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- EMDB-14764: Late assembly intermediate of the proximal proton pumping module ... -

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Basic information

Entry
Database: EMDB / ID: EMD-14764
TitleLate assembly intermediate of the proximal proton pumping module of complex I with assembly factors NDUFAF1 and CIA84
Map dataLate assembly intermediate of the proximal proton pumping module of complex I with assembly factors NDUFAF1 and CIA84.
Sample
  • Complex: Late assembly intermediate of the proximal proton pumping module of complex I with assembly factors NDUFAF1 and CIA84
    • Protein or peptide: x 14 types
  • Ligand: x 5 types
Keywordsassembly respiratory chain membrane protein mitochondria / ELECTRON TRANSPORT
Function / homology
Function and homology information


NADH:ubiquinone reductase (H+-translocating) / : / mitochondrial electron transport, NADH to ubiquinone / NADH dehydrogenase (ubiquinone) activity / ATP synthesis coupled electron transport / : / mitochondrial membrane / mitochondrial intermembrane space / mitochondrial inner membrane / oxidoreductase activity ...NADH:ubiquinone reductase (H+-translocating) / : / mitochondrial electron transport, NADH to ubiquinone / NADH dehydrogenase (ubiquinone) activity / ATP synthesis coupled electron transport / : / mitochondrial membrane / mitochondrial intermembrane space / mitochondrial inner membrane / oxidoreductase activity / mitochondrion / membrane
Similarity search - Function
NADH:ubiquinone oxidoreductase intermediate-associated protein 30 / Complex I intermediate-associated protein 30, mitochondrial / Complex I intermediate-associated protein 30 (CIA30) / NADH-ubiquinone oxidoreductase, 21kDa subunit, C-terminal, fungi / NADH-ubiquinone oxidoreductase 9.5kDa subunit / C-terminal of NADH-ubiquinone oxidoreductase 21 kDa subunit / : / NADH-ubiquinone oxidoreductase, 21kDa subunit, N-terminal / NADH-ubiquinone oxidoreductase complex I, 21 kDa subunit / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex subunit 1 ...NADH:ubiquinone oxidoreductase intermediate-associated protein 30 / Complex I intermediate-associated protein 30, mitochondrial / Complex I intermediate-associated protein 30 (CIA30) / NADH-ubiquinone oxidoreductase, 21kDa subunit, C-terminal, fungi / NADH-ubiquinone oxidoreductase 9.5kDa subunit / C-terminal of NADH-ubiquinone oxidoreductase 21 kDa subunit / : / NADH-ubiquinone oxidoreductase, 21kDa subunit, N-terminal / NADH-ubiquinone oxidoreductase complex I, 21 kDa subunit / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex subunit 1 / NADH-ubiquinone oxidoreductase MWFE subunit / NADH:ubiquinone oxidoreductase, NDUFS5-15kDa / GRIM-19 / GRIM-19 protein / NADH:ubiquinone oxidoreductase, iron-sulphur subunit 5 / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 8 / NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJ / NADH-ubiquinone oxidoreductase chain 4L/K / NADH:ubiquinone/plastoquinone oxidoreductase, chain 6 / NADH-ubiquinone/plastoquinone oxidoreductase chain 6 / NADH-ubiquinone oxidoreductase chain 4L/Mnh complex subunit C1-like / NADH-ubiquinone/plastoquinone oxidoreductase chain 4L / NADH:quinone oxidoreductase/Mrp antiporter, membrane subunit / Proton-conducting membrane transporter / NADH:ubiquinone/plastoquinone oxidoreductase, chain 3 / NADH:ubiquinone oxidoreductase, subunit 3 superfamily / NADH-ubiquinone/plastoquinone oxidoreductase, chain 3 / NADH:ubiquinone oxidoreductase, subunit 1, conserved site / Respiratory-chain NADH dehydrogenase subunit 1 signature 1. / Respiratory-chain NADH dehydrogenase subunit 1 signature 2. / NADH:ubiquinone oxidoreductase, subunit 1/F420H2 oxidoreductase subunit H / NADH dehydrogenase / CHCH / CHCH domain / Coiled coil-helix-coiled coil-helix (CHCH) domain profile. / Galactose-binding-like domain superfamily
Similarity search - Domain/homology
Mitochondrial group I intron splicing factor CCM1 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 / NADH:ubiquinone oxidoreductase intermediate-associated protein 30 domain-containing protein / Uncharacterized protein / Uncharacterized protein / NADH-ubiquinone oxidoreductase complex I, 21 kDa subunit-domain-containing protein / Uncharacterized protein / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13 / NADH-ubiquinone oxidoreductase / NADH-ubiquinone oxidoreductase chain 3 ...Mitochondrial group I intron splicing factor CCM1 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 / NADH:ubiquinone oxidoreductase intermediate-associated protein 30 domain-containing protein / Uncharacterized protein / Uncharacterized protein / NADH-ubiquinone oxidoreductase complex I, 21 kDa subunit-domain-containing protein / Uncharacterized protein / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13 / NADH-ubiquinone oxidoreductase / NADH-ubiquinone oxidoreductase chain 3 / NADH-ubiquinone oxidoreductase chain 1 / NADH-ubiquinone oxidoreductase chain 6 / NADH-ubiquinone oxidoreductase chain 2 / NADH-ubiquinone oxidoreductase chain 4L
Similarity search - Component
Biological speciesYarrowia lipolytica (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsSchiller J / Laube E / Vonck J / Zickermann V
Funding support Germany, 1 items
OrganizationGrant numberCountry
German Research Foundation (DFG)ZI 552/4-2 Germany
CitationJournal: Sci Adv / Year: 2022
Title: Insights into complex I assembly: Function of NDUFAF1 and a link with cardiolipin remodeling.
Authors: Jonathan Schiller / Eike Laube / Ilka Wittig / Werner Kühlbrandt / Janet Vonck / Volker Zickermann /
Abstract: Respiratory complex I is a ~1-MDa proton pump in mitochondria. Its structure has been revealed in great detail, but the structural basis of its assembly, in humans involving at least 15 assembly ...Respiratory complex I is a ~1-MDa proton pump in mitochondria. Its structure has been revealed in great detail, but the structural basis of its assembly, in humans involving at least 15 assembly factors, is essentially unknown. We determined cryo-electron microscopy structures of assembly intermediates associated with assembly factor NDUFAF1 in a yeast model system. Subunits ND2 and NDUFC2 together with assembly factors NDUFAF1 and CIA84 form the nucleation point of the NDUFAF1-dependent assembly pathway. Unexpectedly, the cardiolipin remodeling enzyme tafazzin is an integral component of this core complex. In a later intermediate, all 12 subunits of the proximal proton pump module have assembled. NDUFAF1 locks the central ND3 subunit in an assembly-competent conformation, and major rearrangements of central subunits are required for complex I maturation.
History
DepositionApr 13, 2022-
Header (metadata) releaseNov 23, 2022-
Map releaseNov 23, 2022-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14764.png

Downloads & links

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Map

FileDownload / File: emd_14764.map.gz / Format: CCP4 / Size: 34.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLate assembly intermediate of the proximal proton pumping module of complex I with assembly factors NDUFAF1 and CIA84.
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.21 Å/pix.
x 208 pix.
= 251.1 Å		1.21 Å/pix.
x 208 pix.
= 251.1 Å		1.21 Å/pix.
x 208 pix.
= 251.1 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.20721 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-1.2728627 - 2.341034
Average (Standard dev.)0.009726462 (±0.098803915)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions208208208
Spacing208208208
CellA=B=C: 251.09967 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_14764_msk_1.map
Projections & Slices
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Additional map: map after density modification in Phenix

Fileemd_14764_additional_1.map
Annotationmap after density modification in Phenix
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Half map: #2

Fileemd_14764_half_map_1.map
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Half map: #1

Fileemd_14764_half_map_2.map
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Sample components

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Entire : Late assembly intermediate of the proximal proton pumping module ...

EntireName: Late assembly intermediate of the proximal proton pumping module of complex I with assembly factors NDUFAF1 and CIA84
Components
  • Complex: Late assembly intermediate of the proximal proton pumping module of complex I with assembly factors NDUFAF1 and CIA84
    • Protein or peptide: Subunit NIMM of NADH:Ubiquinone Oxidoreductase (Complex I)
    • Protein or peptide: NADH-ubiquinone oxidoreductase chain 4L
    • Protein or peptide: Subunit NUPM of NADH:Ubiquinone Oxidoreductase (Complex I)
    • Protein or peptide: Subunit NB6M of NADH:Ubiquinone Oxidoreductase (Complex I)
    • Protein or peptide: NADH-ubiquinone oxidoreductase complex I, 21 kDa subunit-domain-containing protein
    • Protein or peptide: NADH-ubiquinone oxidoreductase chain 1
    • Protein or peptide: NADH dehydrogenase subunit 2
    • Protein or peptide: NADH-ubiquinone oxidoreductase chain 3
    • Protein or peptide: NADH-ubiquinone oxidoreductase chain 6
    • Protein or peptide: subunit NI9M of protein NADH:Ubiquinone Oxidoreductase (Complex I)
    • Protein or peptide: Subunit NEBM of NADH:Ubiquinone Oxidoreductase (Complex I)
    • Protein or peptide: Subunit NIPM of NADH:Ubiquinone Oxidoreductase (Complex I)
    • Protein or peptide: assembly factor CIA84
    • Protein or peptide: CIA30 domain-containing protein
  • Ligand: CARDIOLIPIN
  • Ligand: DIUNDECYL PHOSPHATIDYL CHOLINE
  • Ligand: 1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: 1,2-Distearoyl-sn-glycerophosphoethanolamine
  • Ligand: Phosphatidylinositol

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Supramolecule #1: Late assembly intermediate of the proximal proton pumping module ...

SupramoleculeName: Late assembly intermediate of the proximal proton pumping module of complex I with assembly factors NDUFAF1 and CIA84
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#14
Source (natural)Organism: Yarrowia lipolytica (yeast)

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Macromolecule #1: Subunit NIMM of NADH:Ubiquinone Oxidoreductase (Complex I)

MacromoleculeName: Subunit NIMM of NADH:Ubiquinone Oxidoreductase (Complex I)
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Yarrowia lipolytica (yeast)
Molecular weightTheoretical: 9.806238 KDa
SequenceString:
MAIPFEALLP YGIIFGLLTA GGGAMQVLHV YRNGGVRDRF AIDQWDSQMM ERDLRLNGGQ GRKQVDQATA PEAFKHNHVW KSERPLI

UniProtKB: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1

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Macromolecule #2: NADH-ubiquinone oxidoreductase chain 4L

MacromoleculeName: NADH-ubiquinone oxidoreductase chain 4L / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: NADH:ubiquinone reductase (H+-translocating)
Source (natural)Organism: Yarrowia lipolytica (yeast)
Molecular weightTheoretical: 9.84386 KDa
SequenceString:
(FME)FIGTIILVL SFLGFVFNRR NIILAFICLE TMLLGINLIL LRNSVLFDDI SGSLFAIVII ILAGVESAIG LSLLVS YYR LRGVINSYGI

UniProtKB: NADH-ubiquinone oxidoreductase chain 4L

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Macromolecule #3: Subunit NUPM of NADH:Ubiquinone Oxidoreductase (Complex I)

MacromoleculeName: Subunit NUPM of NADH:Ubiquinone Oxidoreductase (Complex I)
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Yarrowia lipolytica (yeast)
Molecular weightTheoretical: 19.355197 KDa
SequenceString:
MPREAAAHWV PFEDKANMPD NVPDVVEVGA TSAPLLSASY FIGAKCKPYN DDFMLCREES QGSGAIDCLK EGRRVTRCAV SVIEDINKS CLDEFRLHWQ CLEQNNHQLS GCRKAEALLN KCVFTKLNLE KKIPGLRPDE EPVFLKKDPW IKPAVDDFKS V RAYAEAKK NGTL

UniProtKB: NADH-ubiquinone oxidoreductase

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Macromolecule #4: Subunit NB6M of NADH:Ubiquinone Oxidoreductase (Complex I)

MacromoleculeName: Subunit NB6M of NADH:Ubiquinone Oxidoreductase (Complex I)
type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Yarrowia lipolytica (yeast)
Molecular weightTheoretical: 14.112429 KDa
SequenceString:
MPSVGQDLPP VGGYEPVQWR RNLPARGFRP LVYLAALCGI CGYGFYRALG GIQERRELKR EKLWARIYLM PLLQAEEDRQ TVRRSIAQL EREKEIMKGT GFDVDKSVYN DGKFHAPALM IPPK

UniProtKB: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13

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Macromolecule #5: NADH-ubiquinone oxidoreductase complex I, 21 kDa subunit-domain-c...

MacromoleculeName: NADH-ubiquinone oxidoreductase complex I, 21 kDa subunit-domain-containing protein
type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Yarrowia lipolytica (yeast)
Molecular weightTheoretical: 18.588209 KDa
SequenceString:
MSSSTPLVKT SVNYSYGDYP LIDADPHFKR VVGYMRPSDY GVIGLATAAL PAGICFAEWL DPVKGKFARP SVKFLRVATM LGFAVGFGA AYARSSLRFF GVTENAREYK KDEAQMAARK AAGLEPYGTS SLTPELQEIA AKNSAHSIAG LFIFPWFNFV N HPYHGREQ K

UniProtKB: NADH-ubiquinone oxidoreductase complex I, 21 kDa subunit-domain-containing protein

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Macromolecule #6: NADH-ubiquinone oxidoreductase chain 1

MacromoleculeName: NADH-ubiquinone oxidoreductase chain 1 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO / EC number: NADH:ubiquinone reductase (H+-translocating)
Source (natural)Organism: Yarrowia lipolytica (yeast)
Molecular weightTheoretical: 38.389277 KDa
SequenceString: (FME)IINIVEILI FLVCVLFSVA YLTVAERKTL AYMQRRLGPN FVGYYGLLQA FADAVKLLLK EIVLPKESNY IILVIS PLI TLITALIGWV VIPLGPGITL GELNLGILFS LAIGSLGVFG SLLSGWSSNS KYSLLGSIRS TAQLISYELI LTSIFII II MFVSSLNITT ...String:
(FME)IINIVEILI FLVCVLFSVA YLTVAERKTL AYMQRRLGPN FVGYYGLLQA FADAVKLLLK EIVLPKESNY IILVIS PLI TLITALIGWV VIPLGPGITL GELNLGILFS LAIGSLGVFG SLLSGWSSNS KYSLLGSIRS TAQLISYELI LTSIFII II MFVSSLNITT IIETQRVVWY CIPLLPLLLI FFIASVAETA RPPFDLTESE SELVAGYFTE YSGSPFVFFF LAEYSNII L ISAFNGYLLL GGYLSFNYSY LFNILFNDYS YVSFLFEGLI NSSAYAIKLV FLMFSFIWVR AAFPRFTYDN LINFCWIIL LPLLFGIFLI IPSTLYIFDS FPTLI

UniProtKB: NADH-ubiquinone oxidoreductase chain 1

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Macromolecule #7: NADH dehydrogenase subunit 2

MacromoleculeName: NADH dehydrogenase subunit 2 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO / EC number: NADH:ubiquinone reductase (H+-translocating)
Source (natural)Organism: Yarrowia lipolytica (yeast)
Molecular weightTheoretical: 53.381367 KDa
SequenceString: (FME)LILAIISLI TFVSMSKLSD NRAIIRLINI YLILVLVLDS FLYLLFLNNQ TYTVMGELLI FNSFTFYIDM LIYFIM IVI SSLYGYNLYN NNLYKTLFEP KKELIILFLI NILGALLIVH SNDFITLFVA IELQSYSIYL ITAIYNSSYK ASKASML YF FMGGILSILI ...String:
(FME)LILAIISLI TFVSMSKLSD NRAIIRLINI YLILVLVLDS FLYLLFLNNQ TYTVMGELLI FNSFTFYIDM LIYFIM IVI SSLYGYNLYN NNLYKTLFEP KKELIILFLI NILGALLIVH SNDFITLFVA IELQSYSIYL ITAIYNSSYK ASKASML YF FMGGILSILI AYSINTYYSV LNSYTLHSLD SLIINTLDLN LILIALSLGL LFKIGIAPLH KWLISIYENT PILITIYI S LIPKISILSY LVLSNISINS LVISILAILT LLVGSVGGLL QIKIKRLLAF SGLTNAGYMM LLLLLNNNEF SYLYYITQY SISHLAIFMI IIFSIYYINY INNQYNPIIY VNQLKGLIHD NAYLVLSMAI VVFSFIGIPP LLGFFGKLNI LMSILNNGYY FISIVLIVA SLISALYYLY LLNVSIQDKN NILINSNETV SSVLSYILSS LIILITFGFI YNSLIIDIFN VYFN

UniProtKB: NADH-ubiquinone oxidoreductase chain 2

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Macromolecule #8: NADH-ubiquinone oxidoreductase chain 3

MacromoleculeName: NADH-ubiquinone oxidoreductase chain 3 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO / EC number: NADH:ubiquinone reductase (H+-translocating)
Source (natural)Organism: Yarrowia lipolytica (yeast)
Molecular weightTheoretical: 14.506339 KDa
SequenceString:
(FME)NTFIIFIIL IPIVGFALLA VNILLAVYKP YNEKLGAFEC GLTSFNQTRL AFNAAFILVA ILFLPFDLEI STLLPY VMS IYLVSNYGFT IVLLFLLILI IGFVYEINTN ALKINKHNKP NTDSLIYKL

UniProtKB: NADH-ubiquinone oxidoreductase chain 3

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Macromolecule #9: NADH-ubiquinone oxidoreductase chain 6

MacromoleculeName: NADH-ubiquinone oxidoreductase chain 6 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO / EC number: NADH:ubiquinone reductase (H+-translocating)
Source (natural)Organism: Yarrowia lipolytica (yeast)
Molecular weightTheoretical: 20.793111 KDa
SequenceString:
(FME)MYLTYYFIE ITIFLAILCT IFIISAKNPM VSILYMIALF VIAAMYLYLI GLGIFSLLYI MIYIGAIAVL FLFIIT LLD INSTELSVKS NIRDLPLVLI SLIVLTISGL MIYSNDSILI NKLLEAFGND YNTIITQDWF NIENTTLLTT IGNVLLT NN AFILLVLAIV LLLGIIGPIS ITMKHKE

UniProtKB: NADH-ubiquinone oxidoreductase chain 6

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Macromolecule #10: subunit NI9M of protein NADH:Ubiquinone Oxidoreductase (Complex I)

MacromoleculeName: subunit NI9M of protein NADH:Ubiquinone Oxidoreductase (Complex I)
type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Yarrowia lipolytica (yeast)
Molecular weightTheoretical: 8.992229 KDa
SequenceString:
MINANPGFWN GPFRYLRWSA HNRPHLFFAF AIGIAGPVAA LTLTPLRRKY LYPDHSPLPQ SYPLPQRARE QLTGFDDE

UniProtKB: Uncharacterized protein

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Macromolecule #11: Subunit NEBM of NADH:Ubiquinone Oxidoreductase (Complex I)

MacromoleculeName: Subunit NEBM of NADH:Ubiquinone Oxidoreductase (Complex I)
type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Yarrowia lipolytica (yeast)
Molecular weightTheoretical: 8.059366 KDa
SequenceString:
MALFTSLVGA SGLGFATKFL SNKIRLKPAG YYPLGYVFSG VAWAGLGLVL HNVHQHSLEV LEKKKTALSE QRTE

UniProtKB: Uncharacterized protein

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Macromolecule #12: Subunit NIPM of NADH:Ubiquinone Oxidoreductase (Complex I)

MacromoleculeName: Subunit NIPM of NADH:Ubiquinone Oxidoreductase (Complex I)
type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Yarrowia lipolytica (yeast)
Molecular weightTheoretical: 10.035651 KDa
SequenceString:
MTAAGISLTG GRNRCFSEWQ SFMHCTAKTD AKSRAQCLPN FEDYMECLHH TKEKARLREI ESVLKQKKEG LEAPPVKVIP VKAIGLVEE

UniProtKB: Uncharacterized protein

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Macromolecule #13: assembly factor CIA84

MacromoleculeName: assembly factor CIA84 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Yarrowia lipolytica (yeast)
Molecular weightTheoretical: 97.098469 KDa
SequenceString: MPKNALLRSA RQVAISRVFA TSRASHVVSH APILASVRPR SNPAPYRRNF SSSRALRNDY GLDTAERSLK ESLVPFNGAP VDRKVVRDQ LMELISVSPG QVFPISVIPV VKSAYYELFR ENERVLSAGD TKTLFGAVAG NNPEDVQDLP FVLAVYHQAE Q AAETNRDS ...String:
MPKNALLRSA RQVAISRVFA TSRASHVVSH APILASVRPR SNPAPYRRNF SSSRALRNDY GLDTAERSLK ESLVPFNGAP VDRKVVRDQ LMELISVSPG QVFPISVIPV VKSAYYELFR ENERVLSAGD TKTLFGAVAG NNPEDVQDLP FVLAVYHQAE Q AAETNRDS RDNILLLGKY FLFQDRLDNF WKLLEAQIKT HDDVDAGFVK QLLELISVDP HLTLGNVARV LQLKTDNHVS SS DELRNAL SATLEQLYYK ENEGSEFFLS LVENHILDSK DFTPSDSVVA MILNTCVNEG REDLGQSVLR NVVSRVGNLS PGQ EDPQNC WGFWSSVAMD LHGSKTDVKA FISRLEALPH RTKATWDILI RYAVFKADLA GRNDLLQVRA LLAEMQKVGF EPDA ETYFD AYRSSKSIKP DVVHLFEAEL DIEKDTSIFA IEMDKALKNH DTLEALSIFY ESFEQGAQWE NKRLHMEAMT ELLIQ YAGL NDTSVADILQ LVQRIEPICA QGRIPYSAET AIAQNVLQRH SDTANFYTFM NRQYGNTADK VTKQDPQIRP HTYQVI HDY IYSCESERAD LAWEMYGLLH KFYVVPFADY YKAIKFFAQD VKRQDYALLT FQQIRKNHDL HGQPAATSEM VAFLFHE FA KTKYKRGIKR LHEVVALETS FDVNRDVLNE MMAAYVSVED LNRVQDCWAQ LQQLPPSIGA NNRSVDVLLS YFKDNIHY T ERTWQGIPEF GLLPTLENYE QYLINNCRTG NYRRALEITK NMEIDSGLKP TAKIIAAVYN YTFTEQRKLE VEQWAEKAH PEMWLELKEG DKLKSLCLPA NSDNDNVESL LKQASADMDE EMSGGIVKVE SV

UniProtKB: Mitochondrial group I intron splicing factor CCM1

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Macromolecule #14: CIA30 domain-containing protein

MacromoleculeName: CIA30 domain-containing protein / type: protein_or_peptide / ID: 14 / Details: NDUFAF1 has a C-terminal strep tag / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Yarrowia lipolytica (yeast)
Molecular weightTheoretical: 32.629998 KDa
Recombinant expressionOrganism: Yarrowia lipolytica (yeast)
SequenceString: MSFLTKALGG LKRLRPTETT EQVLVNFTKP NSLETVLTKC DEELGGYSTV NLALERPTTG KPYGRFFGNL SLDLPKDNKM VTRSGFAMF RTLDQPSSMF KTNAWNWEQY RHLELRVRGD RRKYFVNVQS ATPLASDLYQ HRLFIQTPGE WETVVIPIDD F ILTNKGVV ...String:
MSFLTKALGG LKRLRPTETT EQVLVNFTKP NSLETVLTKC DEELGGYSTV NLALERPTTG KPYGRFFGNL SLDLPKDNKM VTRSGFAMF RTLDQPSSMF KTNAWNWEQY RHLELRVRGD RRKYFVNVQS ATPLASDLYQ HRLFIQTPGE WETVVIPIDD F ILTNKGVV QEQMAMDTAN VYTVGIGLID RQYGPYNLDI EYIKAVAHPP LEFKPKKEYE VEKETILLTP GQPMELGKGK VK ELEENLY FQGAEAAAKE AAAKAWSHPQ FEKGGGSGGG SGGSAWSHPQ FEK

UniProtKB: NADH:ubiquinone oxidoreductase intermediate-associated protein 30 domain-containing protein

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Macromolecule #15: CARDIOLIPIN

MacromoleculeName: CARDIOLIPIN / type: ligand / ID: 15 / Number of copies: 2 / Formula: CDL
Molecular weightTheoretical: 1.464043 KDa
Chemical component information

ChemComp-CDL:
CARDIOLIPIN / phospholipid*YM

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Macromolecule #16: DIUNDECYL PHOSPHATIDYL CHOLINE

MacromoleculeName: DIUNDECYL PHOSPHATIDYL CHOLINE / type: ligand / ID: 16 / Number of copies: 1 / Formula: PLC
Molecular weightTheoretical: 622.834 Da
Chemical component information

ChemComp-PLC:
DIUNDECYL PHOSPHATIDYL CHOLINE / phospholipid*YM

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Macromolecule #17: 1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE

MacromoleculeName: 1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 17 / Number of copies: 1 / Formula: CPL
Molecular weightTheoretical: 758.06 Da
Chemical component information

ChemComp-CPL:
1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / phospholipid*YM

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Macromolecule #18: 1,2-Distearoyl-sn-glycerophosphoethanolamine

MacromoleculeName: 1,2-Distearoyl-sn-glycerophosphoethanolamine / type: ligand / ID: 18 / Number of copies: 1 / Formula: 3PE
Molecular weightTheoretical: 748.065 Da
Chemical component information

ChemComp-3PE:
1,2-Distearoyl-sn-glycerophosphoethanolamine / phospholipid*YM

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Macromolecule #19: Phosphatidylinositol

MacromoleculeName: Phosphatidylinositol / type: ligand / ID: 19 / Number of copies: 1 / Formula: T7X
Molecular weightTheoretical: 887.128 Da
Chemical component information

ChemComp-T7X:
Phosphatidylinositol

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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

Concentration1.2 mg/mL
BufferpH: 7.5
GridModel: C-flat-1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 276 K / Instrument: FEI VITROBOT MARK IV
DetailsThe sample was a mixture of assembly intermediates associated with the assembly factor NDUFAF1

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 6229 / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2048808
Startup modelType of model: OTHER / Details: Ab initio model in CryoSPARC 3.3.1
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.1) / Number images used: 18279
Initial angle assignmentType: OTHER / Software - Name: cryoSPARC (ver. 3.3.1)
Final angle assignmentType: OTHER / Software - Name: cryoSPARC (ver. 3.3.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

7o71


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: OTHER
Output model

PDB-7zkp:
Late assembly intermediate of the proximal proton pumping module of complex I with assembly factors NDUFAF1 and CIA84

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