[English] 日本語
Yorodumi
- PDB-5lnk: Entire ovine respiratory complex I -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5lnk
TitleEntire ovine respiratory complex I
Components
  • (Mitochondrial complex I, ...Respiratory complex I) x 42
  • Acyl carrier protein
  • NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial
KeywordsOXIDOREDUCTASE / NADH:ubiquinone / complex I / mammalian / mitochondrial
Function / homology
Function and homology information


Complex I biogenesis / Respiratory electron transport / mitochondrial respirasome / NADH dehydrogenase activity / respiratory chain complex I / oxidoreductase activity, acting on NAD(P)H / electron transport coupled proton transport / mitochondrial ATP synthesis coupled electron transport / NADH:ubiquinone reductase (H+-translocating) / mitochondrial respiratory chain complex I ...Complex I biogenesis / Respiratory electron transport / mitochondrial respirasome / NADH dehydrogenase activity / respiratory chain complex I / oxidoreductase activity, acting on NAD(P)H / electron transport coupled proton transport / mitochondrial ATP synthesis coupled electron transport / NADH:ubiquinone reductase (H+-translocating) / mitochondrial respiratory chain complex I / apoptotic mitochondrial changes / mitochondrial respiratory chain complex I assembly / mitochondrial electron transport, NADH to ubiquinone / electron transport chain / NADH dehydrogenase (ubiquinone) activity / quinone binding / ATP synthesis coupled electron transport / respirasome / aerobic respiration / ATP metabolic process / reactive oxygen species metabolic process / respiratory electron transport chain / regulation of mitochondrial membrane potential / apoptotic signaling pathway / mitochondrial intermembrane space / 2 iron, 2 sulfur cluster binding / negative regulation of cell growth / circadian rhythm / fatty acid biosynthetic process / NAD binding / FMN binding / 4 iron, 4 sulfur cluster binding / response to oxidative stress / mitochondrial inner membrane / membrane => GO:0016020 / oxidoreductase activity / mitochondrial matrix / negative regulation of DNA-templated transcription / protein-containing complex binding / mitochondrion / nucleoplasm / metal ion binding / cytoplasm
Similarity search - Function
NADH:ubiquinone/plastoquinone oxidoreductase, chain 3 / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain / Rossmann fold - #12280 / Helix Hairpins - #3510 / Ubiquitin-like (UB roll) - #600 / NADH-ubiquinone oxidoreductase 51kDa subunit / de novo design (two linked rop proteins) / Cytochrome-c3 Hydrogenase; chain B / Cytochrome-c3 Hydrogenase, chain B / Complex1_LYR-like ...NADH:ubiquinone/plastoquinone oxidoreductase, chain 3 / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain / Rossmann fold - #12280 / Helix Hairpins - #3510 / Ubiquitin-like (UB roll) - #600 / NADH-ubiquinone oxidoreductase 51kDa subunit / de novo design (two linked rop proteins) / Cytochrome-c3 Hydrogenase; chain B / Cytochrome-c3 Hydrogenase, chain B / Complex1_LYR-like / NADH-ubiquinone oxidoreductase 1 subunit C1 / NADH-ubiquinone oxidoreductase flavoprotein 3 / NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial / NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial / NADH:ubiquinone oxidoreductase, ESSS subunit / ESSS subunit of NADH:ubiquinone oxidoreductase (complex I) / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1, NDUB1 / MNLL subunit / NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial / NADH-ubiquinone oxidoreductase, subunit 10 / NADH-ubiquinone oxidoreductase subunit 10 / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex subunit 1 / NADH-ubiquinone oxidoreductase MWFE subunit / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 / Soluble ligand binding domain / Zinc finger, CHCC-type / Zinc-finger domain / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, metazoa / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, animal type / NADH:ubiquinone oxidoreductase subunit B14.5a (Complex I-B14.5a) / NADH dehydrogenase 1 beta subcomplex subunit 2 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3 / NADH dehydrogenase 1 alpha subcomplex subunit 3 / SLBB domain / NADH dehydrogenase [ubiquinone] 1 subunit C2, NDUC2 / NADH:ubiquinone oxidoreductase, subunit NDUFB4 / NADH-ubiquinone oxidoreductase subunit b14.5b (NDUFC2) / NADH-ubiquinone oxidoreductase B15 subunit (NDUFB4) / NADH dehydrogenase 1, beta subcomplex, subunit 6 / NADH:ubiquinone oxidoreductase, NDUFB6/B17 subunit / NADH:ubiquinone oxidoreductase chain 4, N-terminal / NADH:ubiquinone oxidoreductase, chain 2 / NADH dehydrogenase subunit 2, C-terminal / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial / NADH:ubiquinone oxidoreductase, NDUFB5/SGDH subunit / NADH-ubiquinone oxidoreductase chain 4, amino terminus / NADH dehydrogenase subunit 2 C-terminus / NADH:ubiquinone oxidoreductase, NDUFB5/SGDH subunit / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8 / GRIM-19 / NADH-ubiquinone oxidoreductase ASHI subunit (CI-ASHI or NDUFB8) / GRIM-19 protein / NADH dehydrogenase subunit 5, C-terminal / NADH dehydrogenase subunit 5 C-terminus / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 / NADH-ubiquinone oxidoreductase B12 subunit family / NDUFA6, LYR domain / NADH:ubiquinone oxidoreductase, NDUFS5-15kDa / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7, NDUB7 / NADH-ubiquinone oxidoreductase B18 subunit (NDUFB7) / NADH dehydrogenase ubiquinone Fe-S protein 4-like superfamily / NADH dehydrogenase ubiquinone Fe-S protein 4 / NADH dehydrogenase ubiquinone Fe-S protein 4, mitochondrial / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 2 / NDUFB9, LYR domain / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / NADH ubiquinone oxidoreductase subunit NDUFA12 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 / NADH:ubiquinone oxidoreductase, iron-sulphur subunit 5 / ETC complex I subunit conserved region / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 6 / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 8 / NADH-quinone oxidoreductase, chain G, C-terminal / NADH-ubiquinone oxidoreductase subunit G, C-terminal / Deoxynucleoside kinase domain / Deoxynucleoside kinase / Respiratory-chain NADH dehydrogenase 20 Kd subunit signature. / NADH-ubiquinone oxidoreductase, 20 Kd subunit / NADH-quinone oxidoreductase, chain I / NAD(P)H-quinone oxidoreductase subunit D/H / NADH:ubiquinone oxidoreductase, 49kDa subunit, conserved site / Respiratory chain NADH dehydrogenase 49 Kd subunit signature. / NADH-quinone oxidoreductase, subunit D / Respiratory-chain NADH dehydrogenase, 49 Kd subunit / NADH:ubiquinone oxidoreductase, subunit G / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 3. / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 2. / NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJ / NADH dehydrogenase, subunit C / NADH ubiquinone oxidoreductase, F subunit / Complex 1 LYR protein domain / NADH-plastoquinone oxidoreductase, chain 5 subgroup / NADH:ubiquinone oxidoreductase, 30kDa subunit, conserved site / Respiratory chain NADH dehydrogenase 30 Kd subunit signature. / NADH-quinone oxidoreductase, chain M/4 / Complex 1 protein (LYR family) / 2Fe-2S iron-sulfur cluster binding domain / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 1.
Similarity search - Domain/homology
1,2-Distearoyl-sn-glycerophosphoethanolamine / CARDIOLIPIN / FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / Chem-NDP / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 4'-PHOSPHOPANTETHEINE / IRON/SULFUR CLUSTER / Chem-ZMP / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 ...1,2-Distearoyl-sn-glycerophosphoethanolamine / CARDIOLIPIN / FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / Chem-NDP / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 4'-PHOSPHOPANTETHEINE / IRON/SULFUR CLUSTER / Chem-ZMP / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / NADH-ubiquinone oxidoreductase chain 1 / NADH-ubiquinone oxidoreductase chain 2 / NADH-ubiquinone oxidoreductase chain 3 / NADH-ubiquinone oxidoreductase chain 4L / NADH-ubiquinone oxidoreductase chain 4 / NADH-ubiquinone oxidoreductase chain 5 / NADH-ubiquinone oxidoreductase chain 6 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial / NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial / NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13 / Acyl carrier protein / NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7 / NADH dehydrogenase [ubiquinone] 1 subunit C2 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 / NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 / Complex I-PDSW / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 / NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 5 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial
Similarity search - Component
Biological speciesOvis aries (sheep)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsFiedorczuk, K. / Letts, J.A. / Kaszuba, K. / Sazanov, L.A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MC_U105674180 United Kingdom
CitationJournal: Nature / Year: 2016
Title: Atomic structure of the entire mammalian mitochondrial complex I.
Authors: Karol Fiedorczuk / James A Letts / Gianluca Degliesposti / Karol Kaszuba / Mark Skehel / Leonid A Sazanov /
Abstract: Mitochondrial complex I (also known as NADH:ubiquinone oxidoreductase) contributes to cellular energy production by transferring electrons from NADH to ubiquinone coupled to proton translocation ...Mitochondrial complex I (also known as NADH:ubiquinone oxidoreductase) contributes to cellular energy production by transferring electrons from NADH to ubiquinone coupled to proton translocation across the membrane. It is the largest protein assembly of the respiratory chain with a total mass of 970 kilodaltons. Here we present a nearly complete atomic structure of ovine (Ovis aries) mitochondrial complex I at 3.9 Å resolution, solved by cryo-electron microscopy with cross-linking and mass-spectrometry mapping experiments. All 14 conserved core subunits and 31 mitochondria-specific supernumerary subunits are resolved within the L-shaped molecule. The hydrophilic matrix arm comprises flavin mononucleotide and 8 iron-sulfur clusters involved in electron transfer, and the membrane arm contains 78 transmembrane helices, mostly contributed by antiporter-like subunits involved in proton translocation. Supernumerary subunits form an interlinked, stabilizing shell around the conserved core. Tightly bound lipids (including cardiolipins) further stabilize interactions between the hydrophobic subunits. Subunits with possible regulatory roles contain additional cofactors, NADPH and two phosphopantetheine molecules, which are shown to be involved in inter-subunit interactions. We observe two different conformations of the complex, which may be related to the conformationally driven coupling mechanism and to the active-deactive transition of the enzyme. Our structure provides insight into the mechanism, assembly, maturation and dysfunction of mitochondrial complex I, and allows detailed molecular analysis of disease-causing mutations.
History
DepositionAug 4, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 23, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 22, 2017Group: Refinement description
Revision 1.2Aug 30, 2017Group: Author supporting evidence / Data collection / Experimental preparation
Category: em_sample_support / em_software / pdbx_audit_support
Item: _em_sample_support.grid_type / _em_software.name / _pdbx_audit_support.funding_organization
Revision 1.3Dec 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 1.4Jun 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

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-4093
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
1: Mitochondrial complex I, 51 kDa subunit
2: Mitochondrial complex I, 24 kDa subunit
3: Mitochondrial complex I, 75 kDa subunit
4: Mitochondrial complex I, 49 kDa subunit
5: Mitochondrial complex I, 30 kDa subunit
6: Mitochondrial complex I, PSST subunit
9: Mitochondrial complex I, TYKY subunit
H: Mitochondrial complex I, ND1 subunit
N: Mitochondrial complex I, ND2 subunit
A: Mitochondrial complex I, ND3 subunit
M: Mitochondrial complex I, ND4 subunit
K: Mitochondrial complex I, ND4L subunit
L: Mitochondrial complex I, ND5 subunit
J: Mitochondrial complex I, ND6 subunit
a: Mitochondrial complex I, 10 kDa subunit
b: Mitochondrial complex I, 13 kDa subunit
c: Mitochondrial complex I, 18 kDa subunit
d: Mitochondrial complex I, 39 kDa subunit
e: Mitochondrial complex I, B8 subunit
f: Mitochondrial complex I, B13 subunit
g: Mitochondrial complex I, B14 subunit
h: Mitochondrial complex I, B14.5a subunit
i: Mitochondrial complex I, B17.2 subunit
j: Acyl carrier protein
k: Mitochondrial complex I, 42 kDa subunit
l: Mitochondrial complex I, 15 kDa subunit
m: Mitochondrial complex I, B9 subunit
n: Mitochondrial complex I, B12 subunit
o: Mitochondrial complex I, B14.5b subunit
p: Mitochondrial complex I, B15 subunit
q: Mitochondrial complex I, B16.6 subunit
r: Mitochondrial complex I, B17 subunit
s: Mitochondrial complex I, B18 subunit
t: Mitochondrial complex I, B22 subunit
u: Mitochondrial complex I, AGGG subunit
v: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial
w: Mitochondrial complex I, ESSS subunit
x: Mitochondrial complex I, KFYI subunit
y: Mitochondrial complex I, MNLL subunit
z: Mitochondrial complex I, MWFE subunit
Z: Mitochondrial complex I, PDSW subunit
Y: Mitochondrial complex I, PGIV subunit
X: Acyl carrier protein
W: Mitochondrial complex I, SGDH subunit
V: Mitochondrial complex I, B14.7 subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)978,90270
Polymers962,23745
Non-polymers16,66525
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area261030 Å2
ΔGint-1817 kcal/mol
Surface area296700 Å2
MethodPISA

-
Components

+
Mitochondrial complex I, ... , 42 types, 42 molecules 1234569HNAMKLJabcdefghiklmnopq...

#1: Protein Mitochondrial complex I, 51 kDa subunit


Mass: 48678.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: W5PUX0
#2: Protein Mitochondrial complex I, 24 kDa subunit


Mass: 23840.428 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: W5NRY1
#3: Protein Mitochondrial complex I, 75 kDa subunit


Mass: 77031.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: W5QB34
#4: Protein Mitochondrial complex I, 49 kDa subunit


Mass: 47120.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: W5PJ73
#5: Protein Mitochondrial complex I, 30 kDa subunit


Mass: 26441.793 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: W5PB27
#6: Protein Mitochondrial complex I, PSST subunit


Mass: 20104.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: NCBIProt XP_012033846.2 / Source: (natural) Ovis aries (sheep) / References: UniProt: P42026*PLUS
#7: Protein Mitochondrial complex I, TYKY subunit


Mass: 20219.947 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: NCBIprot XP_011972879.1 / Source: (natural) Ovis aries (sheep) / References: UniProt: P42028*PLUS
#8: Protein Mitochondrial complex I, ND1 subunit / NADH dehydrogenase subunit 1


Mass: 35884.902 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: O78747
#9: Protein Mitochondrial complex I, ND2 subunit / NADH dehydrogenase subunit 2


Mass: 39149.805 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: O78748
#10: Protein Mitochondrial complex I, ND3 subunit / NADH dehydrogenase subunit 3


Mass: 13106.520 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: O78753
#11: Protein Mitochondrial complex I, ND4 subunit / NADH dehydrogenase subunit 4


Mass: 52058.734 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: O78755
#12: Protein Mitochondrial complex I, ND4L subunit / NADH dehydrogenase subunit 4L


Mass: 10840.228 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: O78754
#13: Protein Mitochondrial complex I, ND5 subunit / NADH dehydrogenase subunit 5


Mass: 67554.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: O78756
#14: Protein Mitochondrial complex I, ND6 subunit / NADH dehydrogenase subunit 6


Mass: 19126.619 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: O78757
#15: Protein Mitochondrial complex I, 10 kDa subunit


Mass: 8423.314 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: NCBIprot XP_011991231.1 / Source: (natural) Ovis aries (sheep) / References: UniProt: P25712*PLUS
#16: Protein Mitochondrial complex I, 13 kDa subunit


Mass: 10651.796 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: NCBIprot XP_011980592.1 / Source: (natural) Ovis aries (sheep) / References: UniProt: P23934*PLUS
#17: Protein Mitochondrial complex I, 18 kDa subunit


Mass: 15375.300 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: NCBIprot XP_004017046.1 / Source: (natural) Ovis aries (sheep) / References: UniProt: W5PE07*PLUS
#18: Protein Mitochondrial complex I, 39 kDa subunit


Mass: 38660.488 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: W5PI58
#19: Protein Mitochondrial complex I, B8 subunit


Mass: 10966.627 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: W5QAH8
#20: Protein Mitochondrial complex I, B13 subunit


Mass: 13156.311 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: NCBIprot XP_004005022.1 / Source: (natural) Ovis aries (sheep) / References: UniProt: W5PNX7
#21: Protein Mitochondrial complex I, B14 subunit


Mass: 14923.245 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: W5QC06
#22: Protein Mitochondrial complex I, B14.5a subunit


Mass: 12399.201 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: NCBIprot XP_004008614.1 / Source: (natural) Ovis aries (sheep) / References: UniProt: W5P0I2
#23: Protein Mitochondrial complex I, B17.2 subunit


Mass: 17115.508 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: B9VGZ9
#25: Protein Mitochondrial complex I, 42 kDa subunit


Mass: 36803.762 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: W5QBF5
#26: Protein Mitochondrial complex I, 15 kDa subunit


Mass: 12474.397 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: NCBIprot XP_004001873.1 / Source: (natural) Ovis aries (sheep) / References: UniProt: W5QFF9*PLUS
#27: Protein Mitochondrial complex I, B9 subunit


Mass: 9194.655 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: W5NYM7
#28: Protein Mitochondrial complex I, B12 subunit


Mass: 11015.482 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: W5Q5T4
#29: Protein Mitochondrial complex I, B14.5b subunit


Mass: 14231.420 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: NCBIprot XP_004019479.1 / Source: (natural) Ovis aries (sheep) / References: UniProt: W5P9Q8*PLUS
#30: Protein Mitochondrial complex I, B15 subunit


Mass: 14975.999 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: NCBIprot XP_004003003.1 / Source: (natural) Ovis aries (sheep) / References: UniProt: W5QF73*PLUS
#31: Protein Mitochondrial complex I, B16.6 subunit / Cell death regulatory protein GRIM-19 / Complex I-B16.6 / CI-B16.6 / Gene associated with retinoic- ...Cell death regulatory protein GRIM-19 / Complex I-B16.6 / CI-B16.6 / Gene associated with retinoic-interferon-induced mortality 19 protein / GRIM-19 / NADH-ubiquinone oxidoreductase B16.6 subunit


Mass: 16635.264 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: NCBIprot XP_004008450.1 / Source: (natural) Ovis aries (sheep) / References: UniProt: Q95KV7*PLUS
#32: Protein Mitochondrial complex I, B17 subunit


Mass: 15433.929 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: W5PZE3
#33: Protein Mitochondrial complex I, B18 subunit


Mass: 16282.610 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: W5P5V3
#34: Protein Mitochondrial complex I, B22 subunit


Mass: 21648.715 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: W5PGA3
#35: Protein Mitochondrial complex I, AGGG subunit


Mass: 8500.289 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: W5PVD7
#37: Protein Mitochondrial complex I, ESSS subunit


Mass: 14455.033 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: W5PWF1
#38: Protein/peptide Mitochondrial complex I, KFYI subunit / Complex I-KFYI / CI-KFYI / NADH-ubiquinone oxidoreductase KFYI subunit


Mass: 5808.645 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: NCBIprot XP_004017292.1 / Source: (natural) Ovis aries (sheep) / References: UniProt: Q02376*PLUS
#39: Protein Mitochondrial complex I, MNLL subunit


Mass: 6930.083 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: NCBIprot XP_004018002.1 / Source: (natural) Ovis aries (sheep) / References: UniProt: W5QG39*PLUS
#40: Protein Mitochondrial complex I, MWFE subunit


Mass: 8211.519 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: NCBIprot NP_001305903.1 / Source: (natural) Ovis aries (sheep) / References: UniProt: Q02377*PLUS
#41: Protein Mitochondrial complex I, PDSW subunit


Mass: 20880.752 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: NCBIprot XP_011999786.1 / Source: (natural) Ovis aries (sheep) / References: UniProt: W5Q5Y9*PLUS
#42: Protein Mitochondrial complex I, PGIV subunit


Mass: 20008.014 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: W5PYA5
#43: Protein Mitochondrial complex I, SGDH subunit


Mass: 16714.369 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: W5QHN8
#44: Protein Mitochondrial complex I, B14.7 subunit


Mass: 10145.497 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: UniProt W5PAR2 / Source: (natural) Ovis aries (sheep)

-
Protein , 2 types, 3 molecules jXv

#24: Protein Acyl carrier protein /


Mass: 10119.541 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: W5NQT7
#36: Protein NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial / Complex I-ASHI / NADH-ubiquinone oxidoreductase ASHI subunit


Mass: 18818.070 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: W5Q1B0

-
Non-polymers , 10 types, 25 molecules

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


Mass: 351.640 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe4S4
#46: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#47: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#48: Chemical
ChemComp-3PE / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE / 3-SN-PHOSPHATIDYLETHANOLAMINE / Phosphatidylethanolamine


Mass: 748.065 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C41H82NO8P / Comment: phospholipid*YM
#49: Chemical
ChemComp-PC1 / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 3-SN-PHOSPHATIDYLCHOLINE / Phosphatidylcholine


Mass: 790.145 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C44H88NO8P / Comment: phospholipid*YM
#50: 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.: 4 / Source method: obtained synthetically / Formula: C81H156O17P2 / Comment: phospholipid*YM
#51: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#52: 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
#53: 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
#54: Chemical ChemComp-PNS / 4'-PHOSPHOPANTETHEINE / Phosphopantetheine


Mass: 358.348 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H23N2O7PS

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Mitochondrial complex IRespiratory complex I / Type: COMPLEX / Entity ID: #1-#44 / Source: NATURAL
Molecular weightValue: 0.97 MDa / Experimental value: YES
Source (natural)Organism: Ovis aries (sheep)
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
1100 mMSodium ChlorideNaClSodium chloride1
220 mMHEPES1
32 mMEDTAEthylenediaminetetraacetic acid1
41.5 %Glycerol1
50.2 %Brij-351
SpecimenConc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R0.6/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 277 K / Details: 34s blotting

-
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 FIELDBright-field microscopy / Nominal magnification: 59000 X / Calibrated magnification: 100720 X / Nominal defocus max: 3500 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 1 sec. / Electron dose: 26 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k) / Num. of grids imaged: 2 / Num. of real images: 2600
Image scansSampling size: 14 µm / Width: 4096 / Height: 4096 / Movie frames/image: 7 / Used frames/image: 1-7

-
Processing

SoftwareName: PHENIX / Version: 1.10_2148: / Classification: refinement
EM software
IDNameVersionCategory
2EPUimage acquisition
4GctfCTF correction
7Cootmodel fitting
10RELION1.4final Euler assignment
11RELION1.4classification
12RELION1.43D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 241000
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 82000 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
Atomic model buildingPDB-ID: 4HEA

4hea


Details: For the fourteen core subunits we used as a starting point our previous structure from T. thermophilus (PDB 4HEA) with sequence adjusted to ovine and side-chains rebuilt in SQWRL4. These are ...Details: For the fourteen core subunits we used as a starting point our previous structure from T. thermophilus (PDB 4HEA) with sequence adjusted to ovine and side-chains rebuilt in SQWRL4. These are chains 1, 2, 3, 4, 5, 6, 9, H, A, J, K, N, M and L (with the same chain IDs as in 4HEA). For the remaining supernumerary subunits it was mostly de novo building with some help from homology modeling, which in most cases was not very useful due to low sequence homology. In few cases models produced by Phyre2 server were useful and were used as a starting point, due to the presence of templates with high coverage and confidence: 42kDa (chain k) - PDB ID 1P6X (xray) 39kDa (chain d) - PDB ID 3WJ7 (xray) SDAPs (chains j and X) - PDB ID 2DNW (NMR) B8 (chain e) - PDB ID 1S3A (NMR)
RefinementHighest resolution: 3.9 Å
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00765328
ELECTRON MICROSCOPYf_angle_d1.01788635
ELECTRON MICROSCOPYf_dihedral_angle_d9.54539246
ELECTRON MICROSCOPYf_chiral_restr0.0549813
ELECTRON MICROSCOPYf_plane_restr0.00611218

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

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

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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

Read more