTRF VWDGLRRQRL DRPYIRENGR LRPASW PEA LEAAARAMKG KKIAGLIGDL VPAEAAFSLK QLVEGLGGKV ECRVDGARLP AGNRSAY VG TARIEDIDDA EMIQLIGTNP RDEAPVLNAR IRKAWSKGAK VGLVGEPVDL TYDYAHVG T DRAALESLSS REISDETKAR PSIVIVGQGA IREADGEAVL AHAMKLAENS NSGLLILHT AAGRVGAMDV GAVTEGGLLA AIDGAEVVYN LGADEVDIDQ GPFVIYQGSH GDRGAHRADI ILPGACYTE ESGLFVNTEG RPQLAMRANF APGEGKENWA ILRALSAELG ATQPWDSLAG L RRKLVEAV PHLAQIDQVP QNEWQPLGRF DLGQASFRYA IRDFYLTNPI ARSSPLMGEL SA MAAARKA PAPLAAE MD GDIRKNSYDD GSMDALTGEQ SIRNFNINFG PQHPAAHGVL RMVLELDGEI VERADPHI G LLHRGTEKLM ESRTYLQNLP YLDRLDYVAP MNQEHAWCLA IERLTGTVIP RRASLIRVL YSEIGRILNH LMGVTTGAMD VGALTPPLWG FEAREELMIF YERACGARLH AAYFRPGGVH QDLPPDLLD DIEEWCERFP KLVDDLDTLL TENRIFKQRL VDIGIVTEAD ALDWGYTGVM V RGSGLAWD LRRSQPYECY DEFDFQIPVG RNGDCYDRYL CRMAEMRESC KIMQQAVQKL RA EPAGDVL ARGKLTPPRR AEMKRDMESL IHHFKLYTEG FKVPAGEVYA AVEAPKGEFG VYL VADGTN KPWRAKLRAP GFAHLQSIDW MSRGHMLADV PAIIATLDIV FGEVDR MSE ALSDEALLEL AEHIALRREN DVISTQVAFG ELTVNATLSG VIGLIEFLRN DPNCRFS TL IDITAVDNPA RPARFDVVYH LLSMYQNQRI RVKVQVREDE LVPSLIGVFP GANWYERE V FDLFGILFSG HSDLRRILTD YGFRGHPLRK DFPTTGYVEV RWSDIEKRVV YEPVNLVQE YRQFDFLSPW EGAKYVLPGD EKAPEAKK M MTGLNTAGAD RDLATAELNR ELQDKGFLLT TTEDIINWAR NGSLHWMTFG LACCAVEMM QTSMPRYDLE RFGTAPRASP RQSDLMIVAG TLTNKMAPAL RKVYDQMPEP RYVISMGSCA NGGGYYHYS YSVVRGCDRI VPVDIYVPGC PPTAEALLYG ILQLQRRIRR TGTLVR MAF DFARATKYFL MWDFIKGFGL GMRYFVSPKP TLNYPHEKGP LSPRFRGEHA LRRYPNG EE RCIACKLCEA VCPAQAITID AEPREDGSRR TTRYDIDMTK CIYCGFCQEA CPVDAIVE G PNFEYATETR EELFYDKQKL LANGERWEAE IARNLQLDAP YR MAEFWAS PYGFALSMLL QGLAVIAFVM GSLIFMVYGD RKIWAAVQMR RGPNVVGPWG LLQ TFADAL KYIVKEIVIP AGADKFVYFL APFLSMMLAL FAFVVIPFDE GWVMANINVG ILFI FAASS LEVYGVIMGG WASNSKYPFL ASLRSAAQMI SYEVSLGLII IGIIISTGSM NLTAI VEAQ RGDYGLLNWY WLPHLPMVVL FFVSALAECN RPPFDLVEAE SELVAGFMTE YSSTPY LLF MAGEYIAMYL MCALLSLLFF GGWLSPVPFI ADGWWWMVIK MWFWFYMFAM VKAIVPR YR YDQLMRIGWK VFLPLSLGWV VLVAILARYE ILGGFWARFA VGG MTSLDF STILPEVVLA GYALAALMAG AYLGKDRLAR TLLWVTVAAF LVVAAMVGLG NHVD GAAFH GMFIDDGFSR FAKVVTLVAA AGVLAMSADY MQRRNMLRFE FPIIVALAVL GMMFM VSAG DLLTLYMGLE LQSLALYVVA AMRRDSVRSS EAGLKYFVLG SLSSGLLLYG ASLVYG FAG TTGFEGIIST IEAGHLSLGV LFGLVFMLVG LSFKVSAVPF HMWTPDVYEG SPTPVTA FF ATAPKVAAMA LIARLVFDAF GHVIGDWSQI VAALAVMSMF LGSIAGIGQT NIKRLMAY S SIAHMGFALV GLAAGTAIGV QNMLLYMTIY AVMNIGTFAF ILSMERDGVP VTDLAALNR FAWTDPVKAL AMLVLMFSLA GVPPTLGFFA KFGVLTAAVD AGMGWLAVLG VIASVIGAFY YLRIVYYMY FGGESEGMTS RMGAVQYLAL MVPALAMLVG AISMFGVDSA AGRAAETLVG P VAAIEQPA EAAQAEPVQG E MEYLLQEY LPILVFLGMA SALAIVLILA AAVIAVRNPD PEKVSAYECG FNAFDDARMK FD VRFYLVS ILFIIFDLEV AFLFPWAVSF ASLSDVAFWG MMVFLAVLTV GFAYEWKKGA LEW A MTNL LSIITFLPIV AAIIMALFLR GQDEAAARNA KWLALLTTTA TFVISLFVLF RFDPAN TGF QFVEDHAWIM GLRYKMGVDG ISVLFVLLTT FMMPLTILST WQVQDKVKEY MIAFLVL EG LMIGVFTALD LVLFYLFFEA GLIPMFLIIG IWGGKDRIYA SFKFFLYTFL GSVLMLVA M IAMYRMAGTT DIPTLLTFDF PSENFRLLGM TVVGGMQMLL FLAFFASFAV KMPMWPVHT WLPDAHVQAP TAGSVLLAAV LLKMGGYGFL RFSLPMFPVA SGVAQPYVFW LSAIAIVYTS LVALAQSDM KKVIAYSSVA HMGYVTMGVF AANQIGVDGA IFQMLSHGFI SGALFLCVGV I YDRMHTRE IDAYGGLVNR MPAYAAVFMF FTMANVGLPG TSGFVGEFLT LMGVFRVDTW VA LVATSGV ILSAAYALWL YRRVTLGQLI KESLKSITDM TPRERWVFIP LIAMTLILGV YPR LVTDVT GPAVAALVQD YNQSQPAAPV ATAQASH MI GLTHYLVVGA ILFVTGIFGI FVNRKNVIVI LMSIELMLLA VNINFVAFST HLGDLAGQ V FTMFVLTVAA AEAAIGLAIL VVFFRNRGTI AVEDVNVMKG MEKFVLFAP LIASLIAGLG WRAIGEKAAQ YLTTGVLFLS CLISWYLFLS FDGVPRHIPV L DWVVTGDF HAEWAIRLDR LTAIMLIVVT TVSALVHMYS LGYMAHDDNW THDEHYKARF FA YLSFFTF AMLMLVTADN LLQMFFGWEG VGVASYLLIG FYYKKASANA AAMKAFIVNR VGD FGFLLG IFGIYWLTGS VQFDEIFRQV PQLAQTEMHF LWRDWNAANL LGFLLFVGAM GKSA QLLLH TWLPDAMEGP TPVSALIHAA TMVTAGVFLV CRMSPLYEFA PDAKNFIVII GATTA FFAA TVGLVQNDIK RVIAYSTCSQ LGYMFVAAGV GVYSAAMFHL LTHAFFKAML FLGAGS VIH AMHHEQDMRN YGGLRKKIPL TFWAMMIGTF AITGVGIPLT HLGFAGFLSK DAIIESA YA GSGYAFWLLV IAACFTSFYS WRLIFLTFYG KPRGDHHAHD HAHESPPVMT IPLGVLAI G AVFAGMVWYG PFFGDHHKVT EYFHIAGAHH EAAEGEEAEH ATAEAPVEHA VADTATAEG EAAAEAEHAE IAAPVGGAIY MHPDNHIMDE AHHAPAWVKV SPFVAMVLGL ITAWTFYIAN PSLPRRLAA QQPALYRFLL NKWYFDEIYE FIFVRPAKWL GRVLWKGGDG AVIDGTINGV A MGLIPRLT RAAVRVQSGY LFHYAFAMVL GIVGLLIWVM MRGAH MTFA FYLFAISACV AGFMVVIGRN PVHSVLWLIL AFLSAAGLFV LQGAEFVAML LVVVYV GAV AVLFLFVVMM LDVDFAELKG ELARYLPLAL VIGVVLLAQL GIAFSGWTPS DQAESLR AA PVDAAVENTL GLGLVLYDRY VLMFQLAGLV LLVAMIGAIV LTMRHRKDVK RQNVLEQM W RDPAKTMELK DVKPGQGL M RVRIYKPARN AMQSGTARTR NWVLDFPPAD PRAIDPLMGW TSSDDTQSQV RLRFETRKQ AEDYAREHGL DYEVIEPHTR AANIRPRGYG ENFASDRRAP WTH MTIPAP EIQTVTSWKV ACDGDEARGL GHPRVWLAIP RDTGWVECGY CDKRFVIDRE HAHD DH MS FLLRFLTWWN SQTLNTQVWT KLYGEKVGED DQGNVYYQSG GGKRRWVIYN GESEASRI S PEWHGWLHHT YKEPPTAAPL AHKPWEKPHE PNLTGSSGAY HPAGSLYRAQ PVERRDYDA WQPE MTDFA QRRTMMVDTQ VRPNEVTSYP VIEAMLNVPR EQFVPESRRD VAYVGNNIDL APGRV LLEP RTLGKMMDIL NLQNGDLVLD VGCGYGYSAA VMARIAEAVV AVEEDAAMAA EAEGRL AAQ DVFNVAVVQG ALAEGCPGQA PYDAILIEGA VEQVPEALTE QLREGGRIVA LFREGNL GI VRLGHKLDGR VNWRFAFNAV APLLPGFARP RGFVL

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration2.25 mg/mL
BufferpH: 6.8
Details: 20 mM MES-NaOH (pH 6.8 @ 4 degrees Celsius), 25 mM NaCl
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 1157 / Average exposure time: 3.4 sec. / Average electron dose: 41.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.3000000000000003 µm / Nominal defocus min: 0.9 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: CTFFIND (ver. 4.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.0) / Number images used: 57305
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 3.1.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.0)
Final 3D classificationNumber classes: 5 / Software - Name: RELION (ver. 3.1.0)
FSC plot (resolution estimation)

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