6ADQ

Respiratory Complex CIII2CIV2SOD2 from Mycobacterium smegmatis


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

An electron transfer path connects subunits of a mycobacterial respiratory supercomplex.

Gong, H.Li, J.Xu, A.Tang, Y.Ji, W.Gao, R.Wang, S.Yu, L.Tian, C.Li, J.Yen, H.Y.Man Lam, S.Shui, G.Yang, X.Sun, Y.Li, X.Jia, M.Yang, C.Jiang, B.Lou, Z.Robinson, C.V.Wong, L.L.Guddat, L.W.Sun, F.Wang, Q.Rao, Z.

(2018) Science 362

  • DOI: https://doi.org/10.1126/science.aat8923
  • Primary Citation of Related Structures:  
    6ADQ

  • PubMed Abstract: 

    We report a 3.5-angstrom-resolution cryo-electron microscopy structure of a respiratory supercomplex isolated from Mycobacterium smegmatis. It comprises a complex III dimer flanked on either side by individual complex IV subunits. Complex III and IV associate so that electrons can be transferred from quinol in complex III to the oxygen reduction center in complex IV by way of a bridging cytochrome subunit. We observed a superoxide dismutase-like subunit at the periplasmic face, which may be responsible for detoxification of superoxide formed by complex III. The structure reveals features of an established drug target and provides a foundation for the development of treatments for human tuberculosis.


  • Organizational Affiliation

    Department of Chemistry, University of Oxford, Physical and Theoretical Chemistry Laboratory, South Parks Rd, Oxford, OX1 3QZ, UK.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 2A [auth E],
M [auth Q]
341Mycolicibacterium smegmatis MC2 51Mutation(s): 0 
EC: 1.9.3.1
Membrane Entity: Yes 
UniProt
Find proteins for A0R057 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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UniProt GroupA0R057
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 1B [auth F],
N [auth R]
575Mycolicibacterium smegmatis MC2 51Mutation(s): 0 
EC: 1.9.3.1
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 3C [auth G],
O [auth S]
203Mycolicibacterium smegmatis MC2 51Mutation(s): 0 
EC: 1.9.3.1
Membrane Entity: Yes 
UniProt
Find proteins for A0R049 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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UniProt GroupA0R049
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase polypeptide 4D [auth H],
P [auth T]
139Mycolicibacterium smegmatis MC2 51Mutation(s): 0 
EC: 1.9.3.1
Membrane Entity: Yes 
UniProt
Find proteins for A0R056 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit CtaJE [auth I],
Q [auth U]
79Mycolicibacterium smegmatis MC2 51Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0R1B6 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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UniProt GroupA0R1B6
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized protein MSMEG_4692/MSMEI_4575F [auth J],
R [auth V]
157Mycolicibacterium smegmatis MC2 51Mutation(s): 0 
UniProt
Find proteins for A0R1B5 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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UniProt GroupA0R1B5
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Prokaryotic respiratory supercomplex associate factor 1 PRSAF1G [auth D],
S [auth P]
100Mycolicibacterium smegmatis MC2 51Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0QVH4 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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UniProt GroupA0QVH4
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Superoxide dismutase [Cu-Zn]H [auth Y],
T [auth Z]
236Mycolicibacterium smegmatis MC2 51Mutation(s): 0 
EC: 1.15.1.1
Membrane Entity: Yes 
UniProt
Find proteins for A0QQQ1 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
LpqE proteinI [auth K],
U [auth W]
186Mycolicibacterium smegmatis MC2 51Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0R562 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquinol-cytochrome c reductase cytochrome b subunitJ [auth B],
V [auth N]
546Mycolicibacterium smegmatis MC2 51Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0R052 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome bc1 complex cytochrome c subunitK [auth C],
W [auth O]
294Mycolicibacterium smegmatis MC2 51Mutation(s): 0 
EC: 1.10.2.2
Membrane Entity: Yes 
UniProt
Find proteins for I7FPH1 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Rieske iron-sulfur protein QcrAL [auth A],
X [auth M]
421Mycolicibacterium smegmatis MC2 51Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for I7GD61 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Small Molecules
Ligands 11 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL

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AB [auth B]
CC [auth N]
EA [auth F]
FA [auth F]
FC [auth N]
AB [auth B],
CC [auth N],
EA [auth F],
FA [auth F],
FC [auth N],
GC [auth N],
HA [auth H],
HB [auth A],
HC [auth N],
IA [auth D],
QB [auth R],
RB [auth R],
SA [auth B],
SC [auth M],
TA [auth B],
TB [auth T],
UA [auth B],
UB [auth P]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
9YF
Query on 9YF

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EB [auth C]
IB [auth A]
JB [auth A]
NA [auth K]
OC [auth O]
EB [auth C],
IB [auth A],
JB [auth A],
NA [auth K],
OC [auth O],
QC [auth M],
TC [auth M],
ZB [auth W]
(2R)-2-(hexadecanoyloxy)-3-{[(S)-hydroxy{[(1R,2R,3R,4R,5R,6S)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propyl (9S)-9-methyloctadecanoate
C44 H85 O13 P
GRDWPDVMAXODDM-LZYRCPELSA-N
HEA
Query on HEA

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AA [auth F],
BA [auth F],
MB [auth R],
NB [auth R]
HEME-A
C49 H56 Fe N4 O6
ZGGYGTCPXNDTRV-PRYGPKJJSA-L
MQ9
Query on MQ9

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FB [auth C]
IC [auth N]
JC [auth N]
KC [auth N]
LC [auth N]
FB [auth C],
IC [auth N],
JC [auth N],
KC [auth N],
LC [auth N],
PC [auth O],
WA [auth B],
XA [auth B],
YA [auth B],
ZA [auth B]
MENAQUINONE-9
C56 H80 O2
WCRXHNIUHQUASO-ABFXHILCSA-N
9Y0
Query on 9Y0

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BB [auth B]
GA [auth G]
JA [auth D]
MA [auth K]
SB [auth S]
BB [auth B],
GA [auth G],
JA [auth D],
MA [auth K],
SB [auth S],
VA [auth B],
VB [auth P],
YB [auth W]
(2R)-3-(((2-aminoethoxy)(hydroxy)phosphoryl)oxy)-2-(palmitoyloxy)propyl (E)-octadec-9-enoate
C39 H76 N O8 P
DVXMEPWDARXHCX-OTMQOFQLSA-N
HEC
Query on HEC

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CB [auth C],
DB [auth C],
MC [auth O],
NC [auth O]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
HEM
Query on HEM

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DC [auth N],
EC [auth N],
QA [auth B],
RA [auth B]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
9XX
Query on 9XX

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BC [auth W],
LA [auth Y],
PA [auth K],
XB [auth Z]
(2S)-1-(hexadecanoyloxy)propan-2-yl (10S)-10-methyloctadecanoate
C38 H74 O4
LWLNRPPCJIGPLI-ZPGRZCPFSA-N
PLM
Query on PLM

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AC [auth W],
KA [auth Y],
OA [auth K],
WB [auth Z]
PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
FES
Query on FES

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GB [auth A],
RC [auth M]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
CU
Query on CU

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CA [auth F]
DA [auth F]
KB [auth Q]
LB [auth Q]
OB [auth R]
CA [auth F],
DA [auth F],
KB [auth Q],
LB [auth Q],
OB [auth R],
PB [auth R],
Y [auth E],
Z [auth E]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (China)China2017YFC0840300
Chinese Academy of SciencesChinaXDB08020200
Ministry of Science and Technology (China)China2014CB542800
Ministry of Science and Technology (China)China2014CBA02003
National Natural Science Foundation of ChinaChina813300237
National Natural Science Foundation of ChinaChina81520108019

Revision History  (Full details and data files)

  • Version 1.0: 2018-11-14
    Type: Initial release
  • Version 1.1: 2018-12-26
    Changes: Data collection, Database references
  • Version 1.2: 2019-11-06
    Changes: Data collection, Other