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- EMDB-16000: Cryo-EM structure of the Arabidopsis thaliana I+III2 supercomplex... -

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Entry
Database: EMDB / ID: EMD-16000
TitleCryo-EM structure of the Arabidopsis thaliana I+III2 supercomplex (CI membrane core)
Map data
Sample
  • Complex: Mitochondrial Arabidopsis thaliana I+III2 supercomplex (CI membrane core)
    • Protein or peptide: x 22 types
  • Ligand: x 12 types
Function / homology
Function and homology information


plastid outer membrane / TIM22 mitochondrial import inner membrane insertion complex / anther dehiscence / vegetative to reproductive phase transition of meristem / chloroplast outer membrane / NADH dehydrogenase complex / P450-containing electron transport chain / Lyases; Carbon-oxygen lyases; Hydro-lyases / protein insertion into mitochondrial inner membrane / photorespiration ...plastid outer membrane / TIM22 mitochondrial import inner membrane insertion complex / anther dehiscence / vegetative to reproductive phase transition of meristem / chloroplast outer membrane / NADH dehydrogenase complex / P450-containing electron transport chain / Lyases; Carbon-oxygen lyases; Hydro-lyases / protein insertion into mitochondrial inner membrane / photorespiration / embryo development ending in seed dormancy / response to abscisic acid / plant-type vacuole / respiratory chain complex I / ubiquinone binding / regulation of reactive oxygen species metabolic process / electron transport coupled proton transport / plastid / porin activity / NADH:ubiquinone reductase (H+-translocating) / pore complex / mitochondrial respiratory chain complex I / mitochondrial electron transport, NADH to ubiquinone / protein homotrimerization / NADH dehydrogenase (ubiquinone) activity / ATP synthesis coupled electron transport / respirasome / monoatomic ion transport / aerobic respiration / response to salt stress / chloroplast / mitochondrial membrane / carbonate dehydratase activity / mitochondrial intermembrane space / 2 iron, 2 sulfur cluster binding / peroxisome / mitochondrial inner membrane / mitochondrial outer membrane / copper ion binding / nucleolus / protein homodimerization activity / mitochondrion / extracellular region / identical protein binding / metal ion binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Mitochondrial import inner membrane translocase subunit TIM22 / At2g27730-like / NADH-ubiquinone oxidoreductase 11kDa subunit / NADH-ubiquinone oxidoreductase 11 kDa subunit / : / NADH-ubiquinone oxidoreductase, 21kDa subunit, N-terminal / NADH-ubiquinone oxidoreductase complex I, 21 kDa subunit / Adrenodoxin / NAD(P)H-quinone oxidoreductase subunit 3, bacterial/plastid / NAD(P)H-quinone oxidoreductase, subunit N/subunit 2 ...Mitochondrial import inner membrane translocase subunit TIM22 / At2g27730-like / NADH-ubiquinone oxidoreductase 11kDa subunit / NADH-ubiquinone oxidoreductase 11 kDa subunit / : / NADH-ubiquinone oxidoreductase, 21kDa subunit, N-terminal / NADH-ubiquinone oxidoreductase complex I, 21 kDa subunit / Adrenodoxin / NAD(P)H-quinone oxidoreductase subunit 3, bacterial/plastid / NAD(P)H-quinone oxidoreductase, subunit N/subunit 2 / Tim17/Tim22/Tim23/Pmp24 family / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex subunit 1 / NADH-ubiquinone oxidoreductase MWFE subunit / Hexapeptide repeat / GRIM-19 / GRIM-19 protein / NADH dehydrogenase subunit 5, C-terminal / NADH dehydrogenase subunit 5 C-terminus / NADH:ubiquinone oxidoreductase, NDUFS5-15kDa / NADH:ubiquinone oxidoreductase, iron-sulphur subunit 5 / Bacterial transferase hexapeptide (six repeats) / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 8 / NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJ / NADH-plastoquinone oxidoreductase, chain 5 subgroup / NADH-quinone oxidoreductase, chain M/4 / NADH-ubiquinone oxidoreductase chain 4L/K / NADH:ubiquinone/plastoquinone oxidoreductase, chain 6 / NADH-ubiquinone/plastoquinone oxidoreductase chain 6 / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminal / NADH-quinone oxidoreductase, chain 5-like / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus / NADH-ubiquinone oxidoreductase chain 4L/Mnh complex subunit C1-like / NADH-ubiquinone/plastoquinone oxidoreductase chain 4L / 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 / Trimeric LpxA-like superfamily / NADH dehydrogenase / CHCH / NADH:ubiquinone oxidoreductase / CHCH domain / NADH:quinone oxidoreductase/Mrp antiporter, membrane subunit / Proton-conducting membrane transporter / Coiled coil-helix-coiled coil-helix (CHCH) domain profile. / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-like superfamily
Similarity search - Domain/homology
(thale cress) hypothetical protein / NADH-ubiquinone oxidoreductase chain 6 / (thale cress) hypothetical protein / NADH-ubiquinone oxidoreductase chain 1 / NADH-ubiquinone oxidoreductase chain 5 / NADH-ubiquinone oxidoreductase chain 2 / Outer envelope pore protein 16-3, chloroplastic/mitochondrial / NADH-ubiquinone oxidoreductase chain 3 / NADH-ubiquinone oxidoreductase chain 4 / NADH-ubiquinone oxidoreductase chain 4L ...(thale cress) hypothetical protein / NADH-ubiquinone oxidoreductase chain 6 / (thale cress) hypothetical protein / NADH-ubiquinone oxidoreductase chain 1 / NADH-ubiquinone oxidoreductase chain 5 / NADH-ubiquinone oxidoreductase chain 2 / Outer envelope pore protein 16-3, chloroplastic/mitochondrial / NADH-ubiquinone oxidoreductase chain 3 / NADH-ubiquinone oxidoreductase chain 4 / NADH-ubiquinone oxidoreductase chain 4L / At4g16450 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8-B / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13-A / Uncharacterized protein At1g67785 / Excitatory amino acid transporter / Gamma carbonic anhydrase 2, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 / Gamma carbonic anhydrase 1, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 5-B / Gamma carbonic anhydrase-like 2, mitochondrial / At2g46540/F11C10.23 / Uncharacterized protein At2g27730, mitochondrial
Similarity search - Component
Biological speciesArabidopsis t (thale cress) / thale cress (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.13 Å
AuthorsKlusch N / Kuehlbrandt W
Funding support Germany, 1 items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Nat Plants / Year: 2023
Title: Cryo-EM structure of the respiratory I + III supercomplex from Arabidopsis thaliana at 2 Å resolution.
Authors: Niklas Klusch / Maximilian Dreimann / Jennifer Senkler / Nils Rugen / Werner Kühlbrandt / Hans-Peter Braun /
Abstract: Protein complexes of the mitochondrial respiratory chain assemble into respiratory supercomplexes. Here we present the high-resolution electron cryo-microscopy structure of the Arabidopsis ...Protein complexes of the mitochondrial respiratory chain assemble into respiratory supercomplexes. Here we present the high-resolution electron cryo-microscopy structure of the Arabidopsis respiratory supercomplex consisting of complex I and a complex III dimer, with a total of 68 protein subunits and numerous bound cofactors. A complex I-ferredoxin, subunit B14.7 and P9, a newly defined subunit of plant complex I, mediate supercomplex formation. The component complexes stabilize one another, enabling new detailed insights into their structure. We describe (1) an interrupted aqueous passage for proton translocation in the membrane arm of complex I; (2) a new coenzyme A within the carbonic anhydrase module of plant complex I defining a second catalytic centre; and (3) the water structure at the proton exit pathway of complex III with a co-purified ubiquinone in the Q site. We propose that the main role of the plant supercomplex is to stabilize its components in the membrane.
History
DepositionOct 21, 2022-
Header (metadata) releaseJan 11, 2023-
Map releaseJan 11, 2023-
UpdateFeb 1, 2023-
Current statusFeb 1, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16000.png

Downloads & links

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Map

FileDownload / File: emd_16000.map.gz / Format: CCP4 / Size: 98.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesX (Sec.)Y (Row.)Z (Col.)
0.57 Å/pix.
x 296 pix.
= 169.608 Å		0.57 Å/pix.
x 273 pix.
= 156.429 Å		0.57 Å/pix.
x 319 pix.
= 182.787 Å

Surface

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Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 0.573 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.6
Minimum - Maximum-2.9974337 - 5.559311
Average (Standard dev.)-1.5873237e-12 (±0.26225895)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin186196269
Dimensions273319296
Spacing296273319
CellA: 169.608 Å / B: 156.429 Å / C: 182.787 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_16000_additional_1.map
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_16000_half_map_1.map
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Half map: #1

Fileemd_16000_half_map_2.map
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Sample components

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Entire : Mitochondrial Arabidopsis thaliana I+III2 supercomplex (CI membra...

EntireName: Mitochondrial Arabidopsis thaliana I+III2 supercomplex (CI membrane core)
Components
  • Complex: Mitochondrial Arabidopsis thaliana I+III2 supercomplex (CI membrane core)
    • Protein or peptide: NADH-ubiquinone oxidoreductase chain 3
    • Protein or peptide: NADH-ubiquinone oxidoreductase chain 1
    • Protein or peptide: NADH-ubiquinone oxidoreductase chain 6
    • Protein or peptide: NADH-ubiquinone oxidoreductase chain 4L
    • Protein or peptide: NADH-ubiquinone oxidoreductase chain 5
    • Protein or peptide: NADH-ubiquinone oxidoreductase chain 4
    • Protein or peptide: NADH-ubiquinone oxidoreductase chain 2
    • Protein or peptide: AT3G07480.1
    • Protein or peptide: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8-B
    • Protein or peptide: Outer envelope pore protein 16-3, chloroplastic/mitochondrial
    • Protein or peptide: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13-A
    • Protein or peptide: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1
    • Protein or peptide: At2g46540/F11C10.23
    • Protein or peptide: Excitatory amino acid transporter
    • Protein or peptide: NADH dehydrogenase [ubiquinone] iron-sulfur protein 5-B
    • Protein or peptide: At4g16450
    • Protein or peptide: P1
    • Protein or peptide: Uncharacterized protein At1g67785
    • Protein or peptide: Uncharacterized protein At2g27730, mitochondrial
    • Protein or peptide: Gamma carbonic anhydrase-like 2, mitochondrial
    • Protein or peptide: Gamma carbonic anhydrase 2, mitochondrial
    • Protein or peptide: Gamma carbonic anhydrase 1, mitochondrial
  • Ligand: (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE
  • Ligand: Ubiquinone-9Coenzyme Q10
  • Ligand: PHOSPHATIDYLETHANOLAMINE
  • Ligand: 2-{[(4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranosyl)oxy]methyl}-4-{[(3beta,9beta,14beta,17beta,25R)-spirost-5-en-3-yl]oxy}butyl 4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranoside
  • Ligand: FE (III) ION
  • Ligand: 2,3-DIMETHOXY-5-METHYL-6-(3,11,15,19-TETRAMETHYL-EICOSA-2,6,10,14,18-PENTAENYL)-[1,4]BENZOQUINONE
  • Ligand: (7S)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE
  • Ligand: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE
  • Ligand: CARDIOLIPIN
  • Ligand: ZINC ION
  • Ligand: Butyryl Coenzyme A
  • Ligand: water

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Supramolecule #1: Mitochondrial Arabidopsis thaliana I+III2 supercomplex (CI membra...

SupramoleculeName: Mitochondrial Arabidopsis thaliana I+III2 supercomplex (CI membrane core)
type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#22
Source (natural)Organism: Arabidopsis t (thale cress)

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Macromolecule #1: NADH-ubiquinone oxidoreductase chain 3

MacromoleculeName: NADH-ubiquinone oxidoreductase chain 3 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: NADH:ubiquinone reductase (H+-translocating)
Source (natural)Organism: thale cress (thale cress)
Molecular weightTheoretical: 13.969396 KDa
SequenceString:
(FME)MLEFAPIFI YLVISLLVSL ILLGVPFLFA SNSSTYPEKL SAYECGFDPF GDARSRFDIR FYLVSILFLI FDLEVT FFF PWAVSLNKID LFGFWSMMAF LFILTIGFLY EWKRGALDWE

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Macromolecule #2: NADH-ubiquinone oxidoreductase chain 1

MacromoleculeName: NADH-ubiquinone oxidoreductase chain 1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: NADH:ubiquinone reductase (H+-translocating)
Source (natural)Organism: thale cress (thale cress)
Molecular weightTheoretical: 36.02007 KDa
SequenceString: MYIAVPAEIL GIILPLLLGV AFLVLAERKV MAFVQRRKGP DVVGSFGLLQ PLADGLKLIL KEPISPSSAN FFLFRMAPVA TFMLSLVAW AVVPFDYGMV LSDLNIGLLY LFAISSLGVY GIIIAGRSSN SKYAFLGALR SAAQMVSYEV SIGLILITVL I CVGSCNLS ...String:
MYIAVPAEIL GIILPLLLGV AFLVLAERKV MAFVQRRKGP DVVGSFGLLQ PLADGLKLIL KEPISPSSAN FFLFRMAPVA TFMLSLVAW AVVPFDYGMV LSDLNIGLLY LFAISSLGVY GIIIAGRSSN SKYAFLGALR SAAQMVSYEV SIGLILITVL I CVGSCNLS EIVMAQKQIW FGIPLFPVLV MFFISCLAET NRAPFDLPEA EAELVAGYNV EYSSMGFALF FLGEYANMIL MS GLCTLFF LGGWLPILDL PIFKKIPGSI WFSIKVLFFL FLYIWVRAAF PRYRYDQLMG LGWKVFLPLS LAWVVSVSGL LVT FQWLP

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Macromolecule #3: NADH-ubiquinone oxidoreductase chain 6

MacromoleculeName: NADH-ubiquinone oxidoreductase chain 6 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: NADH:ubiquinone reductase (H+-translocating)
Source (natural)Organism: thale cress (thale cress)
Molecular weightTheoretical: 23.690385 KDa
SequenceString: MILSVLSSLA LVSGLMVVRA KNPVHSVLFF ILVFCDTSGL LLLLGLDFFA MIFLVVYIGA IAVLFLFVVM MFHIQIAEIH EEVLRYLPV SGIIGLIFWW EMFFILDNES IPLLPTQRNT TSLRYTVYAG KVRSWTNLET LGNLLYTYYF VWFLVSSLIL L VAMIGAIV ...String:
MILSVLSSLA LVSGLMVVRA KNPVHSVLFF ILVFCDTSGL LLLLGLDFFA MIFLVVYIGA IAVLFLFVVM MFHIQIAEIH EEVLRYLPV SGIIGLIFWW EMFFILDNES IPLLPTQRNT TSLRYTVYAG KVRSWTNLET LGNLLYTYYF VWFLVSSLIL L VAMIGAIV LTMHRTTKVK RQDVFRRNAI DFRRTIMRRT TDPLTIY

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Macromolecule #4: NADH-ubiquinone oxidoreductase chain 4L

MacromoleculeName: NADH-ubiquinone oxidoreductase chain 4L / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: NADH:ubiquinone reductase (H+-translocating)
Source (natural)Organism: thale cress (thale cress)
Molecular weightTheoretical: 11.193559 KDa
SequenceString:
(FME)DLIKYFTFS MIIFILGIWG ILLNRRNILI MLMSIELMLL AVNLNFLVFS VSLDDMMGQV FALLVLTVAA AESAIG LAI FVITFRVRGT IAVEFINSIQ G

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Macromolecule #5: NADH-ubiquinone oxidoreductase chain 5

MacromoleculeName: NADH-ubiquinone oxidoreductase chain 5 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO / EC number: NADH:ubiquinone reductase (H+-translocating)
Source (natural)Organism: thale cress (thale cress)
Molecular weightTheoretical: 74.497977 KDa
SequenceString: MYLLIVFLPL LGSSVAGFFG RFLGSEGSAI MTTTCVSFSS ILSLIAFYEV ALGASACYLR IAPWISSEMF DASWGFLFDS LTVVMLIVV TFISSLVHLY SISYMSEDPH SPRFMCYLSI FTFFMLMLVT GDNFLQLFLG WEGVGLASYL LIHFWFTRLQ A DKAAIKAM ...String:
MYLLIVFLPL LGSSVAGFFG RFLGSEGSAI MTTTCVSFSS ILSLIAFYEV ALGASACYLR IAPWISSEMF DASWGFLFDS LTVVMLIVV TFISSLVHLY SISYMSEDPH SPRFMCYLSI FTFFMLMLVT GDNFLQLFLG WEGVGLASYL LIHFWFTRLQ A DKAAIKAM LVNRVGDFGL ALGILGCFTL FQTVDFSTIF ACASVPRNSW IFCNMRLNAI SLICILLFIG AVGKSAQIGL HT WLPDAME GPTPVSALIH AATMVTAGVF MIARCSPLFE YSPTALIVIT FAGAMTSFLA ATTGILQNDL KRVIAYSTCS QLG YMIFAC GISNYSVSVF HLMNHAFFKA LLFLSAGSVI HAMSDEQDMR KMGGLASSFP LTYAMMLIGS LSLIGFPFLT GFYS KDVIL ELAYTKYTIS GNFAFWLGSV SVLFTSYYSF RLLFLTFLVP TNSFGRDISR CHDAPIPMAI PLILLALGSL FVGYL AKDM MIGLGTNFWA NSLLVLPKNE ILAESEFAAP TIIKLIPILF STLGAFVAYN VNLVADQFQR AFQTSTFCNR LYSFFN KRW FFDQVLNDFL VRSFLRFGYE VSFEALDKGA IEILGPYGIS YTFRRLAERI SQLQSGFVYH YAFAMLLGLT LFVTFFC MW DSLSSWVDNR LSFILIVSSF YTKSSQE

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Macromolecule #6: NADH-ubiquinone oxidoreductase chain 4

MacromoleculeName: NADH-ubiquinone oxidoreductase chain 4 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO / EC number: NADH:ubiquinone reductase (H+-translocating)
Source (natural)Organism: thale cress (thale cress)
Molecular weightTheoretical: 55.995664 KDa
SequenceString: MLEHFCECYF NLSGLILCPV LGSIILLFIP NSRIRLIRLI GLCASLITFL YSLVLWIQFD SSTAKFQFVE SLRWLPYENI NFYLGIDGI SLFFVILTTF LIPICILVGW SGMRSYGKEY IIAFLICEFL MIAVFCMLDL LLFYVFFESV LIPMFIIIGV W GSRQRKIK ...String:
MLEHFCECYF NLSGLILCPV LGSIILLFIP NSRIRLIRLI GLCASLITFL YSLVLWIQFD SSTAKFQFVE SLRWLPYENI NFYLGIDGI SLFFVILTTF LIPICILVGW SGMRSYGKEY IIAFLICEFL MIAVFCMLDL LLFYVFFESV LIPMFIIIGV W GSRQRKIK AAYQFFLYTL LGSLFMLLAI LLILFQTGTT DLQILLTTEF SERRQIFLWI AFFASFAVKV PMVPVHIWLP EA HVEAPTA GSVILAGILL KFGTYGFLRF SIPMFPEATL CFTPFIYTLS AIAIIYTSLT TLRQIDLKKI IAYSSVAHMN LVT IGMFSL NIQGIGGSIL LMLSHGLVSS ALFLCVGVLY DRHKTRLVRY YGGLVSTMPN FSTIFFFFTL ANMSLPGTSS FIGE FLILV GAFQRNSLVA TLAALGMILG AAYSLWLYNR VVSGNLKPDF LHKFSDLNGR EVFIFIPFLV GLVWMGVYPK VFLDC MHTS VSNLVQHGKF H

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Macromolecule #7: NADH-ubiquinone oxidoreductase chain 2

MacromoleculeName: NADH-ubiquinone oxidoreductase chain 2 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO / EC number: NADH:ubiquinone reductase (H+-translocating)
Source (natural)Organism: thale cress (thale cress)
Molecular weightTheoretical: 55.486836 KDa
SequenceString: MKAEFVRILP HMFNLFLAVF PEIFIINATF ILLIHGVVFS TSKKYDYPPL ASNVGWLGLL SVLITLLLLA AGAPLLTIAH LFWNNLFRR DNFTYFCQIF LLLSTAGTIS MCFDFFDQER FDAFEFIVLI LLSTCGMLFM ISAYDLIAMY LAIELQSLCF Y VIAASKRK ...String:
MKAEFVRILP HMFNLFLAVF PEIFIINATF ILLIHGVVFS TSKKYDYPPL ASNVGWLGLL SVLITLLLLA AGAPLLTIAH LFWNNLFRR DNFTYFCQIF LLLSTAGTIS MCFDFFDQER FDAFEFIVLI LLSTCGMLFM ISAYDLIAMY LAIELQSLCF Y VIAASKRK SEFSTEAGLK YLILGAFSSG ILLFGCSMIY GSTGATHFDQ LAKILTGYEI TGARSSGIFM GILFIAVGFL FK ITAVPFH MWAPDIYEGS PTPVTAFLSI APKISIFANI LRVFIYGSYG ATLQQIFFFC SIASMILGAL AAMAQTKVKR LLA YSSIGH VGYICIGFSC GTIEGIQSLL IGIFIYALMT MDAFAIVLAL RQTRVKYIAD LGALAKTNPI LAITFSITMF SYAG IPPLA GFCSKFYLFF AALGCGAYFL ALVGVVTSVI GCFYYIRLVK RMFFDTPRTW ILYEPMDRNK SLLLAMTSFF ITLFL LYPS PLFSVTHQMA LSLYL

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Macromolecule #8: AT3G07480.1

MacromoleculeName: AT3G07480.1 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: thale cress (thale cress)
Molecular weightTheoretical: 17.626197 KDa
SequenceString:
MATTLQKLSS QIHRLSPFTR SLIVRTSATS APSPSLGSKK VSDRIVKLSA IDPDGYKQDI IGLSGQTLLR ALTHTGLIDP ASHRLDDIE ACSAECEVQI AEEWLEKLPP RTYDEEYVLK RSSRSRILNK HSRLGCQVVL TQELQGMVVA VPEAKPWDIP

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Macromolecule #9: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8-B

MacromoleculeName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8-B
type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: thale cress (thale cress)
Molecular weightTheoretical: 11.985954 KDa
SequenceString:
MSSAVDATGN PIPTSAVLTA SAKHIGMRCM PENVAFLKCK KNDPNPEKCL DKGRDVTRCV LGLLKDLHQK CQKEMDDYVG CMYYYTNEF DLCRKEQEAF EKVCPLK

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Macromolecule #10: Outer envelope pore protein 16-3, chloroplastic/mitochondrial

MacromoleculeName: Outer envelope pore protein 16-3, chloroplastic/mitochondrial
type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: thale cress (thale cress)
Molecular weightTheoretical: 17.017348 KDa
SequenceString:
MDPAEMRYLE EEDGPLMKTI KGSITGFGAG TIYGTILATW KDVPRVERNV ALPGLIRTLK MMGTHGLTFA AIGGVYIGVE QLVQNFRSK RDFYNGAIGG FVAGASVLGY RARSIPTAIA AGATLAVTSA LIDSGGQTTR VDNGREYYPY TVEKRAEADS

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Macromolecule #11: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13-A

MacromoleculeName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13-A
type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: thale cress (thale cress)
Molecular weightTheoretical: 16.145584 KDa
SequenceString:
MTEAMIRNKP GMASVKDMPL LQDGPPPGGF APVRYARRIS NTGPSAMAMF LAVSGAFAWG MYQVGQGNKI RRALKEEKYA ARRTILPIL QAEEDERFVS EWKKYLEYEA DVMKDVPGWK VGENVYNSGR WMPPATGELR PDVW

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Macromolecule #12: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1

MacromoleculeName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1
type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: thale cress (thale cress)
Molecular weightTheoretical: 7.349628 KDa
SequenceString:
MSLVWLEAML PLGIIGGMLC IMGNSQYYIH KAYHGRPKHI GHDEWDVAME RRDKKVVEKA AAPSS

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Macromolecule #13: At2g46540/F11C10.23

MacromoleculeName: At2g46540/F11C10.23 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: thale cress (thale cress)
Molecular weightTheoretical: 6.810177 KDa
SequenceString:
MPVMEKLRMF VAQEPVVAAS CLIGGVGLFL PAVVRPILDS LEASKQVKAP PLTDVIAGVT GKKQS

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Macromolecule #14: Excitatory amino acid transporter

MacromoleculeName: Excitatory amino acid transporter / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: thale cress (thale cress)
Molecular weightTheoretical: 9.220749 KDa
SequenceString:
MPISATMVGA LLGLGTQMYS NALRKLPYMR HPWEHVVGMG LGAVFANQLV KWDVKLKEDL DVMLAKARAA NERRYFDEDR D

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Macromolecule #15: NADH dehydrogenase [ubiquinone] iron-sulfur protein 5-B

MacromoleculeName: NADH dehydrogenase [ubiquinone] iron-sulfur protein 5-B
type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: thale cress (thale cress)
Molecular weightTheoretical: 9.914133 KDa
SequenceString:
MASGWGITGN KGRCYDFWMD FSECMSHCRE PKDCTLLRED YLECLHHSKE FQRRNRIYKE EQRKLRAASR KGEETGDGTH THH

+
Macromolecule #16: At4g16450

MacromoleculeName: At4g16450 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: thale cress (thale cress)
Molecular weightTheoretical: 11.383019 KDa
SequenceString:
(FME)NTDITALEK AQYPVVDRNP AFTKVVGNFS TLDYLRFSTI TGISVTVGYL SGIKPGIKGP SMVTGGLIGL MGGFMY AYQ NSAGRLMGFF PNDGEVASYQ KRGGFSK

+
Macromolecule #17: P1

MacromoleculeName: P1 / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: thale cress (thale cress)
Molecular weightTheoretical: 11.808244 KDa
SequenceString:
MGFIMEFAEN LVLRLMENPE ERDRKAREHI YEMHERCKKI KEMWALPIRP YGFWTFERHN AQLRWDPQIS QVAGRRDPYD DLLEDNYTP PSSSSSSSD

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Macromolecule #18: Uncharacterized protein At1g67785

MacromoleculeName: Uncharacterized protein At1g67785 / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: thale cress (thale cress)
Molecular weightTheoretical: 7.54679 KDa
SequenceString:
MVKVLTYFGM TLAAFAFWQS MDKVHVWIAL HQDEKQERME KEAEVRRVRA ELLRKAREED PLA

+
Macromolecule #19: Uncharacterized protein At2g27730, mitochondrial

MacromoleculeName: Uncharacterized protein At2g27730, mitochondrial / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: thale cress (thale cress)
Molecular weightTheoretical: 11.96552 KDa
SequenceString:
MATRNALRIV SRRFSSGKVL SEEERAAENV FIKKMEQEKL QKLARQGPGE QAAGSASEAK VAGATASASA ESGPKVSEDK NRNYAVVAG VVAIVGSIGW YLKAGGKKQP EVQE

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Macromolecule #20: Gamma carbonic anhydrase-like 2, mitochondrial

MacromoleculeName: Gamma carbonic anhydrase-like 2, mitochondrial / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: thale cress (thale cress)
Molecular weightTheoretical: 27.985113 KDa
SequenceString: MATSLARISK RSITSAVSSN LIRRYFAAEA VAVATTETPK PKSQVTPSPD RVKWDYRGQR QIIPLGQWLP KVAVDAYVAP NVVLAGQVT VWDGSSVWNG AVLRGDLNKI TVGFCSNVQE RCVVHAAWSS PTGLPAQTLI DRYVTVGAYS LLRSCTIEPE C IIGQHSIL ...String:
MATSLARISK RSITSAVSSN LIRRYFAAEA VAVATTETPK PKSQVTPSPD RVKWDYRGQR QIIPLGQWLP KVAVDAYVAP NVVLAGQVT VWDGSSVWNG AVLRGDLNKI TVGFCSNVQE RCVVHAAWSS PTGLPAQTLI DRYVTVGAYS LLRSCTIEPE C IIGQHSIL MEGSLVETRS ILEAGSVLPP GRRIPSGELW GGNPARFIRT LTNEETLEIP KLAVAINHLS GDYFSEFLPY ST IYLEVEK FKKSLGIAI

+
Macromolecule #21: Gamma carbonic anhydrase 2, mitochondrial

MacromoleculeName: Gamma carbonic anhydrase 2, mitochondrial / type: protein_or_peptide / ID: 21 / Number of copies: 1 / Enantiomer: LEVO / EC number: Lyases; Carbon-oxygen lyases; Hydro-lyases
Source (natural)Organism: thale cress (thale cress)
Molecular weightTheoretical: 30.102207 KDa
SequenceString: MGTLGRAIYT VGNWIRGTGQ ALDRVGSLLQ GSHRIEEHLS RHRTLMNVFD KSPLVDKDVF VAPSASVIGD VQIGKGSSIW YGCVLRGDV NNISVGSGTN IQDNTLVHVA KTNISGKVLP TLIGDNVTVG HSAVIHGCTV EDDAFVGMGA TLLDGVVVEK H AMVAAGSL ...String:
MGTLGRAIYT VGNWIRGTGQ ALDRVGSLLQ GSHRIEEHLS RHRTLMNVFD KSPLVDKDVF VAPSASVIGD VQIGKGSSIW YGCVLRGDV NNISVGSGTN IQDNTLVHVA KTNISGKVLP TLIGDNVTVG HSAVIHGCTV EDDAFVGMGA TLLDGVVVEK H AMVAAGSL VKQNTRIPSG EVWGGNPAKF MRKLTDEEIV YISQSAKNYI NLAQIHASEN SKSFEQIEVE RALRKKYARK DE DYDSMLG ITRETPPELI LPDNVLPGGK PVAKVPSTQY F

+
Macromolecule #22: Gamma carbonic anhydrase 1, mitochondrial

MacromoleculeName: Gamma carbonic anhydrase 1, mitochondrial / type: protein_or_peptide / ID: 22 / Number of copies: 1 / Enantiomer: LEVO / EC number: Lyases; Carbon-oxygen lyases; Hydro-lyases
Source (natural)Organism: thale cress (thale cress)
Molecular weightTheoretical: 30.010039 KDa
SequenceString: MGTLGRAFYS VGFWIRETGQ ALDRLGCRLQ GKNYFREQLS RHRTLMNVFD KAPIVDKEAF VAPSASVIGD VHIGRGSSIW YGCVLRGDV NTVSVGSGTN IQDNSLVHVA KSNLSGKVHP TIIGDNVTIG HSAVLHGCTV EDETFIGMGA TLLDGVVVEK H GMVAAGAL ...String:
MGTLGRAFYS VGFWIRETGQ ALDRLGCRLQ GKNYFREQLS RHRTLMNVFD KAPIVDKEAF VAPSASVIGD VHIGRGSSIW YGCVLRGDV NTVSVGSGTN IQDNSLVHVA KSNLSGKVHP TIIGDNVTIG HSAVLHGCTV EDETFIGMGA TLLDGVVVEK H GMVAAGAL VRQNTRIPSG EVWGGNPARF LRKLTDEEIA FISQSATNYS NLAQAHAAEN AKPLNVIEFE KVLRKKHALK DE EYDSMLG IVRETPPELN LPNNILPDKE TKRPSNVN

+
Macromolecule #23: (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-...

MacromoleculeName: (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE
type: ligand / ID: 23 / Number of copies: 5 / Formula: PGT
Molecular weightTheoretical: 751.023 Da
Chemical component information

ChemComp-PGT:
(1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE / phospholipid*YM / Phosphatidylglycerol

+
Macromolecule #24: Ubiquinone-9

MacromoleculeName: Ubiquinone-9 / type: ligand / ID: 24 / Number of copies: 1 / Formula: UQ9
Molecular weightTheoretical: 795.226 Da
Chemical component information

ChemComp-UQ9:
Ubiquinone-9

+
Macromolecule #25: PHOSPHATIDYLETHANOLAMINE

MacromoleculeName: PHOSPHATIDYLETHANOLAMINE / type: ligand / ID: 25 / Number of copies: 10 / Formula: PTY
Molecular weightTheoretical: 734.039 Da
Chemical component information

ChemComp-PTY:
PHOSPHATIDYLETHANOLAMINE / phospholipid*YM / Phosphatidylethanolamine

+
Macromolecule #26: 2-{[(4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranosyl)oxy]methyl...

MacromoleculeName: 2-{[(4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranosyl)oxy]methyl}-4-{[(3beta,9beta,14beta,17beta,25R)-spirost-5-en-3-yl]oxy}butyl 4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranoside
type: ligand / ID: 26 / Number of copies: 4 / Formula: Q7G
Molecular weightTheoretical: 1.165315 KDa
Chemical component information

ChemComp-Q7G:
2-{[(4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranosyl)oxy]methyl}-4-{[(3beta,9beta,14beta,17beta,25R)-spirost-5-en-3-yl]oxy}butyl 4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranoside

+
Macromolecule #27: FE (III) ION

MacromoleculeName: FE (III) ION / type: ligand / ID: 27 / Number of copies: 1 / Formula: FE
Molecular weightTheoretical: 55.845 Da

+
Macromolecule #28: 2,3-DIMETHOXY-5-METHYL-6-(3,11,15,19-TETRAMETHYL-EICOSA-2,6,10,14...

MacromoleculeName: 2,3-DIMETHOXY-5-METHYL-6-(3,11,15,19-TETRAMETHYL-EICOSA-2,6,10,14,18-PENTAENYL)-[1,4]BENZOQUINONE
type: ligand / ID: 28 / Number of copies: 1 / Formula: UQ5
Molecular weightTheoretical: 522.758 Da
Chemical component information

ChemComp-UQ5:
2,3-DIMETHOXY-5-METHYL-6-(3,11,15,19-TETRAMETHYL-EICOSA-2,6,10,14,18-PENTAENYL)-[1,4]BENZOQUINONE

+
Macromolecule #29: (7S)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5...

MacromoleculeName: (7S)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE
type: ligand / ID: 29 / Number of copies: 3 / Formula: PC7
Molecular weightTheoretical: 763.1 Da
Chemical component information

ChemComp-PC7:
(7S)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE / phospholipid*YM / Phosphatidylcholine

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Macromolecule #30: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE

MacromoleculeName: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / type: ligand / ID: 30 / Number of copies: 2 / Formula: 3PH
Molecular weightTheoretical: 704.998 Da
Chemical component information

ChemComp-3PH:
1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / Phosphatidic acid

+
Macromolecule #31: CARDIOLIPIN

MacromoleculeName: CARDIOLIPIN / type: ligand / ID: 31 / Number of copies: 2 / Formula: CDL
Molecular weightTheoretical: 1.464043 KDa
Chemical component information

ChemComp-CDL:
CARDIOLIPIN / phospholipid*YM / Cardiolipin

+
Macromolecule #32: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 32 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #33: Butyryl Coenzyme A

MacromoleculeName: Butyryl Coenzyme A / type: ligand / ID: 33 / Number of copies: 1 / Formula: BCO
Molecular weightTheoretical: 837.624 Da
Chemical component information

ChemComp-BCO:
Butyryl Coenzyme A

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Macromolecule #34: water

MacromoleculeName: water / type: ligand / ID: 34 / Number of copies: 1284 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER / Water

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Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.18 mg/mL
BufferpH: 7.4
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - #0 - Film type ID: 1 / Support film - #0 - Material: CARBON / Support film - #0 - topology: CONTINUOUS / Support film - #1 - Film type ID: 2 / Support film - #1 - Material: GRAPHENE / Support film - #1 - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 70 % / Chamber temperature: 283.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 215000
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Particle selectionNumber selected: 1215138
Startup modelType of model: EMDB MAP
EMDB ID:

11878

Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.3)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.13 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.3) / Number images used: 213993
FSC plot (resolution estimation)

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Atomic model buiding 1

SoftwareName: Coot (ver. 0.9.5)
RefinementSpace: REAL
Output model

PDB-8bef:
Cryo-EM structure of the Arabidopsis thaliana I+III2 supercomplex (CI membrane core)

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