9BPB | pdb_00009bpb

Tethered respiratory III2IV2 supercomplex from Saccharomyces cerevisiae


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.57 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Differential substrate utilization by yeast respiratory supercomplexes

Eldeeb, M.H.Cosner, Z.Mays, J.Carlstrom, A.Rodriguez, G.Berndtsson, J.Ott, M.Fontanesi, F.

To be published.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 1, mitochondrialA,
V [auth K]
457Saccharomyces cerevisiae W303Mutation(s): 0 
UniProt
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 2, mitochondrialB,
W [auth L]
368Saccharomyces cerevisiae W303Mutation(s): 0 
UniProt
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome bC,
X [auth M]
385Saccharomyces cerevisiae W303Mutation(s): 0 
EC: 7.1.1.8
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c1, heme protein, mitochondrialD,
Y [auth N]
309Saccharomyces cerevisiae W303Mutation(s): 0 
EC: 7.1.1.8
UniProt
Find proteins for P07143 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit Rieske, mitochondrialE,
Z [auth O]
215Saccharomyces cerevisiae W303Mutation(s): 0 
EC: 7.1.1.8
UniProt
Find proteins for P08067 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 6, mitochondrialAA [auth P],
F
147Saccharomyces cerevisiae W303Mutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 7, mitochondrial,Cytochrome c oxidase subunit 8, mitochondrialBA [auth Q],
G
183Saccharomyces cerevisiae W303Mutation(s): 0 
Gene Names: QCR7CRO1UCR7YDR529CD9719.32COX8YLR395CL8084.14
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 8, mitochondrialCA [auth R],
H
94Saccharomyces cerevisiae W303Mutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 9, mitochondrialDA [auth S],
I
66Saccharomyces cerevisiae W303Mutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 10, mitochondrialEA [auth T],
J
77Saccharomyces cerevisiae W303Mutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 1FA [auth m],
K [auth a]
534Saccharomyces cerevisiae W303Mutation(s): 0 
EC: 7.1.1.9
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 2GA [auth n],
L [auth b]
251Saccharomyces cerevisiae W303Mutation(s): 0 
EC: 7.1.1.9
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 3HA [auth o],
M [auth c]
269Saccharomyces cerevisiae W303Mutation(s): 0 
EC: 7.1.1.9
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 4, mitochondrialIA [auth p],
N [auth d]
155Saccharomyces cerevisiae W303Mutation(s): 0 
UniProt
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 5A, mitochondrialJA [auth q],
O [auth e]
153Saccharomyces cerevisiae W303Mutation(s): 0 
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 6, mitochondrialKA [auth r],
P [auth f]
148Saccharomyces cerevisiae W303Mutation(s): 0 
UniProt
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 7, mitochondrialLA [auth s],
Q [auth g]
60Saccharomyces cerevisiae W303Mutation(s): 0 
UniProt
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 9, mitochondrialMA [auth u],
R [auth i]
59Saccharomyces cerevisiae W303Mutation(s): 0 
UniProt
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 12, mitochondrialNA [auth v],
S [auth j]
83Saccharomyces cerevisiae W303Mutation(s): 0 
UniProt
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 13, mitochondrialOA [auth w],
T [auth k]
129Saccharomyces cerevisiae W303Mutation(s): 0 
UniProt
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 26, mitochondrialPA [auth x],
U [auth l]
66Saccharomyces cerevisiae W303Mutation(s): 0 
UniProt
Find proteins for Q2V2P9 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Small Molecules
Ligands 19 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL

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BB [auth D]
DB [auth E]
EB [auth H]
IC [auth N]
KC [auth O]
BB [auth D],
DB [auth E],
EB [auth H],
IC [auth N],
KC [auth O],
LC [auth R],
QA [auth A],
YB [auth K]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
HEA
Query on HEA

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JB [auth a],
LB [auth a],
QC [auth m],
SC [auth m]
HEME-A
C49 H56 Fe N4 O6
ZGGYGTCPXNDTRV-PRYGPKJJSA-L
CN3
Query on CN3

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OB [auth a],
VC [auth m]
(2R,5S,11R,14R)-5,8,11-trihydroxy-2-(nonanoyloxy)-5,11-dioxido-16-oxo-14-[(propanoyloxy)methyl]-4,6,10,12,15-pentaoxa-5,11-diphosphanonadec-1-yl undecanoate
C36 H68 O17 P2
FMNZIMGRZPIVKW-XWHIBYANSA-N
PCF
Query on PCF

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DD [auth w]
ED [auth x]
FB [auth H]
HB [auth I]
MC [auth R]
DD [auth w],
ED [auth x],
FB [auth H],
HB [auth I],
MC [auth R],
OC [auth S],
WB [auth k],
XB [auth l]
1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE
C40 H80 N O8 P
KILNVBDSWZSGLL-KXQOOQHDSA-N
PTY
Query on PTY

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AD [auth n]
BD [auth o]
GB [auth I]
MB [auth a]
NC [auth S]
AD [auth n],
BD [auth o],
GB [auth I],
MB [auth a],
NC [auth S],
RB [auth b],
TB [auth b],
TC [auth m],
UB [auth c],
YC [auth n]
PHOSPHATIDYLETHANOLAMINE
C40 H80 N O8 P
NJGIRBISCGPRPF-KXQOOQHDSA-N
8PE
Query on 8PE

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AC [auth M],
SA [auth C]
(2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(tetradecanoyloxy)propyl octadecanoate
C37 H74 N O8 P
RFJQNULIDFTTLL-PGUFJCEWSA-N
PEF
Query on PEF

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GC [auth N]
IB [auth J]
PB [auth a]
PC [auth T]
WC [auth m]
GC [auth N],
IB [auth J],
PB [auth a],
PC [auth T],
WC [auth m],
ZA [auth D]
DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE
C37 H74 N O8 P
SLKDGVPOSSLUAI-PGUFJCEWSA-N
CN5
Query on CN5

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TA [auth C](5S,11R)-5,8,11-trihydroxy-5,11-dioxido-17-oxo-4,6,10,12,16-pentaoxa-5,11-diphosphaoctadec-1-yl pentadecanoate
C26 H52 O13 P2
UKWPDXFRXMWSMQ-VWLOTQADSA-N
HEC
Query on HEC

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AB [auth D],
HC [auth N]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
HEM
Query on HEM

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CC [auth M],
EC [auth M],
VA [auth C],
XA [auth C]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
9PE
Query on 9PE

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DC [auth M],
WA [auth C]
(1R)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(heptanoyloxy)methyl]ethyl octadecanoate
C30 H60 N O8 P
RWBMCOYSJCETON-MUUNZHRXSA-N
UQ6
Query on UQ6

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BC [auth M],
FC [auth M],
UA [auth C],
YA [auth C]
5-(3,7,11,15,19,23-HEXAMETHYL-TETRACOSA-2,6,10,14,18,22-HEXAENYL)-2,3-DIMETHOXY-6-METHYL-BENZENE-1,4-DIOL
C39 H60 O4
DYOSCPIQEYRQEO-XQCASOQKSA-N
6PH
Query on 6PH

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RA [auth C],
ZB [auth M]
(1R)-2-(phosphonooxy)-1-[(tridecanoyloxy)methyl]ethyl pentadecanoate
C31 H61 O8 P
UOOPRMYYAWVCCZ-GDLZYMKVSA-N
FES
Query on FES

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CB [auth E],
JC [auth O]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
CUA
Query on CUA

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SB [auth b],
ZC [auth n]
DINUCLEAR COPPER ION
Cu2
ALKZAGKDWUSJED-UHFFFAOYSA-N
ZN
Query on ZN

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CD [auth p],
VB [auth d]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CU
Query on CU

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KB [auth a],
RC [auth m]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
CA
Query on CA

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NB [auth a],
UC [auth m]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG
Query on MG

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QB [auth b],
XC [auth n]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.57 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTCoot0.9.8.7
RECONSTRUCTIONcryoSPARC4.2

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Defense (DOD, United States)United StatesW911NF-21-1-0359

Revision History  (Full details and data files)

  • Version 1.0: 2025-05-21
    Type: Initial release