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- PDB-6yj4: Structure of Yarrowia lipolytica complex I at 2.7 A -

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Entry
Database: PDB / ID: 6yj4
TitleStructure of Yarrowia lipolytica complex I at 2.7 A
Components
  • (Acyl carrier protein ...) x 2
  • (NADH-ubiquinone oxidoreductase chain ...) x 6
  • NADH dehydrogenase subunit 2
  • NUCM protein
  • NUGM protein
  • Subunit N7BM of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NB2M of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NB4M of protein NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NB5M of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NB6M of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NB8M of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NEBM of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NESM of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NI2M of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NI8M of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NIAM of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NIDM of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NIMM of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NIPM of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NUAM of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NUBM of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NUEM of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NUFM of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NUHM of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NUIM of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NUJM of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NUKM of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NUMM of protein NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NUPM of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NUUM of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NUXM of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NUYM of NADH:Ubiquinone Oxidoreductase (Complex I)
  • Subunit NUZM of NADH:Ubiquinone Oxidoreductase (Complex I)
  • subunit NI9M of protein NADH:Ubiquinone Oxidoreductase (Complex I)
  • subunit NIGM of protein NADH:Ubiquinone Oxidoreductase (Complex I)
  • subunit NUNM of protein NADH:Ubiquinone Oxidoreductase (Complex I)
KeywordsMEMBRANE PROTEIN / NADH:Ubiquinone Oxidoreductase / complex I
Function / homology
Function and homology information


lipoate biosynthetic process / NADH dehydrogenase / TIM23 mitochondrial import inner membrane translocase complex / membrane protein complex / NADH dehydrogenase complex / ubiquinone biosynthetic process / mitochondrial [2Fe-2S] assembly complex / oxidoreductase activity, acting on NAD(P)H / NADH dehydrogenase activity / iron-sulfur cluster assembly ...lipoate biosynthetic process / NADH dehydrogenase / TIM23 mitochondrial import inner membrane translocase complex / membrane protein complex / NADH dehydrogenase complex / ubiquinone biosynthetic process / mitochondrial [2Fe-2S] assembly complex / oxidoreductase activity, acting on NAD(P)H / NADH dehydrogenase activity / iron-sulfur cluster assembly / acyl binding / ubiquinone binding / electron transport coupled proton transport / protein import into mitochondrial matrix / acyl carrier activity / NADH:ubiquinone reductase (H+-translocating) / mitochondrial respiratory chain complex I assembly / mitochondrial electron transport, NADH to ubiquinone / respiratory chain complex I / catalytic complex / NADH dehydrogenase (ubiquinone) activity / quinone binding / ATP synthesis coupled electron transport / aerobic respiration / respiratory electron transport chain / electron transport chain / mitochondrial membrane / mitochondrial intermembrane space / 2 iron, 2 sulfur cluster binding / NAD binding / FMN binding / 4 iron, 4 sulfur cluster binding / response to oxidative stress / oxidoreductase activity / mitochondrial inner membrane / protein-containing complex binding / mitochondrion / metal ion binding / membrane
Similarity search - Function
NADH dehydrogenase [ubiquinone] (complex I), 21kDa subunit, fungi / NADH-ubiquinone oxidoreductase, 21kDa subunit, C-terminal, fungi / NADH-ubiquinone oxidoreductase 9.5kDa subunit / C-terminal of NADH-ubiquinone oxidoreductase 21 kDa subunit / : / NADH-ubiquinone oxidoreductase, 21kDa subunit, N-terminal / NADH-ubiquinone oxidoreductase complex I, 21 kDa subunit / NADH-ubiquinone oxidoreductase 51kDa subunit / SLBB domain / Complex1_LYR-like ...NADH dehydrogenase [ubiquinone] (complex I), 21kDa subunit, fungi / NADH-ubiquinone oxidoreductase, 21kDa subunit, C-terminal, fungi / NADH-ubiquinone oxidoreductase 9.5kDa subunit / C-terminal of NADH-ubiquinone oxidoreductase 21 kDa subunit / : / NADH-ubiquinone oxidoreductase, 21kDa subunit, N-terminal / NADH-ubiquinone oxidoreductase complex I, 21 kDa subunit / NADH-ubiquinone oxidoreductase 51kDa subunit / SLBB domain / Complex1_LYR-like / NADH-ubiquinone oxidoreductase, subunit 10 / NADH-ubiquinone oxidoreductase subunit 10 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 / NADH-ubiquinone oxidoreductase MWFE subunit / : / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex subunit 1 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8 / NADH-ubiquinone oxidoreductase ASHI subunit (CI-ASHI or NDUFB8) / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11 / NADH-ubiquinone oxidoreductase NDSU1/NuoG-like, 4Fe-4S domain / Zinc finger, CHCC-type / Zinc-finger domain / NADH:ubiquinone oxidoreductase, NDUFS5-15kDa / 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:ubiquinone oxidoreductase, iron-sulphur subunit 5 / GRIM-19 / GRIM-19 protein / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / NDUFB9, LYR domain / NDUFA6, LYR domain / NADH dehydrogenase ubiquinone Fe-S protein 4-like superfamily / NADH dehydrogenase ubiquinone Fe-S protein 4 / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 2 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 / NADH dehydrogenase ubiquinone Fe-S protein 4, mitochondrial / ETC complex I subunit conserved region / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / NADH ubiquinone oxidoreductase subunit NDUFA12 / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 6 / : / SLBB domain / : / NADH-quinone oxidoreductase, chain G, C-terminal / NADH-ubiquinone oxidoreductase subunit G, C-terminal / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 8 / : / NADH-quinone oxidoreductase subunit 3, ferredoxin-like domain / Respiratory-chain NADH dehydrogenase 20 Kd subunit signature. / NADH-ubiquinone oxidoreductase, 20 Kd subunit / NADH-quinone oxidoreductase, chain I / NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJ / NADH-plastoquinone oxidoreductase, chain 5 subgroup / NADH-ubiquinone oxidoreductase chain 4L/K / NADH-quinone oxidoreductase, chain M/4 / NADH:ubiquinone/plastoquinone oxidoreductase, chain 6 / NADH-ubiquinone/plastoquinone oxidoreductase chain 6 / NADH-ubiquinone oxidoreductase chain 4L/Mnh complex subunit C1-like / NADH-ubiquinone/plastoquinone oxidoreductase chain 4L / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminal / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus / NAD(P)H-quinone oxidoreductase subunit D/H / NADH-quinone oxidoreductase, chain 5-like / NADH:ubiquinone oxidoreductase, 49kDa subunit, conserved site / Respiratory chain NADH dehydrogenase 49 Kd subunit signature. / NADH:ubiquinone oxidoreductase, subunit G / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 3. / NADH ubiquinone oxidoreductase, F subunit / NADH-quinone oxidoreductase, subunit D / Respiratory-chain NADH dehydrogenase, 49 Kd subunit / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 2. / NADH dehydrogenase, subunit C / Complex 1 LYR protein domain / NADH:ubiquinone oxidoreductase, 30kDa subunit, conserved site / Respiratory chain NADH dehydrogenase 30 Kd subunit signature. / Complex 1 protein (LYR family) / NADH:ubiquinone oxidoreductase / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 1. / : / NADH:ubiquinone oxidoreductase, 30kDa subunit / NADH:ubiquinone oxidoreductase, 30kDa subunit superfamily / Respiratory-chain NADH dehydrogenase, 30 Kd subunit / NADH:quinone oxidoreductase/Mrp antiporter, membrane subunit / NADH:quinone oxidoreductase/Mrp antiporter, TM / NADH:ubiquinone oxidoreductase, 75kDa subunit, conserved site / NADH:ubiquinone/plastoquinone oxidoreductase, chain 3 / NADH:ubiquinone oxidoreductase, subunit 3 superfamily / NADH-ubiquinone/plastoquinone oxidoreductase, chain 3 / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / NADH:ubiquinone oxidoreductase, subunit 1, conserved site / Respiratory-chain NADH dehydrogenase subunit 1 signature 1. / Respiratory-chain NADH dehydrogenase subunit 1 signature 2. / NADH:ubiquinone oxidoreductase, subunit 1/F420H2 oxidoreductase subunit H / NADH dehydrogenase / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 1. / 2Fe-2S iron-sulfur cluster binding domain / Respiratory-chain NADH dehydrogenase 24 Kd subunit signature.
Similarity search - Domain/homology
1,2-Distearoyl-sn-glycerophosphoethanolamine / CARDIOLIPIN / Chem-EHZ / FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / Chem-NDP / DIUNDECYL PHOSPHATIDYL CHOLINE / IRON/SULFUR CLUSTER / Complex 1 LYR protein domain-containing protein / Uncharacterized protein ...1,2-Distearoyl-sn-glycerophosphoethanolamine / CARDIOLIPIN / Chem-EHZ / FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / Chem-NDP / DIUNDECYL PHOSPHATIDYL CHOLINE / IRON/SULFUR CLUSTER / Complex 1 LYR protein domain-containing protein / Uncharacterized protein / Uncharacterized protein / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit / NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 / Uncharacterized protein / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / Uncharacterized protein / Acyl carrier protein / Uncharacterized protein / Uncharacterized protein / NADH-ubiquinone oxidoreductase complex I, 21 kDa subunit-domain-containing protein / NADH dehydrogenase [ubiquinone] iron-sulfur protein 5 / Thioredoxin-like protein / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13 / Acyl carrier protein / Uncharacterized protein / Zinc finger CHCC-type domain-containing protein / NAD-dependent epimerase/dehydratase domain-containing protein / NADH dehydrogenase 1 beta subcomplex subunit 3 / NADH-ubiquinone oxidoreductase / ETC complex I subunit conserved region-domain-containing protein / Uncharacterized protein / Uncharacterized protein / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 / YALI0D10274p / YALI0E23749p / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7 / YALI0A17946p / YALI0F06061p / NADH dehydrogenase [ubiquinone] iron-sulfur protein 5 / YALI0F00924p / YALI0F17248p / NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial / YALI0E29095p / YALI0D00737p / YALI0F02123p / YALI0D05467p / YALI0F14003p / YALI0E28424p / YALI0E23089p / YALI0E11891p / Acyl carrier protein / YALI0D24585p / YALI0D19030p / Acyl carrier protein / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / YALI0D04939p / YALI0C03201p / NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit N7BM / NADH-ubiquinone oxidoreductase / YALI0A02651p / YALI0A01419p / NUWM protein / NUVM protein / NADH-ubiquinone oxidoreductase chain 3 / NADH-ubiquinone oxidoreductase chain 2 / NADH-ubiquinone oxidoreductase chain 5 / NADH-ubiquinone oxidoreductase chain 4L / NADH-ubiquinone oxidoreductase chain 4 / NADH-ubiquinone oxidoreductase chain 1 / NADH-ubiquinone oxidoreductase chain 6 / Subunit NUKM of protein NADH:Ubiquinone oxidoreductase / Subunit NUIM of protein NADH:Ubiquinone oxidoreductase / Subunit NUHM of protein NADH:Ubiquinone oxidoreductase / NUGM protein / NUCM protein / NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial / NUAM protein / NADH-ubiquinone oxidoreductase chain 5 / NADH-ubiquinone oxidoreductase chain 4 / NADH-ubiquinone oxidoreductase chain 3 / NADH-ubiquinone oxidoreductase chain 1 / NADH-ubiquinone oxidoreductase chain 2 / NADH-ubiquinone oxidoreductase chain 4L
Similarity search - Component
Biological speciesYarrowia lipolytica (yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsHirst, J. / Grba, D.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC_U105663141 United Kingdom
Medical Research Council (MRC, United Kingdom)MC_UU_00015/2 United Kingdom
Citation
Journal: Nat Struct Mol Biol / Year: 2020
Title: Mitochondrial complex I structure reveals ordered water molecules for catalysis and proton translocation.
Authors: Daniel N Grba / Judy Hirst /
Abstract: Mitochondrial complex I powers ATP synthesis by oxidative phosphorylation, exploiting the energy from ubiquinone reduction by NADH to drive protons across the energy-transducing inner membrane. ...Mitochondrial complex I powers ATP synthesis by oxidative phosphorylation, exploiting the energy from ubiquinone reduction by NADH to drive protons across the energy-transducing inner membrane. Recent cryo-EM analyses of mammalian and yeast complex I have revolutionized structural and mechanistic knowledge and defined structures in different functional states. Here, we describe a 2.7-Å-resolution structure of the 42-subunit complex I from the yeast Yarrowia lipolytica containing 275 structured water molecules. We identify a proton-relay pathway for ubiquinone reduction and water molecules that connect mechanistically crucial elements and constitute proton-translocation pathways through the membrane. By comparison with known structures, we deconvolute structural changes governing the mammalian 'deactive transition' (relevant to ischemia-reperfusion injury) and their effects on the ubiquinone-binding site and a connected cavity in ND1. Our structure thus provides important insights into catalysis by this enigmatic respiratory machine.
#1: Journal: Nat Struct Mol Biol / Year: 2020
Title: Mitochondrial complex I structure reveals ordered water molecules for catalysis and proton translocation.
Authors: Daniel N Grba / Judy Hirst /
Abstract: Mitochondrial complex I powers ATP synthesis by oxidative phosphorylation, exploiting the energy from ubiquinone reduction by NADH to drive protons across the energy-transducing inner membrane. ...Mitochondrial complex I powers ATP synthesis by oxidative phosphorylation, exploiting the energy from ubiquinone reduction by NADH to drive protons across the energy-transducing inner membrane. Recent cryo-EM analyses of mammalian and yeast complex I have revolutionized structural and mechanistic knowledge and defined structures in different functional states. Here, we describe a 2.7-Å-resolution structure of the 42-subunit complex I from the yeast Yarrowia lipolytica containing 275 structured water molecules. We identify a proton-relay pathway for ubiquinone reduction and water molecules that connect mechanistically crucial elements and constitute proton-translocation pathways through the membrane. By comparison with known structures, we deconvolute structural changes governing the mammalian 'deactive transition' (relevant to ischemia-reperfusion injury) and their effects on the ubiquinone-binding site and a connected cavity in ND1. Our structure thus provides important insights into catalysis by this enigmatic respiratory machine.
History
DepositionApr 2, 2020Deposition site: PDBE / Processing site: PDBE
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Structure visualization

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Assembly

Deposited unit
A: NADH-ubiquinone oxidoreductase chain 3
B: Subunit NUKM of NADH:Ubiquinone Oxidoreductase (Complex I)
C: NUGM protein
D: NUCM protein
E: Subunit NUHM of NADH:Ubiquinone Oxidoreductase (Complex I)
F: Subunit NUBM of NADH:Ubiquinone Oxidoreductase (Complex I)
G: Subunit NUAM of NADH:Ubiquinone Oxidoreductase (Complex I)
H: NADH-ubiquinone oxidoreductase chain 1
I: Subunit NUIM of NADH:Ubiquinone Oxidoreductase (Complex I)
J: NADH-ubiquinone oxidoreductase chain 6
K: NADH-ubiquinone oxidoreductase chain 4L
L: NADH-ubiquinone oxidoreductase chain 5
M: NADH-ubiquinone oxidoreductase chain 4
N: NADH dehydrogenase subunit 2
O: Subunit NUXM of NADH:Ubiquinone Oxidoreductase (Complex I)
P: Subunit NUEM of NADH:Ubiquinone Oxidoreductase (Complex I)
Q: Subunit NUYM of NADH:Ubiquinone Oxidoreductase (Complex I)
R: Subunit NUMM of protein NADH:Ubiquinone Oxidoreductase (Complex I)
S: Subunit NI8M of NADH:Ubiquinone Oxidoreductase (Complex I)
T: Acyl carrier protein ACPM1 of NADH:Ubiquinone Oxidoreductase (Complex I)
U: Acyl carrier protein ACPM2 of NADH:Ubiquinone Oxidoreductase (Complex I)
V: Subunit NUFM of NADH:Ubiquinone Oxidoreductase (Complex I)
W: Subunit NB4M of protein NADH:Ubiquinone Oxidoreductase (Complex I)
X: Subunit NUPM of NADH:Ubiquinone Oxidoreductase (Complex I)
Y: Subunit NUJM of NADH:Ubiquinone Oxidoreductase (Complex I)
Z: Subunit NB6M of NADH:Ubiquinone Oxidoreductase (Complex I)
a: Subunit NIMM of NADH:Ubiquinone Oxidoreductase (Complex I)
b: subunit NI9M of protein NADH:Ubiquinone Oxidoreductase (Complex I)
c: Subunit NUZM of NADH:Ubiquinone Oxidoreductase (Complex I)
d: Subunit NEBM of NADH:Ubiquinone Oxidoreductase (Complex I)
e: Subunit NIPM of NADH:Ubiquinone Oxidoreductase (Complex I)
f: Subunit N7BM of NADH:Ubiquinone Oxidoreductase (Complex I)
g: Subunit NESM of NADH:Ubiquinone Oxidoreductase (Complex I)
h: subunit NUNM of protein NADH:Ubiquinone Oxidoreductase (Complex I)
i: Subunit NUUM of NADH:Ubiquinone Oxidoreductase (Complex I)
j: subunit NIGM of protein NADH:Ubiquinone Oxidoreductase (Complex I)
k: Subunit NB2M of NADH:Ubiquinone Oxidoreductase (Complex I)
l: Subunit NIAM of NADH:Ubiquinone Oxidoreductase (Complex I)
m: Subunit NB5M of NADH:Ubiquinone Oxidoreductase (Complex I)
n: Subunit NI2M of NADH:Ubiquinone Oxidoreductase (Complex I)
o: Subunit NB8M of NADH:Ubiquinone Oxidoreductase (Complex I)
p: Subunit NIDM of NADH:Ubiquinone Oxidoreductase (Complex I)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,020,03592
Polymers985,35142
Non-polymers34,68350
Water4,954275
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

-
NADH-ubiquinone oxidoreductase chain ... , 6 types, 6 molecules AHJKLM

#1: Protein NADH-ubiquinone oxidoreductase chain 3


Mass: 14506.339 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yarrowia lipolytica (yeast) / Gene: nad3, YALI1_M00472r / Production host: Yarrowia lipolytica (yeast)
References: UniProt: S5TMS4, UniProt: Q9B6C7*PLUS, NADH:ubiquinone reductase (H+-translocating)
#8: Protein NADH-ubiquinone oxidoreductase chain 1


Mass: 38389.277 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yarrowia lipolytica (yeast) / Gene: nad1, YALI1_M00064g / Production host: Yarrowia lipolytica (yeast)
References: UniProt: S5U3V2, UniProt: Q9B6E8*PLUS, NADH:ubiquinone reductase (H+-translocating)
#10: Protein NADH-ubiquinone oxidoreductase chain 6 / NADH dehydrogenase subunit 6


Mass: 20793.111 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yarrowia lipolytica (strain CLIB 122 / E 150) (yeast)
Gene: ND6 / Production host: Yarrowia lipolytica (yeast)
References: UniProt: Q9B6E9, NADH:ubiquinone reductase (H+-translocating)
#11: Protein NADH-ubiquinone oxidoreductase chain 4L


Mass: 9843.860 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yarrowia lipolytica (yeast) / Gene: nad4L, YALI1_M00335g / Production host: Yarrowia lipolytica (yeast)
References: UniProt: S5U4U1, UniProt: Q9B6D4*PLUS, NADH:ubiquinone reductase (H+-translocating)
#12: Protein NADH-ubiquinone oxidoreductase chain 5


Mass: 73768.703 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yarrowia lipolytica (yeast) / Gene: nad5, YALI1_M00338r / Production host: Yarrowia lipolytica (yeast)
References: UniProt: S5TF58, UniProt: Q9B6D3*PLUS, NADH:ubiquinone reductase (H+-translocating)
#13: Protein NADH-ubiquinone oxidoreductase chain 4


Mass: 54534.652 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yarrowia lipolytica (yeast) / Gene: nad4, YALI1_M00296g / Production host: Yarrowia lipolytica (yeast)
References: UniProt: S5TMP9, UniProt: Q9B6D6*PLUS, NADH:ubiquinone reductase (H+-translocating)

+
Protein , 34 types, 34 molecules BCDEFGINOPQRSVWXYZabcdefghijkl...

#2: Protein Subunit NUKM of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 23455.176 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yarrowia lipolytica (yeast) / Gene: nukm, YALI1_F09003g / Production host: Yarrowia lipolytica (yeast) / References: UniProt: Q9UUT7, NADH dehydrogenase
#3: Protein NUGM protein


Mass: 33644.910 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: His tagged / Source: (gene. exp.) Yarrowia lipolytica (yeast) / Gene: nugm, B0I71DRAFT_126141 / Production host: Yarrowia lipolytica (yeast)
References: UniProt: Q9UUU0, UniProt: F2Z6D7*PLUS, NADH dehydrogenase
#4: Protein NUCM protein


Mass: 52521.949 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yarrowia lipolytica (yeast) / Gene: nucm, B0I71DRAFT_131656, YALI1_F22993g / Production host: Yarrowia lipolytica (yeast)
References: UniProt: Q9UUU1, UniProt: F2Z626*PLUS, NADH dehydrogenase
#5: Protein Subunit NUHM of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 27247.402 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yarrowia lipolytica (yeast) / Gene: nuhm / Production host: Yarrowia lipolytica (yeast)
References: UniProt: Q9UUT9, UniProt: F2Z6C0*PLUS, NADH dehydrogenase
#6: Protein Subunit NUBM of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 53829.508 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yarrowia lipolytica (yeast) / Gene: nubm, NUO51, YALI1_B26679g / Production host: Yarrowia lipolytica (yeast)
References: UniProt: Q9UUU2, UniProt: F2Z660*PLUS, NADH dehydrogenase, NADH:ubiquinone reductase (H+-translocating)
#7: Protein Subunit NUAM of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 79088.078 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yarrowia lipolytica (yeast) / Gene: nuam, YALI1_D07089g / Production host: Yarrowia lipolytica (yeast)
References: UniProt: Q9UUU3, UniProt: F2Z6F1*PLUS, NADH dehydrogenase
#9: Protein Subunit NUIM of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 25682.305 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yarrowia lipolytica (yeast) / Gene: nuim, YALI1_F01456g / Production host: Yarrowia lipolytica (yeast)
References: UniProt: Q9UUT8, UniProt: F2Z619*PLUS, NADH dehydrogenase
#14: Protein NADH dehydrogenase subunit 2


Mass: 53381.367 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yarrowia lipolytica (yeast) / Gene: nad2, YALI1_M00458g / Production host: Yarrowia lipolytica (yeast)
References: UniProt: S5U4R9, UniProt: Q9B6C8*PLUS, NADH:ubiquinone reductase (H+-translocating)
#15: Protein Subunit NUXM of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 18588.209 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yarrowia lipolytica (yeast) / Gene: YALI1_E33570g / Production host: Yarrowia lipolytica (yeast) / References: UniProt: A0A1D8NKB4, UniProt: Q6C4A6*PLUS
#16: Protein Subunit NUEM of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 42765.738 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yarrowia lipolytica (yeast) / Gene: B0I71DRAFT_137087, BD777DRAFT_111096 / Production host: Yarrowia lipolytica (yeast) / References: UniProt: A0A371BY45, UniProt: Q6C7X4*PLUS
#17: Protein Subunit NUYM of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 18656.080 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yarrowia lipolytica (yeast) / Gene: YALI1_B19507g / Production host: Yarrowia lipolytica (yeast) / References: UniProt: A0A1D8N7X0, UniProt: Q6CEK9*PLUS
#18: Protein Subunit NUMM of protein NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 15148.970 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yarrowia lipolytica (yeast) / Gene: YALI1_D24109g / Production host: Yarrowia lipolytica (yeast) / References: UniProt: A0A1H6Q8Z5, UniProt: Q6C8J9*PLUS
#19: Protein Subunit NI8M of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 9621.051 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yarrowia lipolytica (yeast) / Gene: YALI1_C04281g / Production host: Yarrowia lipolytica (yeast) / References: UniProt: A0A1H6PJS3, UniProt: Q6CD73*PLUS
#22: Protein Subunit NUFM of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 16657.920 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yarrowia lipolytica (yeast) / Gene: B0I71DRAFT_119420, BD777DRAFT_112063 / Production host: Yarrowia lipolytica (yeast) / References: UniProt: A0A371C5F3, UniProt: Q6C4W9*PLUS
#23: Protein Subunit NB4M of protein NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 14778.818 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yarrowia lipolytica (yeast) / Gene: YALI1_A01824g / Production host: Yarrowia lipolytica (yeast) / References: UniProt: A0A1D8N3C8, UniProt: Q6CI60*PLUS
#24: Protein Subunit NUPM of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 19355.197 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yarrowia lipolytica (yeast) / Gene: B0I71DRAFT_134276 / Production host: Yarrowia lipolytica (yeast) / References: UniProt: A0A371C2D0, UniProt: Q6CGB4*PLUS
#25: Protein Subunit NUJM of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 20849.551 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yarrowia lipolytica (yeast) / Gene: B0I71DRAFT_129038, BD777DRAFT_131485 / Production host: Yarrowia lipolytica (yeast) / References: UniProt: A0A371CB65, UniProt: Q6C674*PLUS
#26: Protein Subunit NB6M of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 14112.429 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yarrowia lipolytica (yeast) / Gene: YALI1_E34222g / Production host: Yarrowia lipolytica (yeast) / References: UniProt: A0A1H6PPE5, UniProt: B5FVF8*PLUS
#27: Protein Subunit NIMM of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 9806.238 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yarrowia lipolytica (yeast) / Gene: YALI1_C30086g / Production host: Yarrowia lipolytica (yeast) / References: UniProt: A0A1D8NC63, UniProt: B5FVD3*PLUS
#28: Protein subunit NI9M of protein NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 8992.229 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yarrowia lipolytica (yeast) / Gene: B0I71DRAFT_131413, YALI1_E28107g / Production host: Yarrowia lipolytica (yeast) / References: UniProt: A0A1D8NJR0, UniProt: B5FVF3*PLUS
#29: Protein Subunit NUZM of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 19772.525 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yarrowia lipolytica (yeast) / Gene: B0I71DRAFT_129288, YALI1_A03153g / Production host: Yarrowia lipolytica (yeast) / References: UniProt: A0A1D8N3H5, UniProt: Q6CI10*PLUS
#30: Protein Subunit NEBM of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 8059.366 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yarrowia lipolytica (yeast) / Gene: YALI1_E00527g / Production host: Yarrowia lipolytica (yeast) / References: UniProt: A0A1D8NGI5
#31: Protein Subunit NIPM of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 10035.651 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yarrowia lipolytica (yeast) / Gene: YALI1_F24343g / Production host: Yarrowia lipolytica (yeast) / References: UniProt: A0A1D8NNZ0, UniProt: B5RSL7*PLUS
#32: Protein Subunit N7BM of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 16175.141 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yarrowia lipolytica (yeast) / Gene: B0I71DRAFT_100046, YALI1_B00908g / Production host: Yarrowia lipolytica (yeast) / References: UniProt: A0A1D8N5V2, UniProt: Q6CG53*PLUS
#33: Protein Subunit NESM of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 28479.941 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yarrowia lipolytica (yeast) / Gene: nuwm, B0I71DRAFT_98177, YALI1_E34367g / Production host: Yarrowia lipolytica (yeast)
References: UniProt: Q6ZY23, UniProt: F2Z673*PLUS, NADH dehydrogenase
#34: Protein subunit NUNM of protein NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 15818.789 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yarrowia lipolytica (yeast) / Gene: B0I71DRAFT_126580 / Production host: Yarrowia lipolytica (yeast) / References: UniProt: A0A371CFV9, UniProt: Q6C1R9*PLUS
#35: Protein Subunit NUUM of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 9793.966 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yarrowia lipolytica (yeast) / Gene: B0I71DRAFT_133979, YALI1_D22691g / Production host: Yarrowia lipolytica (yeast) / References: UniProt: A0A1H6Q311
#36: Protein subunit NIGM of protein NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 10765.430 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yarrowia lipolytica (yeast) / Gene: B0I71DRAFT_129560, YALI1_D30003g / Production host: Yarrowia lipolytica (yeast) / References: UniProt: A0A1D8NFX6
#37: Protein Subunit NB2M of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 6948.902 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yarrowia lipolytica (yeast) / Gene: B0I71DRAFT_135324 / Production host: Yarrowia lipolytica (yeast) / References: UniProt: A0A371C0F2, UniProt: B5FVE5*PLUS
#38: Protein Subunit NIAM of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 17328.523 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yarrowia lipolytica (yeast) / Gene: B0I71DRAFT_129122, YALI1_D06302g / Production host: Yarrowia lipolytica (yeast) / References: UniProt: A0A1D8ND94, UniProt: Q6CA88*PLUS
#39: Protein Subunit NB5M of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 10494.885 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yarrowia lipolytica (yeast) / Gene: nuvm, YALI1_F09017g / Production host: Yarrowia lipolytica (yeast)
References: UniProt: Q6ZY24, UniProt: B5RSK9*PLUS, NADH dehydrogenase
#40: Protein Subunit NI2M of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 12902.870 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yarrowia lipolytica (yeast) / Gene: YALI1_D09203g / Production host: Yarrowia lipolytica (yeast) / References: UniProt: A0A1D8NDL1, UniProt: Q6C9Z1*PLUS
#41: Protein Subunit NB8M of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 11219.027 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yarrowia lipolytica (yeast) / Gene: YALI1_E37603g / Production host: Yarrowia lipolytica (yeast) / References: UniProt: A0A1H6PKH9, UniProt: B5FVG1*PLUS
#42: Protein Subunit NIDM of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 11039.276 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yarrowia lipolytica (yeast) / Gene: YALI1_A18188g / Production host: Yarrowia lipolytica (yeast) / References: UniProt: A0A1D8N596, UniProt: B5RSK3*PLUS

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Acyl carrier protein ... , 2 types, 2 molecules TU

#20: Protein Acyl carrier protein ACPM1 of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 12053.585 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yarrowia lipolytica (yeast) / Gene: YALI1_D18037g / Production host: Yarrowia lipolytica (yeast) / References: UniProt: A0A1H6PXT9, UniProt: Q6C926*PLUS
#21: Protein Acyl carrier protein ACPM2 of NADH:Ubiquinone Oxidoreductase (Complex I)


Mass: 14444.458 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yarrowia lipolytica (yeast) / Gene: YALI1_D32594g / Production host: Yarrowia lipolytica (yeast) / References: UniProt: A0A1D8NG21, UniProt: Q6C7X2*PLUS

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Sugars , 1 types, 5 molecules

#45: Sugar
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

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Non-polymers , 10 types, 320 molecules

#43: Chemical
ChemComp-3PE / 1,2-Distearoyl-sn-glycerophosphoethanolamine / 3-SN-PHOSPHATIDYLETHANOLAMINE / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE


Mass: 748.065 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C41H82NO8P / Comment: phospholipid*YM
#44: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe4S4
#46: Chemical
ChemComp-PLC / DIUNDECYL PHOSPHATIDYL CHOLINE


Mass: 622.834 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C32H65NO8P / Comment: phospholipid*YM
#47: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#48: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#49: Chemical
ChemComp-CDL / CARDIOLIPIN / DIPHOSPHATIDYL GLYCEROL / BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL


Mass: 1464.043 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C81H156O17P2 / Comment: phospholipid*YM
#50: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#51: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#52: Chemical ChemComp-EHZ / ~{S}-[2-[3-[[(2~{R})-3,3-dimethyl-2-oxidanyl-4-phosphonooxy-butanoyl]amino]propanoylamino]ethyl] (3~{S})-3-oxidanyltetradecanethioate


Mass: 584.703 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H49N2O9PS
#53: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 275 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Yarrowia lipolytica mitochondrial complex I (NADH:Ubiquinone oxidoreductase)COMPLEX#1-#420MULTIPLE SOURCES
2Yarrowia lipolytica mitochondrial complex ICOMPLEX#1-#9, #11-#421RECOMBINANT
3Entity 10COMPLEX#101RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Yarrowia lipolytica (yeast)4952
23Yarrowia lipolytica (strain CLIB 122 / E 150) (yeast)284591
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
12Yarrowia lipolytica (yeast)4952
23Yarrowia lipolytica (yeast)4952
Buffer solutionpH: 7.45
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: Gold grids pre-treated with PEG thiol reagent / Grid material: GOLD / Grid type: UltrAuFoil
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 130000 X / Calibrated defocus min: -1500 nm / Calibrated defocus max: -2700 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Image recordingElectron dose: 44 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2540
Image scansMovie frames/image: 25

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Processing

EM software
IDNameVersionCategory
1RELION3.1particle selection
2EPUimage acquisition
4RELION3.1CTF correction
5GctfCTF correction
8UCSF Chimera1.13.1model fitting
10RELION3.1initial Euler assignment
11RELION3.1final Euler assignment
12RELION3.1classification
13RELION3.13D reconstruction
14PHENIX1.14model refinement
15PHENIX1.16model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 106302 / Details: Post manual curation of Relion auto-pick
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 49669 / Symmetry type: POINT
Atomic model buildingPDB-ID: 6G2J

6g2j


Accession code: 6G2J / Source name: PDB / Type: experimental model

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