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- PDB-5j4z: Architecture of tight respirasome -

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Entry
Database: PDB / ID: 5j4z
TitleArchitecture of tight respirasome
Components
  • (COMPLEX I B14. ...) x 2
  • (COMPLEX I SDAP/NDUFAB1) x 3
  • (COMPLEX I UNKNOWN SUBUNIT FRAGMENT ...) x 12
  • (COMPLEX III SUBUNIT ...) x 7
  • (Cytochrome b-c1 complex subunit Rieske, ...) x 2
  • (Cytochrome c oxidase subunit ...) x 5
  • COMPLEX I 13KDA/NDUFS6
  • COMPLEX I 15KDA/NDUFS5
  • COMPLEX I 18KDA/NDUFS6
  • COMPLEX I 24KDA/NDUFV2
  • COMPLEX I 30KDA/NDUFS3
  • COMPLEX I 39KDA/NDUFA9
  • COMPLEX I 42KDA/NDUFA10
  • COMPLEX I 49KDA/NDUFS2
  • COMPLEX I 51KDA/NDUFV1
  • COMPLEX I 75KDA/NDUFS1
  • COMPLEX I B13/NDUFA5
  • COMPLEX I B14/NDUFA6
  • COMPLEX I B15/NDUFB4
  • COMPLEX I B16.6/NDUFA13
  • COMPLEX I B17.2/NDUFA12
  • COMPLEX I B18/NDUFB7
  • COMPLEX I B22/NDUFB9
  • COMPLEX I B8/NDUFA2
  • COMPLEX I B9/NDUFA3
  • COMPLEX I ESSS/NDUFB11
  • COMPLEX I KFYI/NDUFC1
  • COMPLEX I MWFE/NDUFA1
  • COMPLEX I ND1
  • COMPLEX I ND2
  • COMPLEX I ND3
  • COMPLEX I ND4
  • COMPLEX I ND4L
  • COMPLEX I ND5
  • COMPLEX I ND6
  • COMPLEX I PDSW/NDUFB10
  • COMPLEX I PGIV/NDUFA8
  • COMPLEX I PSST/NDUFS7
  • COMPLEX I TYKY/NDUFS8
  • COMPLEX IV COX4
  • COMPLEX IV COX5A
  • COMPLEX IV COX5B
  • COMPLEX IV COX6B1
  • COMPLEX IV COX6C
  • COMPLEX IV COX7B
  • COMPLEX IV COX7C
  • COMPLEX IV COX8B
  • Cytochrome b
  • Cytochrome b-c1 complex subunit 6
KeywordsELECTRON TRANSPORT / membrane protein complex / supercomplex / respirasome
Function / homology
Function and homology information


: / : / regulation of oxidative phosphorylation / respiratory chain complex IV assembly / mitochondrial respirasome assembly / : / respiratory chain complex IV / cytochrome-c oxidase / respiratory chain complex III / oxidative phosphorylation ...: / : / regulation of oxidative phosphorylation / respiratory chain complex IV assembly / mitochondrial respirasome assembly / : / respiratory chain complex IV / cytochrome-c oxidase / respiratory chain complex III / oxidative phosphorylation / quinol-cytochrome-c reductase / mitochondrial electron transport, cytochrome c to oxygen / quinol-cytochrome-c reductase activity / cytochrome-c oxidase activity / mitochondrial electron transport, ubiquinol to cytochrome c / electron transport coupled proton transport / membrane => GO:0016020 / ATP synthesis coupled electron transport / metalloendopeptidase activity / 2 iron, 2 sulfur cluster binding / electron transfer activity / oxidoreductase activity / mitochondrial inner membrane / copper ion binding / heme binding / ubiquitin protein ligase binding / proteolysis / nucleoplasm / metal ion binding
Similarity search - Function
Cytochrome b-c1 complex subunit 10 / Single alpha-helix domain superfamily / Ubiquinol-cytochrome C reductase complex, 6.4kD protein / Cytochrome c oxidase, subunit 8 / Mitochondrial cytochrome c oxidase subunit VIc/VIIs / Cytochrome c oxidase, subunit 8 superfamily / Mitochondrial cytochrome c oxidase subunit VIc/VIIs superfamily / : / Cytochrome oxidase c subunit VIII / Cytochrome c oxidase subunit VIc ...Cytochrome b-c1 complex subunit 10 / Single alpha-helix domain superfamily / Ubiquinol-cytochrome C reductase complex, 6.4kD protein / Cytochrome c oxidase, subunit 8 / Mitochondrial cytochrome c oxidase subunit VIc/VIIs / Cytochrome c oxidase, subunit 8 superfamily / Mitochondrial cytochrome c oxidase subunit VIc/VIIs superfamily / : / Cytochrome oxidase c subunit VIII / Cytochrome c oxidase subunit VIc / Cytochrome c oxidase subunit VIIa, metazoa / Cytochrome C oxidase, subunit VIIB / Cytochrome c oxidase subunit IV / Cytochrome C oxidase, subunit VIIB domain superfamily / Cytochrome c oxidase, subunit VIIa superfamily / Cytochrome C oxidase chain VIIB / Cytochrome c oxidase, subunit VIa, conserved site / Cytochrome c oxidase subunit VIa signature. / Cytochrome c oxidase, subunit VIa / Cytochrome c oxidase, subunit VIa superfamily / Cytochrome c oxidase subunit VIa / Ubiquinol-cytochrome c reductase 8kDa, N-terminal / Ubiquinol-cytochrome c reductase 8 kDa, N-terminal / Cytochrome c oxidase, subunit VIb / Cytochrome c oxidase subunit Vb, zinc binding region signature. / Cytochrome c oxidase subunit VIIc / Cytochrome c oxidase subunit IV family / Cytochrome c oxidase, subunit VIb superfamily / Cytochrome c oxidase subunit VIIc superfamily / Cytochrome c oxidase subunit IV superfamily / Cytochrome c oxidase subunit VIIc / Cytochrome c oxidase subunit IV / Cytochrome c oxidase subunit 2, C-terminal / Cytochrome oxidase c subunit VIb / Cytochrome c oxidase, subunit Va/VI / Cytochrome c oxidase, subunit Va/VI superfamily / Cytochrome c oxidase subunit Va / Cytochrome c oxidase subunit VII / Cytochrome c oxidase subunit VII / Globular protein, non-globular alpha/beta subunit / Cytochrome c oxidase, subunit Vb / Cytochrome c oxidase subunit III domain / Cytochrome c oxidase subunit Vb / Cytochrome c oxidase subunit Vb, zinc binding domain profile. / Cytochrome c oxidase, subunit II / Cytochrome c oxidase, subunit Vb superfamily / Cytochrome c oxidase subunit I domain / Cytochrome b-c1 complex, subunit 6 / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome b-c1 complex subunit 8 / Cytochrome C oxidase subunit II, transmembrane domain / UcrQ family / Cytochrome oxidase subunit II transmembrane region profile. / Cytochrome bc1 complex subunit Rieske, transmembrane domain superfamily / Cytochrome c oxidase subunit III / Cytochrome c oxidase subunit III-like / Cytochrome c oxidase, subunit III, 4-helical bundle / Cytochrome c oxidase subunit III / Heme-copper oxidase subunit III family profile. / Cytochrome c oxidase subunit III-like superfamily / Cytochrome b-c1 complex subunit 7 / Cytochrome b-c1 complex subunit 7 superfamily / Ubiquinol-cytochrome C reductase complex 14kD subunit / Cytochrome b-c1 complex subunit 8 superfamily / Cytochrome b-c1 complex subunit Rieske, transmembrane domain / Ubiquinol cytochrome reductase transmembrane region / Cytochrome b-c1 complex subunit 9 / Cytochrome b-c1 complex subunit 9 superfamily / Cytochrome b-c1 complex subunit 9 / Cytochrome c/quinol oxidase subunit II / Ubiquinol-cytochrome C reductase hinge domain / Ubiquinol-cytochrome C reductase hinge domain superfamily / Ubiquinol-cytochrome C reductase hinge protein / Cytochrome c1, transmembrane anchor, C-terminal / : / Cytochrome b / Cytochrome C oxidase subunit II, transmembrane domain superfamily / Ubiquinol-cytochrome c reductase, iron-sulphur subunit / : / Cytochrome c oxidase, subunit I, copper-binding site / Heme-copper oxidase catalytic subunit, copper B binding region signature. / Cytochrome c oxidase-like, subunit I domain / Cytochrome oxidase subunit I profile. / Cytochrome c1 / Cytochrome C1 family / : / Cytochrome b/b6, C-terminal / Cytochrome b(C-terminal)/b6/petD / Cytochrome b/b6 C-terminal region profile. / Peptidase M16, zinc-binding site / Insulinase family, zinc-binding region signature. / Cytochrome c oxidase subunit I / Cytochrome c oxidase-like, subunit I superfamily / Cytochrome C and Quinol oxidase polypeptide I / Cytochrome b/b6, C-terminal domain superfamily / Cytochrome b/b6/petB / Cytochrome C oxidase subunit II, periplasmic domain / Cytochrome c oxidase subunit II-like C-terminal / Cytochrome oxidase subunit II copper A binding domain profile. / Rieske iron-sulphur protein, C-terminal
Similarity search - Domain/homology
COPPER (II) ION / DINUCLEAR COPPER ION / FE2/S2 (INORGANIC) CLUSTER / HEME-A / PROTOPORPHYRIN IX CONTAINING FE / IRON/SULFUR CLUSTER / Cytochrome b-c1 complex subunit 6 / Cytochrome c oxidase subunit 3 / Cytochrome c oxidase subunit 1 / Cytochrome c oxidase subunit 2 ...COPPER (II) ION / DINUCLEAR COPPER ION / FE2/S2 (INORGANIC) CLUSTER / HEME-A / PROTOPORPHYRIN IX CONTAINING FE / IRON/SULFUR CLUSTER / Cytochrome b-c1 complex subunit 6 / Cytochrome c oxidase subunit 3 / Cytochrome c oxidase subunit 1 / Cytochrome c oxidase subunit 2 / Cytochrome b / Cytochrome c oxidase subunit 5A, mitochondrial / Cytochrome b-c1 complex subunit Rieske, mitochondrial / Cytochrome c oxidase subunit / Cytochrome c oxidase subunit 7A1, mitochondrial / Cytochrome b-c1 complex subunit 7 / Complex III subunit 9 / Cytochrome c oxidase subunit 8 / Cytochrome c oxidase subunit / Cytochrome c oxidase subunit 4 / Cytochrome b-c1 complex subunit 10 / Cytochrome b-c1 complex subunit 8 / Cytochrome c oxidase subunit 5B, mitochondrial / Cytochrome c oxidase subunit 6C / cytochrome c1, heme protein, mitochondrial / Cytochrome b-c1 complex subunit 2, mitochondrial / Cytochrome b-c1 complex subunit 1, mitochondrial / Cytochrome c oxidase subunit 7C, mitochondrial / Cytochrome c oxidase subunit 7B, mitochondrial
Similarity search - Component
Biological speciesOvis aries (sheep)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.8 Å
AuthorsLetts, J.A. / Fiedorczuk, 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: The architecture of respiratory supercomplexes.
Authors: James A Letts / Karol Fiedorczuk / Leonid A Sazanov /
Abstract: Mitochondrial electron transport chain complexes are organized into supercomplexes responsible for carrying out cellular respiration. Here we present three architectures of mammalian (ovine) ...Mitochondrial electron transport chain complexes are organized into supercomplexes responsible for carrying out cellular respiration. Here we present three architectures of mammalian (ovine) supercomplexes determined by cryo-electron microscopy. We identify two distinct arrangements of supercomplex CICIIICIV (the respirasome)-a major 'tight' form and a minor 'loose' form (resolved at the resolution of 5.8 Å and 6.7 Å, respectively), which may represent different stages in supercomplex assembly or disassembly. We have also determined an architecture of supercomplex CICIII at 7.8 Å resolution. All observed density can be attributed to the known 80 subunits of the individual complexes, including 132 transmembrane helices. The individual complexes form tight interactions that vary between the architectures, with complex IV subunit COX7a switching contact from complex III to complex I. The arrangement of active sites within the supercomplex may help control reactive oxygen species production. To our knowledge, these are the first complete architectures of the dominant, physiologically relevant state of the electron transport chain.
History
DepositionApr 1, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 21, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2016Group: Derived calculations
Revision 1.2Oct 5, 2016Group: Database references
Revision 1.3Aug 2, 2017Group: Data collection / Structure summary / Category: em_software / entity / Item: _em_software.name / _entity.pdbx_description
Revision 1.4Dec 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 1.5Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_validate_chiral
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
A: COMPLEX I ND3
B: COMPLEX I PSST/NDUFS7
C: COMPLEX I 30KDA/NDUFS3
D: COMPLEX I 49KDA/NDUFS2
E: COMPLEX I 24KDA/NDUFV2
F: COMPLEX I 51KDA/NDUFV1
G: COMPLEX I 75KDA/NDUFS1
H: COMPLEX I ND1
I: COMPLEX I TYKY/NDUFS8
J: COMPLEX I ND6
K: COMPLEX I ND4L
L: COMPLEX I ND5
M: COMPLEX I ND4
N: COMPLEX I ND2
O: COMPLEX I 18KDA/NDUFS6
P: COMPLEX I 13KDA/NDUFS6
Q: COMPLEX I 15KDA/NDUFS5
R: COMPLEX I MWFE/NDUFA1
S: COMPLEX I B8/NDUFA2
T: COMPLEX I B9/NDUFA3
U: COMPLEX I B13/NDUFA5
V: COMPLEX I B14/NDUFA6
W: COMPLEX I PGIV/NDUFA8
X: COMPLEX I 39KDA/NDUFA9
Y: COMPLEX I 42KDA/NDUFA10
Z: COMPLEX I B14.7/NDUFA11
a: COMPLEX I B17.2/NDUFA12
b: COMPLEX I B16.6/NDUFA13
c: COMPLEX I SDAP/NDUFAB1
d: COMPLEX I B8/NDUFA2
e: COMPLEX I SDAP/NDUFAB1
f: COMPLEX I SDAP/NDUFAB1
g: COMPLEX I B15/NDUFB4
h: COMPLEX I B18/NDUFB7
i: COMPLEX I B22/NDUFB9
j: COMPLEX I PDSW/NDUFB10
k: COMPLEX I ESSS/NDUFB11
0: COMPLEX I KFYI/NDUFC1
1: COMPLEX I B14.5B/NDUFC2
2: COMPLEX I UNKNOWN SUBUNIT FRAGMENT 1
3: COMPLEX I UNKNOWN SUBUNIT FRAGMENT 2
4: COMPLEX I UNKNOWN SUBUNIT FRAGMENT 2
5: COMPLEX I UNKNOWN SUBUNIT FRAGMENT 3
6: COMPLEX I UNKNOWN SUBUNIT FRAGMENT 4
7: COMPLEX I UNKNOWN SUBUNIT FRAGMENT 5
8: COMPLEX I UNKNOWN SUBUNIT FRAGMENT 6
9: COMPLEX I B18/NDUFB7
z: COMPLEX I B18/NDUFB7
y: COMPLEX I UNKNOWN SUBUNIT FRAGMENT 11
x: COMPLEX I UNKNOWN SUBUNIT FRAGMENT 12
w: COMPLEX I UNKNOWN SUBUNIT FRAGMENT 13
v: COMPLEX I UNKNOWN SUBUNIT FRAGMENT 14
u: COMPLEX I UNKNOWN SUBUNIT FRAGMENT 15
t: COMPLEX I UNKNOWN SUBUNIT FRAGMENT 16
AA: COMPLEX III SUBUNIT 1 / CORE 1
AB: COMPLEX III SUBUNIT 2 / CORE 2
AC: Cytochrome b
AD: COMPLEX III SUBUNIT 4 / CYTOCHROME C1
AE: Cytochrome b-c1 complex subunit Rieske, mitochondrial
AF: COMPLEX III SUBUNIT 7 / 14KDA
AG: COMPLEX III SUBUNIT 8 / QP-C
AH: Cytochrome b-c1 complex subunit 6
AI: Cytochrome b-c1 complex subunit Rieske, mitochondrial
AJ: COMPLEX III SUBUNIT 9 / 7.2KDA
AK: COMPLEX III SUBUNIT 10 / 6.4KDA
AL: COMPLEX III SUBUNIT 1 / CORE 1
AM: COMPLEX III SUBUNIT 2 / CORE 2
AN: Cytochrome b
AO: COMPLEX III SUBUNIT 4 / CYTOCHROME C1
AP: Cytochrome b-c1 complex subunit Rieske, mitochondrial
AQ: COMPLEX III SUBUNIT 7 / 14KDA
AR: COMPLEX III SUBUNIT 8 / QP-C
AS: Cytochrome b-c1 complex subunit 6
AT: Cytochrome b-c1 complex subunit Rieske, mitochondrial
AU: COMPLEX III SUBUNIT 9 / 7.2KDA
AV: COMPLEX III SUBUNIT 10 / 6.4KDA
BN: Cytochrome c oxidase subunit 1
BO: Cytochrome c oxidase subunit 2
BC: Cytochrome c oxidase subunit 3
BD: COMPLEX IV COX4
BE: COMPLEX IV COX5A
BP: COMPLEX IV COX5B
BG: Cytochrome c oxidase subunit 6A, mitochondrial
BH: COMPLEX IV COX6B1
BI: COMPLEX IV COX6C
BJ: Cytochrome c oxidase subunit 7A1, mitochondrial
BK: COMPLEX IV COX7B
BL: COMPLEX IV COX7C
BM: COMPLEX IV COX8B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,285,297109
Polymers1,276,88989
Non-polymers8,40820
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 40 types, 45 molecules ABCDEFGHIJKLMNOPQSdTUVWXYabcef...

#1: Protein COMPLEX I ND3


Mass: 8698.714 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIA
#2: Protein COMPLEX I PSST/NDUFS7


Mass: 13196.322 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIA
#3: Protein COMPLEX I 30KDA/NDUFS3


Mass: 16528.332 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIA
#4: Protein COMPLEX I 49KDA/NDUFS2


Mass: 32698.209 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIA
#5: Protein COMPLEX I 24KDA/NDUFV2


Mass: 16174.965 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIA
#6: Protein COMPLEX I 51KDA/NDUFV1


Mass: 36600.117 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIA
#7: Protein COMPLEX I 75KDA/NDUFS1


Mass: 55757.980 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIA
#8: Protein COMPLEX I ND1


Mass: 25294.037 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIA
#9: Protein COMPLEX I TYKY/NDUFS8


Mass: 14715.244 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIA
#10: Protein COMPLEX I ND6


Mass: 14570.941 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIA
#11: Protein COMPLEX I ND4L


Mass: 7932.770 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIA
#12: Protein COMPLEX I ND5


Mass: 48953.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIA
#13: Protein COMPLEX I ND4


Mass: 38740.727 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIA
#14: Protein COMPLEX I ND2


Mass: 29379.080 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIA
#15: Protein COMPLEX I 18KDA/NDUFS6


Mass: 8868.924 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIA
#16: Protein COMPLEX I 13KDA/NDUFS6


Mass: 7251.930 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIA
#17: Protein COMPLEX I 15KDA/NDUFS5


Mass: 5634.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIA
#19: Protein COMPLEX I B8/NDUFA2


Mass: 6826.406 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIA
#20: Protein COMPLEX I B9/NDUFA3


Mass: 4528.573 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIA
#21: Protein COMPLEX I B13/NDUFA5


Mass: 8188.084 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIA
#22: Protein COMPLEX I B14/NDUFA6


Mass: 9549.763 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIA
#23: Protein COMPLEX I PGIV/NDUFA8


Mass: 8783.818 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIA
#24: Protein COMPLEX I 39KDA/NDUFA9


Mass: 26315.285 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIA
#25: Protein COMPLEX I 42KDA/NDUFA10


Mass: 27421.645 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIA
#27: Protein COMPLEX I B17.2/NDUFA12


Mass: 9464.658 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIA
#28: Protein COMPLEX I B16.6/NDUFA13


Mass: 7847.665 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIA
#29: Protein COMPLEX I SDAP/NDUFAB1


Mass: 6741.301 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIA
#30: Protein COMPLEX I SDAP/NDUFAB1


Mass: 4698.783 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIA
#31: Protein COMPLEX I SDAP/NDUFAB1


Mass: 5039.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIA
#32: Protein COMPLEX I B15/NDUFB4


Mass: 11081.651 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIA
#33: Protein COMPLEX I B18/NDUFB7


Mass: 5379.623 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIA
#34: Protein COMPLEX I B22/NDUFB9


Mass: 5975.357 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIA
#36: Protein COMPLEX I ESSS/NDUFB11


Mass: 7081.720 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIA
#53: Protein Cytochrome b / Complex III subunit 3 / Complex III subunit III / Cytochrome b-c1 complex subunit 3 / Ubiquinol- ...Complex III subunit 3 / Complex III subunit III / Cytochrome b-c1 complex subunit 3 / Ubiquinol-cytochrome-c reductase complex cytochrome b subunit


Mass: 42684.602 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIA / References: UniProt: P24959
#58: Protein Cytochrome b-c1 complex subunit 6 / Complex III subunit 6 / Mitochondrial hinge protein


Mass: 7920.902 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIA / References: UniProt: B9VH04
#65: Protein COMPLEX IV COX4


Mass: 16899.340 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIA / References: UniProt: W5PPE8
#66: Protein COMPLEX IV COX5A


Mass: 12083.727 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIA / References: UniProt: W5NXT8
#67: Protein COMPLEX IV COX5B


Mass: 10670.012 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIA / References: UniProt: W5PW27
#69: Protein COMPLEX IV COX6B1


Mass: 9411.600 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIA / References: UniProt: W5P4E7
#70: Protein COMPLEX IV COX6C


Mass: 8466.968 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIA / References: UniProt: W5PXG3

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Protein/peptide , 6 types, 6 molecules Rj0BKBLBM

#18: Protein/peptide COMPLEX I MWFE/NDUFA1


Mass: 2486.056 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIA
#35: Protein/peptide COMPLEX I PDSW/NDUFB10


Mass: 3762.629 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIA
#37: Protein/peptide COMPLEX I KFYI/NDUFC1


Mass: 3081.790 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIA
#72: Protein/peptide COMPLEX IV COX7B


Mass: 5461.107 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIA / References: UniProt: W5QE72
#73: Protein/peptide COMPLEX IV COX7C


Mass: 5362.319 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIA / References: UniProt: W5Q6E1
#74: Protein/peptide COMPLEX IV COX8B


Mass: 4738.523 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIA / References: UniProt: W5PFK9

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COMPLEX I B14. ... , 2 types, 2 molecules Z1

#26: Protein COMPLEX I B14.7/NDUFA11


Mass: 10145.497 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIA
#38: Protein/peptide COMPLEX I B14.5B/NDUFC2


Mass: 2571.161 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIA

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COMPLEX I UNKNOWN SUBUNIT FRAGMENT ... , 12 types, 13 molecules 2345678yxwvut

#39: Protein/peptide COMPLEX I UNKNOWN SUBUNIT FRAGMENT 1


Mass: 3252.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIA
#40: Protein/peptide COMPLEX I UNKNOWN SUBUNIT FRAGMENT 2


Mass: 2400.951 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIA
#41: Protein/peptide COMPLEX I UNKNOWN SUBUNIT FRAGMENT 3


Mass: 2911.580 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIA
#42: Protein/peptide COMPLEX I UNKNOWN SUBUNIT FRAGMENT 4


Mass: 1805.216 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIA
#43: Protein/peptide COMPLEX I UNKNOWN SUBUNIT FRAGMENT 5


Mass: 3337.105 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIA
#44: Protein/peptide COMPLEX I UNKNOWN SUBUNIT FRAGMENT 6


Mass: 2315.846 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIA
#45: Protein/peptide COMPLEX I UNKNOWN SUBUNIT FRAGMENT 11


Mass: 3932.839 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIA
#46: Protein/peptide COMPLEX I UNKNOWN SUBUNIT FRAGMENT 12


Mass: 1124.378 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIA
#47: Protein/peptide COMPLEX I UNKNOWN SUBUNIT FRAGMENT 13


Mass: 2060.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIA
#48: Protein/peptide COMPLEX I UNKNOWN SUBUNIT FRAGMENT 14


Mass: 1549.902 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIA
#49: Protein/peptide COMPLEX I UNKNOWN SUBUNIT FRAGMENT 15


Mass: 1379.692 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIA
#50: Protein/peptide COMPLEX I UNKNOWN SUBUNIT FRAGMENT 16


Mass: 1039.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIA

-
COMPLEX III SUBUNIT ... , 7 types, 14 molecules AAALABAMADAOAFAQAGARAJAUAKAV

#51: Protein COMPLEX III SUBUNIT 1 / CORE 1


Mass: 49652.738 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIA / References: UniProt: W5Q5G6
#52: Protein COMPLEX III SUBUNIT 2 / CORE 2


Mass: 45189.773 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIA / References: UniProt: W5Q0F9
#54: Protein COMPLEX III SUBUNIT 4 / CYTOCHROME C1


Mass: 27323.277 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIA / References: UniProt: W5Q0A9
#56: Protein COMPLEX III SUBUNIT 7 / 14KDA


Mass: 12949.756 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIA / References: UniProt: W5P642
#57: Protein COMPLEX III SUBUNIT 8 / QP-C


Mass: 8884.331 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIA / References: UniProt: W5PUP9
#60: Protein COMPLEX III SUBUNIT 9 / 7.2KDA


Mass: 6937.975 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIA / References: UniProt: W5P6B2
#61: Protein COMPLEX III SUBUNIT 10 / 6.4KDA


Mass: 5932.946 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIA / References: UniProt: W5PSD1

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Cytochrome b-c1 complex subunit Rieske, ... , 2 types, 4 molecules AEAPAIAT

#55: Protein Cytochrome b-c1 complex subunit Rieske, mitochondrial / COMPLEX III SUBUNIT 5 / RIESKE ISP


Mass: 21654.607 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIA / References: UniProt: W5P2X9, quinol-cytochrome-c reductase
#59: Protein Cytochrome b-c1 complex subunit Rieske, mitochondrial / COMPLEX III SUBUNIT 11 / 8KDA


Mass: 5824.802 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIA / References: UniProt: W5P2X9, quinol-cytochrome-c reductase

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Cytochrome c oxidase subunit ... , 5 types, 5 molecules BNBOBCBGBJ

#62: Protein Cytochrome c oxidase subunit 1 / Cytochrome c oxidase polypeptide I / COMPLEX IV COX1


Mass: 57075.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIA / References: UniProt: O78749, cytochrome-c oxidase
#63: Protein Cytochrome c oxidase subunit 2 / Cytochrome c oxidase polypeptide II / COMPLEX IV COX2


Mass: 26015.426 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIA / References: UniProt: O78750
#64: Protein Cytochrome c oxidase subunit 3 / Cytochrome c oxidase polypeptide III / COMPLEX IV COX3


Mass: 29655.195 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIA / References: UniProt: O21619
#68: Protein Cytochrome c oxidase subunit 6A, mitochondrial / Cytochrome c oxidase polypeptide VIa / COMPLEX IV COX6A2


Mass: 9538.775 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIA / References: UniProt: W5PI52
#71: Protein Cytochrome c oxidase subunit 7A1, mitochondrial / COMPLEX IV COX7A2


Mass: 6535.508 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIA / References: UniProt: W5P5H0

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Non-polymers , 6 types, 20 molecules

#75: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


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


Mass: 175.820 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe2S2
#77: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#78: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#79: Chemical ChemComp-HEA / HEME-A


Mass: 852.837 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C49H56FeN4O6
#80: Chemical ChemComp-CUA / DINUCLEAR COPPER ION


Mass: 127.092 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu2

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Details

Has protein modificationY

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Experimental details

-
Experiment

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

-
Sample preparation

Component
IDNameTypeDetailsEntity IDParent-IDSource
1tight respirasomeCOMPLEXSupercomplex I-III2-IV#1-#760NATURAL
2Complex ICOMPLEXNADH-ubiquinone oxidoreductase#1-#521NATURAL
3Complex IIICOMPLEXcytochrom bc1 complex#53-#631NATURAL
4Complex IVCOMPLEXCytochrome c oxidase#64-#761NATURAL
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
111.64 MDaNO
220.96 MDaNO
330.48 MDaNO
440.20 MDaNO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Ovis aries (sheep)9940
32Ovis aries (sheep)9940
43Ovis aries (sheep)9940
54Ovis aries (sheep)9940
Buffer solutionpH: 7.7
Buffer component
IDConc.NameFormulaBuffer-ID
1100 mMsodium chlorideNaCl1
220 mMHEPESC8H18N2O4S1
30.1 %DigitoninC56H92O291
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Single particles dispersed in digitonin
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: 100 % / Chamber temperature: 277 K / Details: Blotted 32 seconds

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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: 47000 X / Calibrated magnification: 81935 X / Nominal defocus max: 5000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 4 sec. / Electron dose: 34 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k) / Num. of grids imaged: 3 / Num. of real images: 1608
Details: Images collected in movie mode with 17 frames per second
Image scansSampling size: 14 µm / Width: 4096 / Height: 4096 / Movie frames/image: 69 / Used frames/image: 1-32

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Processing

EM software
IDNameVersionCategory
1RELION1.4particle selection
4GctfCTF correction
7UCSF Chimeramodel fitting
8Cootmodel fitting
10RELION1.4initial Euler assignment
11RELION1.4final Euler assignment
12RELION1.4classification
13RELION1.43D reconstruction
14PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 67650
3D reconstructionResolution: 5.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 18379 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: BACKBONE TRACE / Space: REAL
RefinementHighest resolution: 5.8 Å

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