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Crystal structure of porcine heart mitochondrial complex II with an empty quinone-binding pocket

Source organism: Sus scrofa
Biochemical function: electron transfer activity
Biological process: tricarboxylic acid cycle
Cellular component: membrane

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EC 1.3.5.1: Succinate dehydrogenase (quinone)

Reaction catalysed:
Succinate + a quinone = fumarate + a quinol
Systematic name:
Succinate:quinone oxidoreductase
Alternative Name(s):
  • Complex II
  • SDH
  • Succinate dehydrogenase (ubiquinone)
  • Succinate dehydrogenase complex
  • Succinate:ubiquinone oxidoreductase
  • Succinic dehydrogenase

GO terms

Biochemical function:
Biological process:
Cellular component:

Sequence families

Pfam Protein families (Pfam)
PF05328
Domain description: CybS, succinate dehydrogenase cytochrome B small subunit
Occurring in:
  1. Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial
The deposited structure of PDB entry 3aef contains 1 copy of Pfam domain PF05328 (CybS, succinate dehydrogenase cytochrome B small subunit) in Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial. Showing 1 copy in chain D.

PF01127
Domain description: Succinate dehydrogenase/Fumarate reductase transmembrane subunit
Occurring in:
  1. Succinate dehydrogenase cytochrome b560 subunit, mitochondrial
The deposited structure of PDB entry 3aef contains 1 copy of Pfam domain PF01127 (Succinate dehydrogenase/Fumarate reductase transmembrane subunit) in Succinate dehydrogenase cytochrome b560 subunit, mitochondrial. Showing 1 copy in chain C.

PF13534
Domain description: 4Fe-4S dicluster domain
Occurring in:
  1. Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial
The deposited structure of PDB entry 3aef contains 1 copy of Pfam domain PF13534 (4Fe-4S dicluster domain) in Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial. Showing 1 copy in chain B.

PF13085
Domain description: 2Fe-2S iron-sulfur cluster binding domain
Occurring in:
  1. Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial
The deposited structure of PDB entry 3aef contains 1 copy of Pfam domain PF13085 (2Fe-2S iron-sulfur cluster binding domain) in Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial. Showing 1 copy in chain B.

PF02910
Domain description: Fumarate reductase flavoprotein C-term
Occurring in:
  1. Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial
The deposited structure of PDB entry 3aef contains 1 copy of Pfam domain PF02910 (Fumarate reductase flavoprotein C-term) in Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial. Showing 1 copy in chain A.

PF00890
Domain description: FAD binding domain
Occurring in:
  1. Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial
The deposited structure of PDB entry 3aef contains 1 copy of Pfam domain PF00890 (FAD binding domain) in Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial. Showing 1 copy in chain A.

InterPro InterPro annotations
IPR034804
Domain description: Fumarate reductase/succinate dehydrogenase, transmembrane subunit
Occurring in:
  1. Succinate dehydrogenase cytochrome b560 subunit, mitochondrial
  2. Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial
IPR014314
Domain description: Succinate dehydrogenase, cytochrome b556 subunit
Occurring in:
  1. Succinate dehydrogenase cytochrome b560 subunit, mitochondrial
IPR007992
Domain description: Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, CybS
Occurring in:
  1. Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial
IPR018495
Domain description: Succinate dehydrogenase, cytochrome b subunit, conserved site
Occurring in:
  1. Succinate dehydrogenase cytochrome b560 subunit, mitochondrial
IPR001041
Domain description: 2Fe-2S ferredoxin-type iron-sulfur binding domain
Occurring in:
  1. Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial
IPR027477
Domain description: Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain superfamily
Occurring in:
  1. Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial
IPR036188
Domain description: FAD/NAD(P)-binding domain superfamily
Occurring in:
  1. Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial
IPR000701
Domain description: Succinate dehydrogenase/fumarate reductase type B, transmembrane subunit
Occurring in:
  1. Succinate dehydrogenase cytochrome b560 subunit, mitochondrial
IPR017900
Domain description: 4Fe-4S ferredoxin, iron-sulphur binding, conserved site
Occurring in:
  1. Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial
IPR017896
Domain description: 4Fe-4S ferredoxin-type, iron-sulphur binding domain
Occurring in:
  1. Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial
IPR009051
Domain description: Alpha-helical ferredoxin
Occurring in:
  1. Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial
IPR006058
Domain description: 2Fe-2S ferredoxin, iron-sulphur binding site
Occurring in:
  1. Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial
IPR004489
Domain description: Succinate dehydrogenase/fumarate reductase iron-sulphur protein
Occurring in:
  1. Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial
IPR025192
Domain description: Succinate dehydogenase/fumarate reductase N-terminal
Occurring in:
  1. Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial
IPR036010
Domain description: 2Fe-2S ferredoxin-like superfamily
Occurring in:
  1. Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial
IPR012675
Domain description: Beta-grasp domain superfamily
Occurring in:
  1. Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial
IPR015939
Domain description: Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal
Occurring in:
  1. Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial
IPR037099
Domain description: Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal domain superfamily
Occurring in:
  1. Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial
IPR003952
Domain description: Fumarate reductase/succinate dehydrogenase, FAD-binding site
Occurring in:
  1. Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial
IPR014006
Domain description: Succinate dehydrogenase/fumarate reductase, flavoprotein subunit
Occurring in:
  1. Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial
IPR003953
Domain description: FAD-dependent oxidoreductase 2, FAD binding domain
Occurring in:
  1. Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial
IPR011281
Domain description: Succinate dehydrogenase, flavoprotein subunit
Occurring in:
  1. Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial
IPR030664
Domain description: FAD-dependent oxidoreductase SdhA/FrdA/AprA
Occurring in:
  1. Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial

Structure domains

CATH CATH domains
1.20.1300.10
Class: Mainly Alpha
Architecture: Up-down Bundle
Topology: 3 helical TM bundles of succinate and fumarate reductases
Homology: Fumarate reductase/succinate dehydrogenase, transmembrane subunit
Occurring in:
  1. Succinate dehydrogenase cytochrome b560 subunit, mitochondrial
  2. Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial
The deposited structure of PDB entry 3aef contains 1 copy of CATH domain 1.20.1300.10 (3 helical TM bundles of succinate and fumarate reductases) in Succinate dehydrogenase cytochrome b560 subunit, mitochondrial. Showing 1 copy in chain C.
The deposited structure of PDB entry 3aef contains 1 copy of CATH domain 1.20.1300.10 (3 helical TM bundles of succinate and fumarate reductases) in Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial. Showing 1 copy in chain D.
3.50.50.60
Class: Alpha Beta
Architecture: 3-Layer(bba) Sandwich
Topology: FAD/NAD(P)-binding domain
Homology: FAD/NAD(P)-binding domain
Occurring in:
  1. Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial
The deposited structure of PDB entry 3aef contains 1 copy of CATH domain 3.50.50.60 (FAD/NAD(P)-binding domain) in Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial. Showing 1 copy in chain A.
1.20.5.540
Class: Mainly Alpha
Architecture: Up-down Bundle
Topology: Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homology: Single helix bin
Occurring in:
  1. Succinate dehydrogenase cytochrome b560 subunit, mitochondrial
The deposited structure of PDB entry 3aef contains 1 copy of CATH domain 1.20.5.540 (Single alpha-helices involved in coiled-coils or other helix-helix interfaces) in Succinate dehydrogenase cytochrome b560 subunit, mitochondrial. Showing 1 copy in chain C.
1.10.1060.10
Class: Mainly Alpha
Architecture: Orthogonal Bundle
Topology: Fumarate Reductase Iron-sulfur Protein; Chain B, domain 2
Homology: Alpha-helical ferredoxin
Occurring in:
  1. Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial
The deposited structure of PDB entry 3aef contains 1 copy of CATH domain 1.10.1060.10 (Fumarate Reductase Iron-sulfur Protein; Chain B, domain 2) in Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial. Showing 1 copy in chain B.
3.10.20.30
Class: Alpha Beta
Architecture: Roll
Topology: Ubiquitin-like (UB roll)
Homology: Ubiquitin-like (UB roll)
Occurring in:
  1. Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial
The deposited structure of PDB entry 3aef contains 1 copy of CATH domain 3.10.20.30 (Ubiquitin-like (UB roll)) in Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial. Showing 1 copy in chain B.
4.10.80.40
Class: Few Secondary Structures
Architecture: Irregular
Topology: Rhinovirus 14, subunit 4
Homology: succinate dehydrogenase protein domain
Occurring in:
  1. Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial
The deposited structure of PDB entry 3aef contains 1 copy of CATH domain 4.10.80.40 (Rhinovirus 14, subunit 4) in Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial. Showing 1 copy in chain A.
1.20.58.100
Class: Mainly Alpha
Architecture: Up-down Bundle
Topology: Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homology: Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal domain
Occurring in:
  1. Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial
The deposited structure of PDB entry 3aef contains 1 copy of CATH domain 1.20.58.100 (Methane Monooxygenase Hydroxylase; Chain G, domain 1) in Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial. Showing 1 copy in chain A.
3.90.700.10
Class: Alpha Beta
Architecture: Alpha-Beta Complex
Topology: Flavocytochrome C3; Chain A, domain 1
Homology: Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain
Occurring in:
  1. Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial
The deposited structure of PDB entry 3aef contains 1 copy of CATH domain 3.90.700.10 (Flavocytochrome C3; Chain A, domain 1) in Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial. Showing 1 copy in chain A.

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