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- EMDB-4384: CryoEM structure of respiratory complex I from Yarrowia lipolytica -

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Basic information

Entry
Database: EMDB / ID: 4384
TitleCryoEM structure of respiratory complex I from Yarrowia lipolytica
Map data
SampleMitochondrial NADH:ubiquinone oxidoreductase:
75-KDA PROTEIN (NUAM) / 51-KDA PROTEIN (NUBM) / 49-KDA PROTEIN (NUCM) / NIMM SUBUNIT / NUEM SUBUNIT / NUFM SUBUNIT / 30-KDA PROTEIN (NUGM) / 24-KDA SUBUNIT (NUHM) / TYKY SUBUNIT (NUIM) / NUJM SUBUNIT ...75-KDA PROTEIN (NUAM) / 51-KDA PROTEIN (NUBM) / 49-KDA PROTEIN (NUCM) / NIMM SUBUNIT / NUEM SUBUNIT / NUFM SUBUNIT / 30-KDA PROTEIN (NUGM) / 24-KDA SUBUNIT (NUHM) / TYKY SUBUNIT (NUIM) / NUJM SUBUNIT / PSST SUBUNIT (NUKM) / ND4L SUBUNIT (NULM) / NUMM SUBUNIT / ACPM1 SUBUNIT / NB4M SUBUNIT / ACPM2 SUBUNIT / NI2M SUBUNIT / NESM SUBUNIT / NUPM SUBUNIT / NB6M SUBUNIT / NUXM SUBUNIT / NUYM SUBUNIT / NUZM SUBUNIT / NIAM SUBUNIT / NEBM SUBUNIT / NB2M SUBUNIT / NIDM SUBUNIT / NUUM SUBUNIT / NI8M SUBUNIT / NI9M SUBUNIT / N7BM SUBUNIT / UNKNOWN SUBUNIT / NB5M SUBUNIT / NUNM SUBUNIT / ND1 SUBUNIT (NU1M) / ND2 SUBUNIT (NU2M) / ND3 SUBUNIT (NU3M) / ND4 SUBUNIT (NU4M) / ND5 SUBUNIT (NU5M) / ND6 SUBUNIT (NU6M) / NB8M SUBUNIT / NIPM SUBUNIT / (ligand) x 8
Function / homologyNAD(P)-binding domain superfamily / NADH-plastoquinone oxidoreductase, chain 5 subgroup / [NiFe]-hydrogenase, large subunit / NADH-ubiquinone oxidoreductase, 21kDa subunit, C-terminal, fungi / NAD(P)H-quinone oxidoreductase subunit D/H / NADH:ubiquinone oxidoreductase, 30kDa subunit, conserved site / Complex I subunit NDUFS6 / NADH-ubiquinone oxidoreductase, 21kDa subunit, N-terminal / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain / NADH:ubiquinone oxidoreductase, subunit G, iron-sulphur binding ...NAD(P)-binding domain superfamily / NADH-plastoquinone oxidoreductase, chain 5 subgroup / [NiFe]-hydrogenase, large subunit / NADH-ubiquinone oxidoreductase, 21kDa subunit, C-terminal, fungi / NAD(P)H-quinone oxidoreductase subunit D/H / NADH:ubiquinone oxidoreductase, 30kDa subunit, conserved site / Complex I subunit NDUFS6 / NADH-ubiquinone oxidoreductase, 21kDa subunit, N-terminal / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain / NADH:ubiquinone oxidoreductase, subunit G, iron-sulphur binding / Soluble ligand binding domain / Zinc finger, CHCC-type / NADH-ubiquinone oxidoreductase, subunit 10 / NADH:ubiquinone oxidoreductase, iron-sulphur subunit 5 / NADH:ubiquinone oxidoreductase, subunit 1, conserved site / 2Fe-2S ferredoxin-like superfamily / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex subunit 1 / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 8 / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 6 / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 2 / NADH-quinone oxidoreductase, chain G, C-terminal / NADH:ubiquinone oxidoreductase, 49kDa subunit, conserved site / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain / NADH ubiquinone oxidoreductase, F subunit / CHCH / NADH:ubiquinone oxidoreductase, subunit G / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / Thioredoxin-like superfamily / NADH-quinone oxidoreductase, chain I / NADH-ubiquinone/plastoquinone oxidoreductase chain 6 / GRIM-19 protein / NADH-ubiquinone oxidoreductase B18 subunit (NDUFB7) / Complex 1 protein (LYR family) / NADH ubiquinone oxidoreductase subunit NDUFA12 / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / ETC complex I subunit conserved region / ETC complex I subunit conserved region / Respiratory-chain NADH dehydrogenase 51 Kd subunit / NAD dependent epimerase/dehydratase family / NADH ubiquinone oxidoreductase, 20 Kd subunit / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus / Phosphopantetheine attachment site / NADH-ubiquinone/plastoquinone oxidoreductase, chain 3 / NADH-ubiquinone/plastoquinone oxidoreductase chain 4L / NADH-ubiquinone oxidoreductase subunit G, C-terminal / Molybdopterin oxidoreductase / Proton-conducting membrane transporter / Respiratory-chain NADH dehydrogenase, 49 Kd subunit / Respiratory-chain NADH dehydrogenase, 30 Kd subunit / NADH dehydrogenase / NADH-ubiquinone oxidoreductase chain 4L/Mnh complex subunit C1-like / NADH dehydrogenase ubiquinone Fe-S protein 4-like superfamily / NADH:ubiquinone oxidoreductase, subunit 3 superfamily / NADH-quinone oxidoreductase, subunit D superfamily / NADH:ubiquinone oxidoreductase, 30kDa subunit superfamily / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain superfamily / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain superfamily / ACP-like superfamily / NADH-quinone oxidoreductase, chain M/4 / NADH dehydrogenase, subunit C / NADH-ubiquinone oxidoreductase B12 subunit family / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 1. / Zinc-finger domain / SLBB domain / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / NADH-ubiquinone oxidoreductase complex I, 21 kDa subunit / 4Fe-4S dicluster domain / C-terminal of NADH-ubiquinone oxidoreductase 21 kDa subunit / NADH-ubiquinone oxidoreductase MWFE subunit / Phosphopantetheine attachment site. / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / Respiratory chain NADH dehydrogenase 49 Kd subunit signature. / Respiratory chain NADH dehydrogenase 30 Kd subunit signature. / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 2. / GRIM-19 / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 3. / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 1. / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 2. / Respiratory-chain NADH dehydrogenase subunit 1 signature 1. / Respiratory-chain NADH dehydrogenase subunit 1 signature 2. / Respiratory-chain NADH dehydrogenase 24 Kd subunit signature. / Respiratory-chain NADH dehydrogenase 20 Kd subunit signature. / Carrier protein (CP) domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / Prokaryotic molybdopterin oxidoreductases 4Fe-4S domain profile. / His(Cys)3-ligated-type [4Fe-4S] domain profile. / NADH-ubiquinone oxidoreductase subunit 10 / NADH:ubiquinone oxidoreductase, NDUFS5-15kDa / CHCH domain / NADH:ubiquinone oxidoreductase, 75kDa subunit, conserved site / Phosphopantetheine binding ACP domain / NADH:ubiquinone oxidoreductase, B18 subunit / Complex 1 LYR protein / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / Ribosomal protein/NADH dehydrogenase domain
Function and homology information
SourceYarrowia lipolytica (yeast)
Methodsingle particle reconstruction / cryo EM / 4.32 Å resolution
AuthorsParey K / Vonck J
CitationJournal: Elife / Year: 2018
Title: Cryo-EM structure of respiratory complex I at work.
Authors: Kristian Parey / Ulrich Brandt / Hao Xie / Deryck J Mills / Karin Siegmund / Janet Vonck / Werner Kühlbrandt / Volker Zickermann
Abstract: Mitochondrial complex I has a key role in cellular energy metabolism, generating a major portion of the proton motive force that drives aerobic ATP synthesis. The hydrophilic arm of the L-shaped ~1 ...Mitochondrial complex I has a key role in cellular energy metabolism, generating a major portion of the proton motive force that drives aerobic ATP synthesis. The hydrophilic arm of the L-shaped ~1 MDa membrane protein complex transfers electrons from NADH to ubiquinone, providing the energy to drive proton pumping at distant sites in the membrane arm. The critical steps of energy conversion are associated with the redox chemistry of ubiquinone. We report the cryo-EM structure of complete mitochondrial complex I from the aerobic yeast both in the deactive form and after capturing the enzyme during steady-state activity. The site of ubiquinone binding observed during turnover supports a two-state stabilization change mechanism for complex I.
Validation ReportPDB-ID: 6gcs

SummaryFull reportAbout validation report
DateDeposition: Apr 19, 2018 / Header (metadata) release: Jul 18, 2018 / Map release: Oct 10, 2018 / Last update: Oct 10, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.045
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.045
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6gcs
  • Surface level: 0.045
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_4384.map.gz (map file in CCP4 format, 379276 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
456 pix
1.09 Å/pix.
= 497.04 Å
456 pix
1.09 Å/pix.
= 497.04 Å
456 pix
1.09 Å/pix.
= 497.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.09 Å
Density
Contour Level:0.045 (by author), 0.045 (movie #1):
Minimum - Maximum-0.0568656 - 0.25599003
Average (Standard dev.)0.00036767506 (0.004647704)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions456456456
Origin0.00.00.0
Limit455.0455.0455.0
Spacing456456456
CellA=B=C: 497.04 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.091.091.09
M x/y/z456456456
origin x/y/z0.0000.0000.000
length x/y/z497.040497.040497.040
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS456456456
D min/max/mean-0.0570.2560.000

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Supplemental data

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Sample components

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Entire Mitochondrial NADH:ubiquinone oxidoreductase

EntireName: Mitochondrial NADH:ubiquinone oxidoreductase / Number of components: 51

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Component #1: protein, Mitochondrial NADH:ubiquinone oxidoreductase

ProteinName: Mitochondrial NADH:ubiquinone oxidoreductase / Recombinant expression: No
MassTheoretical: 963.7 MDa
SourceSpecies: Yarrowia lipolytica (yeast)

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Component #2: protein, 75-KDA PROTEIN (NUAM)

ProteinName: 75-KDA PROTEIN (NUAM) / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 78.996305 kDa
SourceSpecies: Yarrowia lipolytica (yeast)

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Component #3: protein, 51-KDA PROTEIN (NUBM)

ProteinName: 51-KDA PROTEIN (NUBM) / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 53.754871 kDa
SourceSpecies: Yarrowia lipolytica (yeast)

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Component #4: protein, 49-KDA PROTEIN (NUCM)

ProteinName: 49-KDA PROTEIN (NUCM) / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 52.42934 kDa
SourceSpecies: Yarrowia lipolytica (yeast)

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Component #5: protein, NIMM SUBUNIT

ProteinName: NIMM SUBUNIT / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.793137 kDa
SourceSpecies: Yarrowia lipolytica (yeast)

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Component #6: protein, NUEM SUBUNIT

ProteinName: NUEM SUBUNIT / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 42.705246 kDa
SourceSpecies: Yarrowia lipolytica (yeast)

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Component #7: protein, NUFM SUBUNIT

ProteinName: NUFM SUBUNIT / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.63474 kDa
SourceSpecies: Yarrowia lipolytica (yeast)

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Component #8: protein, 30-KDA PROTEIN (NUGM)

ProteinName: 30-KDA PROTEIN (NUGM) / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 32.345217 kDa
SourceSpecies: Yarrowia lipolytica (yeast)

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Component #9: protein, 24-KDA SUBUNIT (NUHM)

ProteinName: 24-KDA SUBUNIT (NUHM) / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 27.216158 kDa
SourceSpecies: Yarrowia lipolytica (yeast)

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Component #10: protein, TYKY SUBUNIT (NUIM)

ProteinName: TYKY SUBUNIT (NUIM) / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 25.651062 kDa
SourceSpecies: Yarrowia lipolytica (yeast)

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Component #11: protein, NUJM SUBUNIT

ProteinName: NUJM SUBUNIT / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 20.827379 kDa
SourceSpecies: Yarrowia lipolytica (yeast)

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Component #12: protein, PSST SUBUNIT (NUKM)

ProteinName: PSST SUBUNIT (NUKM) / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 23.42998 kDa
SourceSpecies: Yarrowia lipolytica (yeast)

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Component #13: protein, ND4L SUBUNIT (NULM)

ProteinName: ND4L SUBUNIT (NULM) / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.477428 kDa
SourceSpecies: Yarrowia lipolytica (yeast)

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Component #14: protein, NUMM SUBUNIT

ProteinName: NUMM SUBUNIT / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.128812 kDa
SourceSpecies: Yarrowia lipolytica (yeast)

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Component #15: protein, ACPM1 SUBUNIT

ProteinName: ACPM1 SUBUNIT / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.040483 kDa
SourceSpecies: Yarrowia lipolytica (yeast)

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Component #16: protein, NB4M SUBUNIT

ProteinName: NB4M SUBUNIT / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.757652 kDa
SourceSpecies: Yarrowia lipolytica (yeast)

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Component #17: protein, ACPM2 SUBUNIT

ProteinName: ACPM2 SUBUNIT / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.428331 kDa
SourceSpecies: Yarrowia lipolytica (yeast)

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Component #18: protein, NI2M SUBUNIT

ProteinName: NI2M SUBUNIT / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.879689 kDa
SourceSpecies: Yarrowia lipolytica (yeast)

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Component #19: protein, NESM SUBUNIT

ProteinName: NESM SUBUNIT / Details: Polyalanine / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.549694 kDa
SourceSpecies: Yarrowia lipolytica (yeast)

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Component #20: protein, NUPM SUBUNIT

ProteinName: NUPM SUBUNIT / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 19.326977 kDa
SourceSpecies: Yarrowia lipolytica (yeast)

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Component #21: protein, NB6M SUBUNIT

ProteinName: NB6M SUBUNIT / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.091265 kDa
SourceSpecies: Yarrowia lipolytica (yeast)

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Component #22: protein, NUXM SUBUNIT

ProteinName: NUXM SUBUNIT / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 18.565029 kDa
SourceSpecies: Yarrowia lipolytica (yeast)

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Component #23: protein, NUYM SUBUNIT

ProteinName: NUYM SUBUNIT / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 18.626852 kDa
SourceSpecies: Yarrowia lipolytica (yeast)

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Component #24: protein, NUZM SUBUNIT

ProteinName: NUZM SUBUNIT / Details: Polyalanine / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.677386 kDa
SourceSpecies: Yarrowia lipolytica (yeast)

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Component #25: protein, NIAM SUBUNIT

ProteinName: NIAM SUBUNIT / Details: Polyalanine / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.528504 kDa
SourceSpecies: Yarrowia lipolytica (yeast)

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Component #26: protein, NEBM SUBUNIT

ProteinName: NEBM SUBUNIT / Details: Polyalanine / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 5.464728 kDa
SourceSpecies: Yarrowia lipolytica (yeast)

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Component #27: protein, NB2M SUBUNIT

ProteinName: NB2M SUBUNIT / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.935799 kDa
SourceSpecies: Yarrowia lipolytica (yeast)

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Component #28: protein, NIDM SUBUNIT

ProteinName: NIDM SUBUNIT / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.021135 kDa
SourceSpecies: Yarrowia lipolytica (yeast)

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Component #29: protein, NUUM SUBUNIT

ProteinName: NUUM SUBUNIT / Details: Polyalanine / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 3.847734 kDa
SourceSpecies: Yarrowia lipolytica (yeast)

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Component #30: protein, NI8M SUBUNIT

ProteinName: NI8M SUBUNIT / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.603918 kDa
SourceSpecies: Yarrowia lipolytica (yeast)

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Component #31: protein, NI9M SUBUNIT

ProteinName: NI9M SUBUNIT / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.224273 kDa
SourceSpecies: Yarrowia lipolytica (yeast)

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Component #32: protein, N7BM SUBUNIT

ProteinName: N7BM SUBUNIT / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.152969 kDa
SourceSpecies: Yarrowia lipolytica (yeast)

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Component #33: protein, UNKNOWN SUBUNIT

ProteinName: UNKNOWN SUBUNIT / Details: Unknown sequence Polyalanine / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 4.528573 kDa
SourceSpecies: Yarrowia lipolytica (yeast)

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Component #34: protein, NB5M SUBUNIT

ProteinName: NB5M SUBUNIT / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.478759 kDa
SourceSpecies: Yarrowia lipolytica (yeast)

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Component #35: protein, NUNM SUBUNIT

ProteinName: NUNM SUBUNIT / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.93277 kDa
SourceSpecies: Yarrowia lipolytica (yeast)

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Component #36: protein, ND1 SUBUNIT (NU1M)

ProteinName: ND1 SUBUNIT (NU1M) / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 38.347148 kDa
SourceSpecies: Yarrowia lipolytica (yeast)

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Component #37: protein, ND2 SUBUNIT (NU2M)

ProteinName: ND2 SUBUNIT (NU2M) / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 53.33118 kDa
SourceSpecies: Yarrowia lipolytica (yeast)

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Component #38: protein, ND3 SUBUNIT (NU3M)

ProteinName: ND3 SUBUNIT (NU3M) / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.470267 kDa
SourceSpecies: Yarrowia lipolytica (yeast)

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Component #39: protein, ND4 SUBUNIT (NU4M)

ProteinName: ND4 SUBUNIT (NU4M) / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 54.48041 kDa
SourceSpecies: Yarrowia lipolytica (yeast)

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Component #40: protein, ND5 SUBUNIT (NU5M)

ProteinName: ND5 SUBUNIT (NU5M) / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 73.704398 kDa
SourceSpecies: Yarrowia lipolytica (yeast)

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Component #41: protein, ND6 SUBUNIT (NU6M)

ProteinName: ND6 SUBUNIT (NU6M) / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 20.758047 kDa
SourceSpecies: Yarrowia lipolytica (yeast)

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Component #42: protein, NB8M SUBUNIT

ProteinName: NB8M SUBUNIT / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.19887 kDa
SourceSpecies: Yarrowia lipolytica (yeast)

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Component #43: protein, NIPM SUBUNIT

ProteinName: NIPM SUBUNIT / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.018518 kDa
SourceSpecies: Yarrowia lipolytica (yeast)

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Component #44: ligand, IRON/SULFUR CLUSTER

LigandName: IRON/SULFUR CLUSTERIron–sulfur cluster / Number of Copies: 6 / Recombinant expression: No
MassTheoretical: 0.35164 kDa

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Component #45: ligand, FE2/S2 (INORGANIC) CLUSTER

LigandName: FE2/S2 (INORGANIC) CLUSTER / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 0.17582 kDa

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Component #46: ligand, FLAVIN MONONUCLEOTIDE

LigandName: FLAVIN MONONUCLEOTIDE / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.456344 kDa

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Component #47: ligand, NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

LigandName: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.745421 kDa

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Component #48: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

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Component #49: ligand, S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)but...

LigandName: S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] tetradecanethioate
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.568704 kDa

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Component #50: ligand, CARDIOLIPIN

LigandName: CARDIOLIPIN / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 1.464043 kDa

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Component #51: ligand, 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE

LigandName: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 0.748065 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 2 mg/ml / pH: 7.2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 283 K / Humidity: 70 %

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
ImagingMicroscope: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 60.5 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 200000.0 X (nominal), 45872.0 X (calibrated) / Cs: 2 mm / Imaging mode: OTHER / Defocus: -1.5 - -3.0 nm / Energy filter: GIF Bioquantum
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 3110

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 124626
3D reconstructionSoftware: RELION / Resolution: 4.32 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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Atomic model buiding

Modeling #1Refinement space: REAL
Output model

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