9HZL | pdb_00009hzl

High resolution cryo-EM structure of human complex III in mitochondria


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.52 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural basis for late maturation steps of mitochondrial respiratory chain complex IV within the human respirasome.

Nguyen, M.D.Sierra-Magro, A.Singh, V.Khawaja, A.Timon-Gomez, A.Barrientos, A.Rorbach, J.

(2026) Nat Commun 

  • DOI: https://doi.org/10.1038/s41467-025-68274-3
  • Primary Citation of Related Structures:  
    9HZL, 9I6F, 9I7U, 9TI4

  • PubMed Abstract: 

    The mitochondrial respiratory chain comprises four multimeric complexes (CI-CIV) that drive oxidative phosphorylation by transferring electrons to oxygen and generating the proton gradient required for ATP synthesis. These complexes can associate into supercomplexes (SCs), such as the CI + CIII₂ + CIV respirasome, but how SCs form, by joining preassembled complexes or by engaging partially assembled intermediates, remains unresolved. Here, we use cryo-electron microscopy to determine high-resolution structures of native human CI + CIII₂ + CIV late-assembly intermediates. Together with biochemical analyses, these structures show that respirasome biogenesis concludes with the final maturation of CIV while it is associated with fully assembled CI and CIII₂. We identify HIGD2A as a placeholder factor within isolated and supercomplexed CIV that is replaced by subunit NDUFA4 during the last step of CIV and respirasome assembly. This mechanism suggests that placeholders such as HIGD2A act as molecular timers, preventing premature incorporation of NDUFA4 or its isoforms and ensuring the orderly progression of pre-SC particles into functional respirasomes. Since defects in CIV assembly, including NDUFA4 deficiencies, cause severe encephalomyopathies and neurodegenerative disorders, understanding the molecular architecture and assembly pathways of isolated and supercomplexed CIV offers insight into the pathogenic mechanisms underlying these conditions.


  • Organizational Affiliation
    • Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 8A,
L [auth N]
82Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000164405 
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UniProt GroupO14949
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit Rieske, mitochondrialB,
C,
M [auth O],
N [auth P]
274Homo sapiensMutation(s): 0 
EC: 7.1.1.8
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GTEx:  ENSG00000169021 
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UniProt GroupP47985
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 9D,
O [auth Q]
63Homo sapiensMutation(s): 0 
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PHAROS:  Q9UDW1
GTEx:  ENSG00000184076 
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UniProt GroupQ9UDW1
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 6, mitochondrialE,
P [auth R]
91Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000173660 
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UniProt GroupP07919
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 7F,
Q [auth S]
111Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000156467 
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UniProt GroupP14927
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 10G,
R [auth T]
56Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000127540 
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UniProt GroupO14957
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c1, heme protein, mitochondrialH,
S [auth U]
325Homo sapiensMutation(s): 0 
EC: 7.1.1.8
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GTEx:  ENSG00000179091 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome bI [auth J],
T [auth V]
380Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000198727 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 2, mitochondrialJ [auth K],
U [auth W]
453Homo sapiensMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b-c1 complex subunit 1, mitochondrialK [auth L],
V [auth Y]
480Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000010256 
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Small Molecules
Ligands 9 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL (Subject of Investigation/LOI)
Query on CDL

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BA [auth G]
DA [auth H]
HA [auth J]
KA [auth J]
OA [auth T]
BA [auth G],
DA [auth H],
HA [auth J],
KA [auth J],
OA [auth T],
SA [auth U],
W [auth A],
YA [auth V],
ZA [auth Y]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
U10 (Subject of Investigation/LOI)
Query on U10

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IA [auth J],
JA [auth J],
VA [auth V],
WA [auth V]
UBIQUINONE-10
C59 H90 O4
ACTIUHUUMQJHFO-UPTCCGCDSA-N
PC1
Query on PC1

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NA [auth P]1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C44 H88 N O8 P
NRJAVPSFFCBXDT-HUESYALOSA-N
PLX
Query on PLX

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AA [auth D],
PA [auth T]
(9R,11S)-9-({[(1S)-1-HYDROXYHEXADECYL]OXY}METHYL)-2,2-DIMETHYL-5,7,10-TRIOXA-2LAMBDA~5~-AZA-6LAMBDA~5~-PHOSPHAOCTACOSANE-6,6,11-TRIOL
C42 H89 N O8 P
YVNJQRQLQPWVSQ-IWSHAHEXSA-O
3PE
Query on 3PE

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AB [auth Y]
LA [auth L]
QA [auth U]
X [auth C]
XA [auth V]
AB [auth Y],
LA [auth L],
QA [auth U],
X [auth C],
XA [auth V],
Z [auth C]
1,2-Distearoyl-sn-glycerophosphoethanolamine
C41 H82 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-N
PEE
Query on PEE

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GA [auth J]1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
C41 H78 N O8 P
MWRBNPKJOOWZPW-NYVOMTAGSA-N
HEC (Subject of Investigation/LOI)
Query on HEC

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CA [auth H],
RA [auth U]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
HEM (Subject of Investigation/LOI)
Query on HEM

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EA [auth J],
FA [auth J],
TA [auth V],
UA [auth V]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
FES
Query on FES

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MA [auth P],
Y [auth C]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.52 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21rc1_5156

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Knut and Alice Wallenberg FoundationSweden023405053

Revision History  (Full details and data files)

  • Version 1.0: 2025-11-12
    Type: Initial release
  • Version 1.1: 2026-01-21
    Changes: Data collection, Database references