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- PDB-5j8k: Architecture of supercomplex I-III2 -

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Basic information

Entry
Database: PDB / ID: 5j8k
TitleArchitecture of supercomplex I-III2
Components
  • (COMPLEX I B14. ...) x 2
  • (COMPLEX I UNKNOWN SUBUNIT FRAGMENT ...) x 14
  • (COMPLEX III SUBUNIT ...Coenzyme Q – cytochrome c reductase) x 7
  • (Cytochrome b-c1 complex subunit Rieske, ...) x 2
  • 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 SDAP/NDUFAB1
  • COMPLEX I TYKY/NDUFS8
  • Cytochrome b-c1 complex subunit 6
  • Cytochrome b
KeywordsMEMBRANE PROTEIN / membrane protein complex / supercomplex
Function / homology
Function and homology information


respiratory chain complex III / mitochondrial respiratory chain complex III / mitochondrial respiratory chain complex IV / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / respirasome / respiratory electron transport chain / 2 iron, 2 sulfur cluster binding / metalloendopeptidase activity ...respiratory chain complex III / mitochondrial respiratory chain complex III / mitochondrial respiratory chain complex IV / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / respirasome / respiratory electron transport chain / 2 iron, 2 sulfur cluster binding / metalloendopeptidase activity / mitochondrial inner membrane / electron transfer activity / membrane => GO:0016020 / ubiquitin protein ligase binding / heme 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 / Ubiquinol-cytochrome c reductase 8kDa, N-terminal / Ubiquinol-cytochrome c reductase 8 kDa, N-terminal / Globular protein, non-globular alpha/beta subunit / Cytochrome b-c1 complex, subunit 6 / Cytochrome b-c1 complex subunit 8 / UcrQ family / Cytochrome bc1 complex subunit Rieske, transmembrane domain superfamily ...Cytochrome b-c1 complex subunit 10 / Single alpha-helix domain superfamily / Ubiquinol-cytochrome C reductase complex, 6.4kD protein / Ubiquinol-cytochrome c reductase 8kDa, N-terminal / Ubiquinol-cytochrome c reductase 8 kDa, N-terminal / Globular protein, non-globular alpha/beta subunit / Cytochrome b-c1 complex, subunit 6 / Cytochrome b-c1 complex subunit 8 / UcrQ family / Cytochrome bc1 complex subunit Rieske, transmembrane domain 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 9 / Cytochrome b-c1 complex subunit 8 superfamily / Cytochrome b-c1 complex subunit 9 superfamily / Ubiquinol-cytochrome C reductase, UQCRX/QCR9 like / Cytochrome b-c1 complex subunit Rieske, transmembrane domain / Ubiquinol cytochrome reductase transmembrane region / 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 / : / : / Ubiquinol-cytochrome c reductase, iron-sulphur subunit / 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 b/b6, C-terminal domain superfamily / Cytochrome b/b6/petB / Rieske iron-sulphur protein, C-terminal / Cytochrome b/b6, N-terminal / Cytochrome b/b6-like domain superfamily / Cytochrome b/b6 N-terminal region profile. / Di-haem cytochrome, transmembrane / Rieske iron-sulphur protein / Peptidase M16, C-terminal / Peptidase M16 inactive domain / Peptidase M16, N-terminal / Insulinase (Peptidase family M16) / Metalloenzyme, LuxS/M16 peptidase-like / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / PROTOPORPHYRIN IX CONTAINING FE / IRON/SULFUR CLUSTER / Cytochrome b-c1 complex subunit 6 / Cytochrome b / Cytochrome b-c1 complex subunit Rieske, mitochondrial / Cytochrome b-c1 complex subunit 7 / Complex III subunit 9 / Cytochrome b-c1 complex subunit 10 / Cytochrome b-c1 complex subunit 8 ...FE2/S2 (INORGANIC) CLUSTER / PROTOPORPHYRIN IX CONTAINING FE / IRON/SULFUR CLUSTER / Cytochrome b-c1 complex subunit 6 / Cytochrome b / Cytochrome b-c1 complex subunit Rieske, mitochondrial / Cytochrome b-c1 complex subunit 7 / Complex III subunit 9 / Cytochrome b-c1 complex subunit 10 / Cytochrome b-c1 complex subunit 8 / cytochrome c1, heme protein, mitochondrial / Cytochrome b-c1 complex subunit 2, mitochondrial / Cytochrome b-c1 complex subunit 1, mitochondrial
Similarity search - Component
Biological speciesOvis aries (sheep)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.8 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 8, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 21, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2016Group: Database references
Revision 1.2Aug 2, 2017Group: Data collection / Experimental preparation / Structure summary
Category: em_sample_support / em_software / entity
Item: _em_sample_support.grid_type / _em_software.name / _entity.pdbx_description
Revision 1.3Dec 11, 2019Group: Advisory / Other / Category: atom_sites / cell / pdbx_unobs_or_zero_occ_atoms
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

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Structure visualization

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Structure viewerMolecule:
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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 B15/NDUFB4
f: COMPLEX I B18/NDUFB7
g: COMPLEX I B22/NDUFB9
h: COMPLEX I PDSW/NDUFB10
i: COMPLEX I ESSS/NDUFB11
j: COMPLEX I KFYI/NDUFC1
k: COMPLEX I B14.5B/NDUFC2
0: COMPLEX I UNKNOWN SUBUNIT FRAGMENT 1
1: COMPLEX I UNKNOWN SUBUNIT FRAGMENT 2
2: COMPLEX I UNKNOWN SUBUNIT FRAGMENT 3
3: COMPLEX I UNKNOWN SUBUNIT FRAGMENT 4
4: COMPLEX I UNKNOWN SUBUNIT FRAGMENT 4
5: COMPLEX I UNKNOWN SUBUNIT FRAGMENT 5
6: COMPLEX I UNKNOWN SUBUNIT FRAGMENT 6
7: COMPLEX I UNKNOWN SUBUNIT FRAGMENT 7
8: COMPLEX I UNKNOWN SUBUNIT FRAGMENT 8
9: COMPLEX I PDSW/NDUFB10
z: COMPLEX I PDSW/NDUFB10
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,080,95292
Polymers1,074,44076
Non-polymers6,51216
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1

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Components

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Protein , 34 types, 39 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: MITOCHONDRIAMitochondrion
#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: MITOCHONDRIAMitochondrion
#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: MITOCHONDRIAMitochondrion
#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: MITOCHONDRIAMitochondrion
#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: MITOCHONDRIAMitochondrion
#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: MITOCHONDRIAMitochondrion
#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: MITOCHONDRIAMitochondrion
#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: MITOCHONDRIAMitochondrion
#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: MITOCHONDRIAMitochondrion
#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: MITOCHONDRIAMitochondrion
#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: MITOCHONDRIAMitochondrion
#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: MITOCHONDRIAMitochondrion
#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: MITOCHONDRIAMitochondrion
#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: MITOCHONDRIAMitochondrion
#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: MITOCHONDRIAMitochondrion
#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: MITOCHONDRIAMitochondrion
#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: MITOCHONDRIAMitochondrion
#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: MITOCHONDRIAMitochondrion
#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: MITOCHONDRIAMitochondrion
#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: MITOCHONDRIAMitochondrion
#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: MITOCHONDRIAMitochondrion
#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: MITOCHONDRIAMitochondrion
#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: MITOCHONDRIAMitochondrion
#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: MITOCHONDRIAMitochondrion
#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: MITOCHONDRIAMitochondrion
#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: MITOCHONDRIAMitochondrion
#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: MITOCHONDRIAMitochondrion
#30: Protein COMPLEX I B15/NDUFB4


Mass: 4698.783 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIAMitochondrion
#31: Protein COMPLEX I B18/NDUFB7


Mass: 5039.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIAMitochondrion
#32: Protein COMPLEX I B22/NDUFB9


Mass: 11081.651 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIAMitochondrion
#33: Protein COMPLEX I PDSW/NDUFB10


Mass: 5379.623 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIAMitochondrion
#34: Protein COMPLEX I ESSS/NDUFB11


Mass: 5975.357 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIAMitochondrion
#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: MITOCHONDRIAMitochondrion / 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: MITOCHONDRIAMitochondrion / References: UniProt: B9VH04

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Protein/peptide , 2 types, 2 molecules Rj

#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: MITOCHONDRIAMitochondrion
#35: Protein/peptide COMPLEX I KFYI/NDUFC1


Mass: 3762.629 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIAMitochondrion

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

#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: MITOCHONDRIAMitochondrion
#36: Protein COMPLEX I B14.5B/NDUFC2


Mass: 7081.720 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIAMitochondrion

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COMPLEX I UNKNOWN SUBUNIT FRAGMENT ... , 14 types, 15 molecules 012345678yxwvut

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


Mass: 3081.790 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIAMitochondrion
#38: Protein/peptide COMPLEX I UNKNOWN SUBUNIT FRAGMENT 2


Mass: 2571.161 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIAMitochondrion
#39: Protein/peptide COMPLEX I UNKNOWN SUBUNIT FRAGMENT 3


Mass: 3252.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIAMitochondrion
#40: Protein/peptide COMPLEX I UNKNOWN SUBUNIT FRAGMENT 4


Mass: 2400.951 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIAMitochondrion
#41: Protein/peptide COMPLEX I UNKNOWN SUBUNIT FRAGMENT 5


Mass: 2911.580 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIAMitochondrion
#42: Protein/peptide COMPLEX I UNKNOWN SUBUNIT FRAGMENT 6


Mass: 1805.216 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIAMitochondrion
#43: Protein/peptide COMPLEX I UNKNOWN SUBUNIT FRAGMENT 7


Mass: 3337.105 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIAMitochondrion
#44: Protein/peptide COMPLEX I UNKNOWN SUBUNIT FRAGMENT 8


Mass: 2315.846 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIAMitochondrion
#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: MITOCHONDRIAMitochondrion
#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: MITOCHONDRIAMitochondrion
#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: MITOCHONDRIAMitochondrion
#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: MITOCHONDRIAMitochondrion
#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: MITOCHONDRIAMitochondrion
#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: MITOCHONDRIAMitochondrion

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

#51: Protein COMPLEX III SUBUNIT 1 / CORE 1 / Coenzyme Q – cytochrome c reductase


Mass: 49385.414 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: HEART / Organelle: MITOCHONDRIAMitochondrion / References: UniProt: W5Q5G6
#52: Protein COMPLEX III SUBUNIT 2 / CORE 2 / Coenzyme Q – cytochrome c reductase


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


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


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


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


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


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


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


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

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Non-polymers , 3 types, 16 molecules

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


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


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


Mass: 616.487 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C34H32FeN4O4

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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: Supercomplex I-III2 / Type: COMPLEX
Details: Supercomplex formed by respiratory complexes I and III
Entity ID: #1-#62 / Source: NATURAL
Molecular weightValue: 1.4 MDa / Experimental value: NO
Source (natural)Organism: Ovis aries (sheep) / Organ: Heart / Organelle: mitochondria
Buffer solutionpH: 7.7
Buffer component
IDConc.NameFormulaBuffer-ID
1100 mMNaClSodium chloride1
220 mMHEPES1
30.1 %Digitonin1
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 FIELDBright-field microscopy / Nominal magnification: 47000 X / Calibrated magnification: 81395 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 were 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: 7.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 9844 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: BACKBONE TRACE / Space: REAL

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