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- EMDB-16003: Cryo-EM structure of the Arabidopsis thaliana I+III2 supercomplex... -

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Basic information

Entry
Database: EMDB / ID: EMD-16003
TitleCryo-EM structure of the Arabidopsis thaliana I+III2 supercomplex (CI membrane tip)
Map data
Sample
  • Complex: Mitochondrial Arabidopsis thaliana I+III2 supercomplex (CI membrane tip)
    • Protein or peptide: x 13 types
  • Ligand: x 6 types
Function / homology
Function and homology information


photorespiration / plant-type vacuole / NADH dehydrogenase activity / respiratory chain complex I / ubiquinone binding / electron transport coupled proton transport / plastid / acyl carrier activity / NADH:ubiquinone reductase (H+-translocating) / mitochondrial respiratory chain complex I ...photorespiration / plant-type vacuole / NADH dehydrogenase activity / respiratory chain complex I / ubiquinone binding / electron transport coupled proton transport / plastid / acyl carrier activity / NADH:ubiquinone reductase (H+-translocating) / mitochondrial respiratory chain complex I / mitochondrial electron transport, NADH to ubiquinone / NADH dehydrogenase (ubiquinone) activity / ATP synthesis coupled electron transport / aerobic respiration / electron transport chain / mitochondrial membrane / mitochondrial intermembrane space / fatty acid biosynthetic process / mitochondrial inner membrane / carbohydrate metabolic process / mitochondrial matrix / mitochondrion / plasma membrane / cytosol
Similarity search - Function
Putative NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, plant/fungi / NADH-ubiquinone oxidoreductase 11kDa subunit / NADH-ubiquinone oxidoreductase 11 kDa subunit / NADH-ubiquinone oxidoreductase, subunit 10 / NADH-ubiquinone oxidoreductase subunit 10 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 / NADH dehydrogenase subunit 5, C-terminal / NADH dehydrogenase subunit 5 C-terminus / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 ...Putative NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, plant/fungi / NADH-ubiquinone oxidoreductase 11kDa subunit / NADH-ubiquinone oxidoreductase 11 kDa subunit / NADH-ubiquinone oxidoreductase, subunit 10 / NADH-ubiquinone oxidoreductase subunit 10 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 / NADH dehydrogenase subunit 5, C-terminal / NADH dehydrogenase subunit 5 C-terminus / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 / NADH-ubiquinone oxidoreductase B12 subunit family / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7, NDUB7 / NADH-ubiquinone oxidoreductase B18 subunit (NDUFB7) / NDUFB9, LYR domain / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / NADH-plastoquinone oxidoreductase, chain 5 subgroup / NADH-quinone oxidoreductase, chain M/4 / 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 / NADH:quinone oxidoreductase/Mrp antiporter, membrane subunit / Proton-conducting membrane transporter / Coiled coil-helix-coiled coil-helix (CHCH) domain profile. / Acyl carrier protein (ACP) / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain
Similarity search - Domain/homology
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3-A / NADH-ubiquinone oxidoreductase chain 5 / Acyl carrier protein 1, mitochondrial / NADH-ubiquinone oxidoreductase chain 4 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2 / Transmembrane protein / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10-B / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial / At1g67350 ...NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3-A / NADH-ubiquinone oxidoreductase chain 5 / Acyl carrier protein 1, mitochondrial / NADH-ubiquinone oxidoreductase chain 4 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2 / Transmembrane protein / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10-B / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial / At1g67350 / At2g31490 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7 / ESSS subunit of NADH:ubiquinone oxidoreductase (Complex I) protein
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress) / thale cress (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.29 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_16003.png

Downloads & links

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Map

FileDownload / File: emd_16003.map.gz / Format: CCP4 / Size: 50.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.57 Å/pix.
x 221 pix.
= 126.633 Å		0.57 Å/pix.
x 244 pix.
= 139.812 Å		0.57 Å/pix.
x 245 pix.
= 140.385 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

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-3.8083503 - 5.5876684
Average (Standard dev.)1.7096541e-12 (±0.32870996)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin313283366
Dimensions244245221
Spacing221244245
CellA: 126.633 Å / B: 139.812 Å / C: 140.38501 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_16003_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_16003_half_map_1.map
Projections & Slices
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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_16003_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram (log scale)

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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 tip)
Components
  • Complex: Mitochondrial Arabidopsis thaliana I+III2 supercomplex (CI membrane tip)
    • Protein or peptide: NADH-ubiquinone oxidoreductase chain 5
    • Protein or peptide: NADH-ubiquinone oxidoreductase chain 4
    • Protein or peptide: Acyl carrier protein 1, mitochondrial
    • Protein or peptide: Transmembrane protein
    • Protein or peptide: ESSS subunit of NADH:ubiquinone oxidoreductase (Complex I) protein
    • Protein or peptide: At1g67350
    • Protein or peptide: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2
    • Protein or peptide: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3-A
    • Protein or peptide: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial
    • Protein or peptide: AT2G31490 protein
    • Protein or peptide: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9
    • Protein or peptide: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7
    • Protein or peptide: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10-B
  • Ligand: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE
  • Ligand: (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE
  • Ligand: PHOSPHATIDYLETHANOLAMINE
  • Ligand: (7S)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE
  • Ligand: S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate
  • 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 tip)
type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#13
Source (natural)Organism: Arabidopsis thaliana (thale cress)

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Macromolecule #1: NADH-ubiquinone oxidoreductase chain 5

MacromoleculeName: NADH-ubiquinone oxidoreductase chain 5 / 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: 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 #2: NADH-ubiquinone oxidoreductase chain 4

MacromoleculeName: NADH-ubiquinone oxidoreductase chain 4 / 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: 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 #3: Acyl carrier protein 1, mitochondrial

MacromoleculeName: Acyl carrier protein 1, mitochondrial / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: thale cress (thale cress)
Molecular weightTheoretical: 13.735628 KDa
SequenceString:
MALRNAILRH LRVPVQTLGL NQSKIGFLGT IRSFSSHDDH LSREAVVDRV LDVVKSFPKV DPSKVTPEVH FQNDLGLDSL DTVEIVMAI EEEFKLEIPD KEADKIDSCS LAIEYVYNHP MSS

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Macromolecule #4: Transmembrane protein

MacromoleculeName: Transmembrane protein / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: thale cress (thale cress)
Molecular weightTheoretical: 9.876422 KDa
SequenceString:
MGGGDHGHGA EGGDFRAKVW SMTGGPNCRP KHWRRNTAIA MFGVFLVCIP IAKLSAKLEQ RPHMPVRPIP SQIWCKNFGT KDDYEKEH

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Macromolecule #5: ESSS subunit of NADH:ubiquinone oxidoreductase (Complex I) protein

MacromoleculeName: ESSS subunit of NADH:ubiquinone oxidoreductase (Complex I) protein
type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: thale cress (thale cress)
Molecular weightTheoretical: 12.648286 KDa
SequenceString:
MPSTQSLTVA AKTLRNRIFS RSGSTSAGPS RWATPGHEER PKGYFMNRTP PAPGQSRKWE DWELPCYITS FLTIVILGVG LNAKPDLSI ETWAHQKALE RLEMEKLATA GDSSD

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Macromolecule #6: At1g67350

MacromoleculeName: At1g67350 / type: protein_or_peptide / ID: 6 / 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 #7: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2

MacromoleculeName: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2
type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: thale cress (thale cress)
Molecular weightTheoretical: 7.58259 KDa
SequenceString:
MGGGGHGGGI TYKGVTVHTP KTWHTVTGKG LCAVMWFWIL YRAKQDGPVV MGWRHPWDGH GDHGHGDHH

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Macromolecule #8: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3-A

MacromoleculeName: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3-A
type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: thale cress (thale cress)
Molecular weightTheoretical: 8.064313 KDa
SequenceString:
MAKPLGTTGE FFRRRDEWRK HPMLSNQMRH ALPGIGIGVG AFCVYLVGEQ IYSKLMAPSS QSSHQKQPAP SH

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Macromolecule #9: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mito...

MacromoleculeName: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial
type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: thale cress (thale cress)
Molecular weightTheoretical: 13.225222 KDa
SequenceString:
MAGRLSGVAS RIMGGNGVVA RSVGSSLRQR AGMGLPVGKH IVPDKPLSVN DELMWDNGTA FPEPCIDRIA DTVGKYEALA WLSGGLGFF VGLGLLAVLN DKASKVPFTP RVYPYDNLRV ELGGEP

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Macromolecule #10: AT2G31490 protein

MacromoleculeName: AT2G31490 protein / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: thale cress (thale cress)
Molecular weightTheoretical: 8.305539 KDa
SequenceString:
MGGGMETNKN KFIEDWGSAR ENLEHNFRWT RRNFALIGIF GIALPIIVYK GIVKDFHMQD EDAGRPHRKF L

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Macromolecule #11: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9

MacromoleculeName: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9
type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: thale cress (thale cress)
Molecular weightTheoretical: 13.638335 KDa
SequenceString:
MSGVSTAAYF ARRAAQKERV RILYRRALKD TLNWAVHRHI FYRDASDLRE KFNVNQDVED VDRIDKLIAH GEAEYNKWRH PDPYIVPWA PGGSKFCRNP TPPAGIEIVY NYGLEDNP

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Macromolecule #12: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7

MacromoleculeName: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7
type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: thale cress (thale cress)
Molecular weightTheoretical: 11.757832 KDa
SequenceString:
MEVPGSSKKM IATQEEMSAA KIALGSRDMC AHLLIPLNKC RQAEFYLPWK CEDERHVYEK CEYELVMERM LAMKKIREEE ALAKQNKLQ GNAAVPLIPK TANA

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Macromolecule #13: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10-B

MacromoleculeName: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10-B
type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: thale cress (thale cress)
Molecular weightTheoretical: 12.462276 KDa
SequenceString:
MGRKKGLPEF EESAPDGFDP ENPYKDPVAM VEMREHIVRE KWIQIEKAKI LREKVKWCYR VEGVNHYQKC RHLVQQYLDS TRGVGWGKD HRPISLHGPK PEAVEAE

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Macromolecule #14: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE

MacromoleculeName: 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / type: ligand / ID: 14 / Number of copies: 3 / Formula: 3PH
Molecular weightTheoretical: 704.998 Da
Chemical component information

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

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Macromolecule #15: (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: 15 / Number of copies: 1 / 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

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Macromolecule #16: PHOSPHATIDYLETHANOLAMINE

MacromoleculeName: PHOSPHATIDYLETHANOLAMINE / type: ligand / ID: 16 / Number of copies: 1 / Formula: PTY
Molecular weightTheoretical: 734.039 Da
Chemical component information

ChemComp-PTY:
PHOSPHATIDYLETHANOLAMINE / phospholipid*YM / Phosphatidylethanolamine

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Macromolecule #17: (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: 17 / Number of copies: 1 / 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 #18: S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-b...

MacromoleculeName: S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate
type: ligand / ID: 18 / Number of copies: 1 / Formula: 8Q1
Molecular weightTheoretical: 540.651 Da
Chemical component information

ChemComp-8Q1:
S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate

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Macromolecule #19: water

MacromoleculeName: water / type: ligand / ID: 19 / Number of copies: 617 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER / Water

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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

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

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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: 2.29 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-8beh:
Cryo-EM structure of the Arabidopsis thaliana I+III2 supercomplex (CI membrane tip)

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Jul 12, 2017. Major update of PDB

Major update of PDB

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External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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