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- EMDB-11874: Cryo-EM structure of Arabidopsis thaliana Complex-I (membrane tip) -

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Basic information

Entry
Database: EMDB / ID: EMD-11874
TitleCryo-EM structure of Arabidopsis thaliana Complex-I (membrane tip)
Map data
Sample
  • Complex: Arabidopsis complex I - membrane tip
    • Protein or peptide: x 13 types
  • Ligand: x 3 types
KeywordsComplex-I / ELECTRON TRANSPORT
Function / homology
Function and homology information


photorespiration / plant-type vacuole / plastid / acyl carrier activity / NADH:ubiquinone reductase (H+-translocating) / mitochondrial electron transport, NADH to ubiquinone / respiratory chain complex I / NADH dehydrogenase (ubiquinone) activity / ATP synthesis coupled electron transport / proton transmembrane transport ...photorespiration / plant-type vacuole / plastid / acyl carrier activity / NADH:ubiquinone reductase (H+-translocating) / mitochondrial electron transport, NADH to ubiquinone / respiratory chain complex I / NADH dehydrogenase (ubiquinone) activity / ATP synthesis coupled electron transport / proton transmembrane transport / electron transport chain / mitochondrial membrane / mitochondrial intermembrane space / fatty acid biosynthetic process / carbohydrate metabolic process / mitochondrial inner membrane / mitochondrial matrix / mitochondrion / membrane / plasma membrane / cytosol
Similarity search - Function
NADH-ubiquinone oxidoreductase 11kDa subunit / Putative NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial / NADH-ubiquinone oxidoreductase 11 kDa subunit / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, plant/fungi / 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 11kDa subunit / Putative NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial / NADH-ubiquinone oxidoreductase 11 kDa subunit / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, plant/fungi / 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) / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / NDUFB9, LYR domain / NADH-plastoquinone oxidoreductase, chain 5 subgroup / NADH-quinone oxidoreductase, chain M/4 / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminal / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus / NADH-quinone oxidoreductase, chain 5-like / NADH:ubiquinone oxidoreductase / NADH:quinone oxidoreductase/Mrp antiporter, membrane subunit / NADH:quinone oxidoreductase/Mrp antiporter, TM / 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
(thale cress) hypothetical protein / (thale cress) hypothetical protein / NADH-ubiquinone oxidoreductase chain 4 / NADH-ubiquinone oxidoreductase chain 5 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3-A / Acyl carrier protein 1, mitochondrial / 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 ...(thale cress) hypothetical protein / (thale cress) hypothetical protein / NADH-ubiquinone oxidoreductase chain 4 / NADH-ubiquinone oxidoreductase chain 5 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3-A / Acyl carrier protein 1, mitochondrial / 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 / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.17 Å
AuthorsKlusch N / Kuehlbrandt W
Funding support Germany, 1 items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Plant Cell / Year: 2021
Title: A ferredoxin bridge connects the two arms of plant mitochondrial complex I.
Authors: Niklas Klusch / Jennifer Senkler / Özkan Yildiz / Werner Kühlbrandt / Hans-Peter Braun /
Abstract: Mitochondrial complex I is the main site for electron transfer to the respiratory chain and generates much of the proton gradient across the inner mitochondrial membrane. Complex I is composed of two ...Mitochondrial complex I is the main site for electron transfer to the respiratory chain and generates much of the proton gradient across the inner mitochondrial membrane. Complex I is composed of two arms, which form a conserved L-shape. We report the structures of the intact, 47-subunit mitochondrial complex I from Arabidopsis thaliana and the 51-subunit complex I from the green alga Polytomella sp., both at around 2.9 Å resolution. In both complexes, a heterotrimeric γ-carbonic anhydrase domain is attached to the membrane arm on the matrix side. Two states are resolved in A. thaliana complex I, with different angles between the two arms and different conformations of the ND1 (NADH dehydrogenase subunit 1) loop near the quinol binding site. The angle appears to depend on a bridge domain, which links the peripheral arm to the membrane arm and includes an unusual ferredoxin. We propose that the bridge domain participates in regulating the activity of plant complex I.
History
DepositionOct 23, 2020-
Header (metadata) releaseDec 8, 2021-
Map releaseDec 8, 2021-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.013
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.013
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7aqw
  • Surface level: 0.013
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11874.png

Downloads & links

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Map

FileDownload / File: emd_11874.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 600 pix.
= 502.2 Å		0.84 Å/pix.
x 600 pix.
= 502.2 Å		0.84 Å/pix.
x 600 pix.
= 502.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.837 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.013 / Movie #1: 0.013
Minimum - Maximum-0.02553981 - 0.053030346
Average (Standard dev.)0.000015151327 (±0.00052796333)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 502.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8370.8370.837
M x/y/z600600600
origin x/y/z0.0000.0000.000
length x/y/z502.200502.200502.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS600600600
D min/max/mean-0.0260.0530.000

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Supplemental data

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Half map: #2

Fileemd_11874_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_11874_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Arabidopsis complex I - membrane tip

EntireName: Arabidopsis complex I - membrane tip
Components
  • Complex: Arabidopsis complex I - 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: P1
    • 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: B15 -- 1 beta subcomplex subunit 4
    • 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: 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

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Supramolecule #1: Arabidopsis complex I - membrane tip

SupramoleculeName: Arabidopsis complex I - membrane tip / type: complex / ID: 1 / 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: Arabidopsis thaliana (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

UniProtKB: NADH-ubiquinone oxidoreductase chain 5

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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: Arabidopsis thaliana (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

UniProtKB: NADH-ubiquinone oxidoreductase chain 4

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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: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 13.735628 KDa
SequenceString:
MALRNAILRH LRVPVQTLGL NQSKIGFLGT IRSFSSHDDH LSREAVVDRV LDVVKSFPKV DPSKVTPEVH FQNDLGLDSL DTVEIVMAI EEEFKLEIPD KEADKIDSCS LAIEYVYNHP MSS

UniProtKB: Acyl carrier protein 1, mitochondrial

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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: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 9.876422 KDa
SequenceString:
MGGGDHGHGA EGGDFRAKVW SMTGGPNCRP KHWRRNTAIA MFGVFLVCIP IAKLSAKLEQ RPHMPVRPIP SQIWCKNFGT KDDYEKEH

UniProtKB: Transmembrane protein

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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: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 12.648286 KDa
SequenceString:
MPSTQSLTVA AKTLRNRIFS RSGSTSAGPS RWATPGHEER PKGYFMNRTP PAPGQSRKWE DWELPCYITS FLTIVILGVG LNAKPDLSI ETWAHQKALE RLEMEKLATA GDSSD

UniProtKB: ESSS subunit of NADH:ubiquinone oxidoreductase (Complex I) protein

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Macromolecule #6: P1

MacromoleculeName: P1 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 11.808244 KDa
SequenceString:
MGFIMEFAEN LVLRLMENPE ERDRKAREHI YEMHERCKKI KEMWALPIRP YGFWTFERHN AQLRWDPQIS QVAGRRDPYD DLLEDNYTP PSSSSSSSD

UniProtKB: (thale cress) hypothetical protein

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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: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 7.58259 KDa
SequenceString:
MGGGGHGGGI TYKGVTVHTP KTWHTVTGKG LCAVMWFWIL YRAKQDGPVV MGWRHPWDGH GDHGHGDHH

UniProtKB: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2

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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: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 8.064313 KDa
SequenceString:
MAKPLGTTGE FFRRRDEWRK HPMLSNQMRH ALPGIGIGVG AFCVYLVGEQ IYSKLMAPSS QSSHQKQPAP SH

UniProtKB: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3-A

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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: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 13.225222 KDa
SequenceString:
MAGRLSGVAS RIMGGNGVVA RSVGSSLRQR AGMGLPVGKH IVPDKPLSVN DELMWDNGTA FPEPCIDRIA DTVGKYEALA WLSGGLGFF VGLGLLAVLN DKASKVPFTP RVYPYDNLRV ELGGEP

UniProtKB: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial

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Macromolecule #10: B15 -- 1 beta subcomplex subunit 4

MacromoleculeName: B15 -- 1 beta subcomplex subunit 4 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 8.305539 KDa
SequenceString:
MGGGMETNKN KFIEDWGSAR ENLEHNFRWT RRNFALIGIF GIALPIIVYK GIVKDFHMQD EDAGRPHRKF L

UniProtKB: (thale cress) hypothetical protein

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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: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 13.638335 KDa
SequenceString:
MSGVSTAAYF ARRAAQKERV RILYRRALKD TLNWAVHRHI FYRDASDLRE KFNVNQDVED VDRIDKLIAH GEAEYNKWRH PDPYIVPWA PGGSKFCRNP TPPAGIEIVY NYGLEDNP

UniProtKB: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9

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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: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 11.757832 KDa
SequenceString:
MEVPGSSKKM IATQEEMSAA KIALGSRDMC AHLLIPLNKC RQAEFYLPWK CEDERHVYEK CEYELVMERM LAMKKIREEE ALAKQNKLQ GNAAVPLIPK TANA

UniProtKB: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7

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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: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 12.462276 KDa
SequenceString:
MGRKKGLPEF EESAPDGFDP ENPYKDPVAM VEMREHIVRE KWIQIEKAKI LREKVKWCYR VEGVNHYQKC RHLVQQYLDS TRGVGWGKD HRPISLHGPK PEAVEAE

UniProtKB: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10-B

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Macromolecule #14: PHOSPHATIDYLETHANOLAMINE

MacromoleculeName: PHOSPHATIDYLETHANOLAMINE / type: ligand / ID: 14 / Number of copies: 1 / Formula: PTY
Molecular weightTheoretical: 734.039 Da
Chemical component information

ChemComp-PTY:
PHOSPHATIDYLETHANOLAMINE / phospholipid*YM

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Macromolecule #15: (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: 15 / 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

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Macromolecule #16: 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: 16 / 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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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 43.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.17 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 459177
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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