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- PDB-6gcs: Cryo-EM structure of respiratory complex I from Yarrowia lipolytica -

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Basic information

Entry
Database: PDB / ID: 6gcs
TitleCryo-EM structure of respiratory complex I from Yarrowia lipolytica
Components
  • 24-KDA SUBUNIT (NUHM)
  • 30-KDA PROTEIN (NUGM)
  • 49-KDA PROTEIN (NUCM)
  • 51-KDA PROTEIN (NUBM)
  • 75-KDA PROTEIN (NUAM)
  • ACPM1 SUBUNIT
  • ACPM2 SUBUNIT
  • N7BM SUBUNIT
  • NB2M SUBUNIT
  • NB4M SUBUNIT
  • NB5M SUBUNIT
  • NB6M SUBUNIT
  • NB8M SUBUNIT
  • ND1 SUBUNIT (NU1M)
  • ND2 SUBUNIT (NU2M)
  • ND3 SUBUNIT (NU3M)
  • ND4 SUBUNIT (NU4M)
  • ND4L SUBUNIT (NULM)
  • ND5 SUBUNIT (NU5M)
  • ND6 SUBUNIT (NU6M)
  • NEBM SUBUNIT
  • NESM SUBUNIT
  • NI2M SUBUNIT
  • NI8M SUBUNIT
  • NI9M SUBUNIT
  • NIAM SUBUNIT
  • NIDM SUBUNIT
  • NIMM SUBUNIT
  • NIPM SUBUNIT
  • NUEM SUBUNIT
  • NUFM SUBUNIT
  • NUJM SUBUNIT
  • NUMM SUBUNIT
  • NUNM SUBUNIT
  • NUPM SUBUNIT
  • NUUM SUBUNIT
  • NUXM SUBUNIT
  • NUYM SUBUNIT
  • NUZM SUBUNIT
  • PSST SUBUNIT (NUKM)
  • TYKY SUBUNIT (NUIM)
  • UNKNOWN SUBUNIT
KeywordsOXIDOREDUCTASE / Complex I / NADH dehydrogenase / Mitochondrion Proton pumping / Ubiquinone
Function / homology
Function and homology information


NADH dehydrogenase / TIM23 mitochondrial import inner membrane translocase complex / ubiquinone-6 biosynthetic process / oxidoreductase activity, acting on NAD(P)H / protein import into mitochondrial matrix / integral component of mitochondrial inner membrane / NADH dehydrogenase activity / NADH:ubiquinone reductase (H+-translocating) / electron transport coupled proton transport / acyl binding ...NADH dehydrogenase / TIM23 mitochondrial import inner membrane translocase complex / ubiquinone-6 biosynthetic process / oxidoreductase activity, acting on NAD(P)H / protein import into mitochondrial matrix / integral component of mitochondrial inner membrane / NADH dehydrogenase activity / NADH:ubiquinone reductase (H+-translocating) / electron transport coupled proton transport / acyl binding / mitochondrial respiratory chain complex I assembly / mitochondrial electron transport, NADH to ubiquinone / acyl carrier activity / ATP synthesis coupled electron transport / ubiquinone binding / NADH dehydrogenase (ubiquinone) activity / electron transport chain / quinone binding / aerobic respiration / respirasome / respiratory electron transport chain / mitochondrial membrane / catalytic activity / 2 iron, 2 sulfur cluster binding / mitochondrial intermembrane space / fatty acid biosynthetic process / NAD binding / 4 iron, 4 sulfur cluster binding / FMN binding / mitochondrial inner membrane / response to oxidative stress / oxidoreductase activity / protein-containing complex binding / mitochondrion / membrane / integral component of membrane / metal ion binding
Similarity search - Function
Complex1_LYR-like / C-terminal of NADH-ubiquinone oxidoreductase 21 kDa subunit / NADH-ubiquinone oxidoreductase, 21kDa subunit, C-terminal, fungi / NADH-ubiquinone oxidoreductase 9.5kDa subunit / NADH-ubiquinone oxidoreductase complex I, 21 kDa subunit / NADH-ubiquinone oxidoreductase, 21kDa subunit, N-terminal / NADH-ubiquinone oxidoreductase subunit 10 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 / NADH-ubiquinone oxidoreductase, subunit 10 / NADH-plastoquinone oxidoreductase, chain 5 subgroup ...Complex1_LYR-like / C-terminal of NADH-ubiquinone oxidoreductase 21 kDa subunit / NADH-ubiquinone oxidoreductase, 21kDa subunit, C-terminal, fungi / NADH-ubiquinone oxidoreductase 9.5kDa subunit / NADH-ubiquinone oxidoreductase complex I, 21 kDa subunit / NADH-ubiquinone oxidoreductase, 21kDa subunit, N-terminal / NADH-ubiquinone oxidoreductase subunit 10 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 / NADH-ubiquinone oxidoreductase, subunit 10 / NADH-plastoquinone oxidoreductase, chain 5 subgroup / NADH-ubiquinone oxidoreductase MWFE subunit / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex subunit 1 / Zinc finger, CHCC-type / Zinc-finger domain / GRIM-19 protein / GRIM-19 / 2Fe-2S iron-sulfur cluster binding domain / Thioredoxin-like [2Fe-2S] ferredoxin / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11 / NADH-quinone oxidoreductase, chain I / NADH-ubiquinone oxidoreductase B12 subunit family / Respiratory-chain NADH dehydrogenase 20 Kd subunit signature. / NADH-ubiquinone oxidoreductase, 20 Kd subunit / NAD(P)H-quinone oxidoreductase subunit D/H / Respiratory chain NADH dehydrogenase 49 Kd subunit signature. / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7, NDUB7 / NADH:ubiquinone oxidoreductase, 49kDa subunit, conserved site / NADH-ubiquinone oxidoreductase B18 subunit (NDUFB7) / NADH dehydrogenase ubiquinone Fe-S protein 4 / NADH dehydrogenase ubiquinone Fe-S protein 4, mitochondrial / NADH dehydrogenase ubiquinone Fe-S protein 4-like superfamily / Respiratory-chain NADH dehydrogenase, 49 Kd subunit / NADH-quinone oxidoreductase, subunit D / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 6 / ETC complex I subunit conserved region / NADH ubiquinone oxidoreductase subunit NDUFA12 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 2 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / NADH:ubiquinone oxidoreductase, iron-sulphur subunit 5 / NADH:ubiquinone oxidoreductase, NDUFS5-15kDa / NADH-quinone oxidoreductase, chain G, C-terminal / NADH-ubiquinone oxidoreductase subunit G, C-terminal / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 8 / NADH:ubiquinone oxidoreductase, subunit G / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 3. / NADH ubiquinone oxidoreductase, F subunit / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 1. / NADH:ubiquinone oxidoreductase, 75kDa subunit, conserved site / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 2. / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJ / NADH-quinone oxidoreductase, chain 5-like / NuoE domain / Respiratory-chain NADH dehydrogenase 24 Kd subunit signature. / NADH-quinone oxidoreductase, chain M/4 / NADH:ubiquinone oxidoreductase, subunit 3 superfamily / NADH:ubiquinone/plastoquinone oxidoreductase, chain 3 / NADH-ubiquinone/plastoquinone oxidoreductase, chain 3 / Respiratory chain NADH dehydrogenase 30 Kd subunit signature. / NADH-ubiquinone/plastoquinone oxidoreductase chain 6 / NADH:ubiquinone oxidoreductase, 30kDa subunit, conserved site / NADH:ubiquinone/plastoquinone oxidoreductase, chain 6 / NADH-ubiquinone oxidoreductase chain 4L/K / NADH dehydrogenase, subunit C / NADH:ubiquinone oxidoreductase / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminal / NADH-quinone oxidoreductase subunit E-like / Soluble ligand binding domain / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus / SLBB domain / Respiratory-chain NADH dehydrogenase subunit 1 signature 2. / NADH:ubiquinone oxidoreductase, subunit 1, conserved site / Respiratory-chain NADH dehydrogenase subunit 1 signature 1. / NADH-quinone oxidoreductase subunit E, N-terminal / Respiratory-chain NADH dehydrogenase, 30 Kd subunit / NADH:ubiquinone oxidoreductase, 30kDa subunit superfamily / NADH:ubiquinone oxidoreductase, 30kDa subunit / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 1. / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 2. / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain superfamily / Respiratory-chain NADH dehydrogenase 51 Kd subunit / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain superfamily / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain / NADH:ubiquinone oxidoreductase, 51kDa subunit, conserved site / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / NADH dehydrogenase / NADH:ubiquinone oxidoreductase, subunit 1/F420H2 oxidoreductase subunit H / NADH-ubiquinone/plastoquinone oxidoreductase chain 4L / NADH-ubiquinone oxidoreductase chain 4L/Mnh complex subunit C1-like / NADH:quinone oxidoreductase/Mrp antiporter, membrane subunit / Proton-conducting membrane transporter / NADH:ubiquinone oxidoreductase, subunit G, iron-sulphur binding / His(Cys)3-ligated-type [4Fe-4S] domain profile. / Complex 1 protein (LYR family)
Similarity search - Domain/homology
NADH-ubiquinone oxidoreductase / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit N7BM / NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial / YALI0C03201p / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / NADH-ubiquinone oxidoreductase 19.3 kDa subunit / Acyl carrier protein / NUVM protein / YALI0D19030p / YALI0D24585p ...NADH-ubiquinone oxidoreductase / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit N7BM / NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial / YALI0C03201p / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / NADH-ubiquinone oxidoreductase 19.3 kDa subunit / Acyl carrier protein / NUVM protein / YALI0D19030p / YALI0D24585p / Acyl carrier protein / Complex I-B14.7 / YALI0A01419p / NADH-ubiquinone oxidoreductase chain 5 / NADH-ubiquinone oxidoreductase chain 3 / NADH-ubiquinone oxidoreductase chain 2 / NADH-ubiquinone oxidoreductase 24 kDa subunit / NADH-ubiquinone oxidoreductase chain 4L / NADH-ubiquinone oxidoreductase chain 4 / NADH-ubiquinone oxidoreductase chain 1 / NADH-ubiquinone oxidoreductase chain 6 / NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial / YALI0E28424p / NADH-ubiquinone oxidoreductase 23 kDa subunit / NADH-ubiquinone oxidoreductase 49 kDa subunit / NADH-ubiquinone oxidoreductase 30.4 kDa subunit / YALI0E23089p / 1,2-Distearoyl-sn-glycerophosphoethanolamine / YALI0F18359p / Acyl carrier protein / FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / Chem-NDP / IRON/SULFUR CLUSTER / Chem-ZMP / CARDIOLIPIN / NADH-ubiquinone oxidoreductase 14.8 kDa subunit / NADH-ubiquinone oxidoreductase 12 kDa subunit / NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / NADH-ubiquinone oxidoreductase 9.5 kDa subunit / YALI0A17946p / NADH-ubiquinone oxidoreductase 20.9 kDa subunit / NADH dehydrogenase [ubiquinone] iron-sulfur protein 5-A / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13 / Acyl carrier protein / Lactobacillus shifted 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 / NADH-ubiquinone oxidoreductase 78 kDa subunit
Similarity search - Component
Biological speciesYarrowia lipolytica (yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.32 Å
AuthorsParey, K. / Vonck, J.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationEXC 115 Germany
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.
History
DepositionApr 19, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 10, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2019Group: Data collection / Structure summary
Category: em_admin / entity ...em_admin / entity / pdbx_database_proc / pdbx_seq_map_depositor_info / struct
Item: _em_admin.last_update / _em_admin.title ..._em_admin.last_update / _em_admin.title / _entity.formula_weight / _pdbx_seq_map_depositor_info.one_letter_code / _pdbx_seq_map_depositor_info.one_letter_code_mod / _struct.title
Revision 1.2Dec 11, 2019Group: Other / Category: atom_sites / cell
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.Z_PDB
Revision 1.3Jun 2, 2021Group: Derived calculations / Category: struct_conn / struct_conn_type
Item: _struct_conn.conn_type_id / _struct_conn.id ..._struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id

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Structure visualization

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Assembly

Deposited unit
A: 75-KDA PROTEIN (NUAM)
B: 51-KDA PROTEIN (NUBM)
C: 49-KDA PROTEIN (NUCM)
D: NIMM SUBUNIT
E: NUEM SUBUNIT
F: NUFM SUBUNIT
G: 30-KDA PROTEIN (NUGM)
H: 24-KDA SUBUNIT (NUHM)
I: TYKY SUBUNIT (NUIM)
J: NUJM SUBUNIT
K: PSST SUBUNIT (NUKM)
L: ND4L SUBUNIT (NULM)
M: NUMM SUBUNIT
O: ACPM1 SUBUNIT
P: NB4M SUBUNIT
Q: ACPM2 SUBUNIT
R: NI2M SUBUNIT
S: NESM SUBUNIT
U: NUPM SUBUNIT
W: NB6M SUBUNIT
X: NUXM SUBUNIT
Y: NUYM SUBUNIT
Z: NUZM SUBUNIT
a: NIAM SUBUNIT
b: NEBM SUBUNIT
c: NB2M SUBUNIT
d: NIDM SUBUNIT
e: NUUM SUBUNIT
f: NI8M SUBUNIT
g: NI9M SUBUNIT
h: N7BM SUBUNIT
i: UNKNOWN SUBUNIT
j: NB5M SUBUNIT
n: NUNM SUBUNIT
1: ND1 SUBUNIT (NU1M)
2: ND2 SUBUNIT (NU2M)
3: ND3 SUBUNIT (NU3M)
4: ND4 SUBUNIT (NU4M)
5: ND5 SUBUNIT (NU5M)
6: ND6 SUBUNIT (NU6M)
8: NB8M SUBUNIT
9: NIPM SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)935,29758
Polymers927,29242
Non-polymers8,00616
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 41 types, 41 molecules ABCDEFGHIJKLMOPQRSUWXYZabcdfgh...

#1: Protein 75-KDA PROTEIN (NUAM)


Mass: 79088.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: Q9UUU3, NADH dehydrogenase
#2: Protein 51-KDA PROTEIN (NUBM)


Mass: 53829.508 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast)
References: UniProt: Q9UUU2, NADH:ubiquinone reductase (H+-translocating), NADH dehydrogenase
#3: Protein 49-KDA PROTEIN (NUCM)


Mass: 52494.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: Q9UUU1, NADH dehydrogenase
#4: Protein NIMM SUBUNIT


Mass: 9806.238 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: A0A1D8NC63, UniProt: B5FVD3*PLUS
#5: Protein NUEM SUBUNIT


Mass: 42765.738 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: Q6C7X4
#6: Protein NUFM SUBUNIT


Mass: 16657.920 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: Q6C4W9
#7: Protein 30-KDA PROTEIN (NUGM)


Mass: 32389.568 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: Q9UUU0, NADH dehydrogenase
#8: Protein 24-KDA SUBUNIT (NUHM)


Mass: 27247.402 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: Q9UUT9, NADH dehydrogenase
#9: Protein TYKY SUBUNIT (NUIM)


Mass: 25682.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: Q9UUT8, NADH dehydrogenase
#10: Protein NUJM SUBUNIT


Mass: 20849.551 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: Q6C674
#11: Protein PSST SUBUNIT (NUKM) /


Mass: 23455.176 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: Q9UUT7, NADH dehydrogenase
#12: Protein ND4L SUBUNIT (NULM)


Mass: 9482.467 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast)
References: UniProt: Q9B6D4, NADH:ubiquinone reductase (H+-translocating)
#13: Protein NUMM SUBUNIT


Mass: 15148.970 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: A0A1H6Q8Z5, UniProt: Q6C8J9*PLUS
#14: Protein ACPM1 SUBUNIT


Mass: 12053.585 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: A0A1H6PXT9, UniProt: Q6C926*PLUS
#15: Protein NB4M SUBUNIT


Mass: 14778.818 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: A0A1D8N3C8, UniProt: Q6CI60*PLUS
#16: Protein ACPM2 SUBUNIT


Mass: 14444.458 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: A0A1D8NG21, UniProt: Q6C7X2*PLUS
#17: Protein NI2M SUBUNIT


Mass: 12902.870 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: A0A1D8NDL1, UniProt: Q6C9Z1*PLUS
#18: Protein NESM SUBUNIT


Mass: 13549.694 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Polyalanine / Source: (natural) Yarrowia lipolytica (yeast) / References: NADH:ubiquinone reductase (H+-translocating)
#19: Protein NUPM SUBUNIT


Mass: 19355.197 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: Q6CGB4
#20: Protein NB6M SUBUNIT


Mass: 14112.429 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: A0A1H6PPE5, UniProt: B5FVF8*PLUS
#21: Protein NUXM SUBUNIT


Mass: 18588.209 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: A0A1D8NKB4, UniProt: Q6C4A6*PLUS
#22: Protein NUYM SUBUNIT


Mass: 18656.080 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: A0A1D8N7X0, UniProt: Q6CEK9*PLUS
#23: Protein NUZM SUBUNIT


Mass: 11677.386 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Polyalanine / Source: (natural) Yarrowia lipolytica (yeast) / References: NADH:ubiquinone reductase (H+-translocating)
#24: Protein NIAM SUBUNIT


Mass: 8528.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Polyalanine / Source: (natural) Yarrowia lipolytica (yeast) / References: NADH:ubiquinone reductase (H+-translocating)
#25: Protein NEBM SUBUNIT


Mass: 5464.728 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Polyalanine / Source: (natural) Yarrowia lipolytica (yeast) / References: NADH:ubiquinone reductase (H+-translocating)
#26: Protein NB2M SUBUNIT


Mass: 6948.902 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: B5FVE5
#27: Protein NIDM SUBUNIT


Mass: 11039.276 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: A0A1D8N596, UniProt: B5RSK3*PLUS
#29: Protein NI8M SUBUNIT


Mass: 9621.051 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: A0A1H6PJS3, UniProt: Q6CD73*PLUS
#30: Protein NI9M SUBUNIT


Mass: 7233.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: A0A1D8NJR0, UniProt: B5FVF3*PLUS
#31: Protein N7BM SUBUNIT


Mass: 16175.141 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: Q6CG53
#32: Protein UNKNOWN SUBUNIT


Mass: 4528.573 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Unknown sequence Polyalanine / Source: (natural) Yarrowia lipolytica (yeast) / References: NADH:ubiquinone reductase (H+-translocating)
#33: Protein NB5M SUBUNIT


Mass: 10494.885 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: Q6ZY24, NADH dehydrogenase
#34: Protein NUNM SUBUNIT


Mass: 7932.770 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: NADH:ubiquinone reductase (H+-translocating)
#35: Protein ND1 SUBUNIT (NU1M) / NADH dehydrogenase subunit 1


Mass: 38361.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast)
References: UniProt: Q9B6E8, NADH:ubiquinone reductase (H+-translocating)
#36: Protein ND2 SUBUNIT (NU2M) / NADH dehydrogenase subunit 2


Mass: 53353.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast)
References: UniProt: Q9B6C8, NADH:ubiquinone reductase (H+-translocating)
#37: Protein ND3 SUBUNIT (NU3M) / NADH dehydrogenase subunit 3


Mass: 14478.329 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast)
References: UniProt: Q9B6C7, NADH:ubiquinone reductase (H+-translocating)
#38: Protein ND4 SUBUNIT (NU4M) / NADH dehydrogenase subunit 4


Mass: 54506.641 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast)
References: UniProt: Q9B6D6, NADH:ubiquinone reductase (H+-translocating)
#39: Protein ND5 SUBUNIT (NU5M) / NADH dehydrogenase subunit 5


Mass: 73740.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast)
References: UniProt: Q9B6D3, NADH:ubiquinone reductase (H+-translocating)
#40: Protein ND6 SUBUNIT (NU6M) / NADH dehydrogenase subunit 6


Mass: 20765.102 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast)
References: UniProt: Q9B6E9, NADH:ubiquinone reductase (H+-translocating)
#41: Protein NB8M SUBUNIT


Mass: 11219.027 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: A0A1H6PKH9, UniProt: B5FVG1*PLUS
#42: Protein NIPM SUBUNIT


Mass: 10035.651 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Yarrowia lipolytica (yeast) / References: UniProt: A0A1D8NNZ0, UniProt: B5RSL7*PLUS

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Protein/peptide , 1 types, 1 molecules e

#28: Protein/peptide NUUM SUBUNIT


Mass: 3847.734 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Polyalanine / Source: (natural) Yarrowia lipolytica (yeast) / References: NADH:ubiquinone reductase (H+-translocating)

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Non-polymers , 8 types, 16 molecules

#43: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe4S4
#44: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


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


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#46: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate


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


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#48: Chemical ChemComp-ZMP / S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] tetradecanethioate


Mass: 568.704 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H49N2O8PS
#49: Chemical ChemComp-CDL / CARDIOLIPIN / DIPHOSPHATIDYL GLYCEROL / BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL / Cardiolipin


Mass: 1464.043 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C81H156O17P2 / Comment: phospholipid*YM
#50: Chemical ChemComp-3PE / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE / 3-SN-PHOSPHATIDYLETHANOLAMINE / Phosphatidylethanolamine


Mass: 748.065 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C41H82NO8P / Comment: phospholipid*YM

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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

ComponentName: Mitochondrial NADH:ubiquinone oxidoreductase / Type: COMPLEX / Entity ID: #1-#42 / Source: NATURAL
Molecular weightValue: 963.7 kDa/nm / Experimental value: NO
Source (natural)Organism: Yarrowia lipolytica (yeast)
Buffer solutionpH: 7.2
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMTris1
2100 mMsodium clorideNaClSodium chloride1
31 mMEDTAEthylenediaminetetraacetic acid1
40.025 %DDM1
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: C-flat-1/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 70 % / Chamber temperature: 283 K

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: OTHER / Nominal magnification: 200000 X / Calibrated magnification: 45872 X / Nominal defocus max: -3 nm / Nominal defocus min: -1.5 nm / Cs: 2 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 8 sec. / Electron dose: 60.5 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 3110
EM imaging opticsEnergyfilter name: GIF Bioquantum
Image scansMovie frames/image: 40

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Processing

SoftwareName: PHENIX / Version: 1.12_2829: / Classification: refinement
EM software
IDNameVersionCategory
2Leginon1image acquisition
4CTFFIND4CTF correction
7Coot0.8.8.model fitting
9RELION2.1initial Euler assignment
10RELION2.1final Euler assignment
11RELION2.1classification
12RELION2.13D reconstruction
13PHENIX1.12_2829model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 271443
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.32 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 124626 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL
RefinementHighest resolution: 4.32 Å
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01356446
ELECTRON MICROSCOPYf_angle_d1.24376824
ELECTRON MICROSCOPYf_dihedral_angle_d13.15233649
ELECTRON MICROSCOPYf_chiral_restr0.0638984
ELECTRON MICROSCOPYf_plane_restr0.0089860

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