2H88

Avian Mitochondrial Respiratory Complex II at 1.8 Angstrom Resolution

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.179 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history. 


Literature

Crystallographic studies of the binding of ligands to the dicarboxylate site of Complex II, and the identity of the ligand in the

Huang, L.S., Shen, J.T., Wang, A.C., Berry, E.A.

(null) Biochim Biophys Acta 1757: 1073-1083

  • DOI: https://doi.org/10.1016/j.bbabio.2006.06.015
  • Primary Citation of Related Structures:  
    2H88, 2H89

  • PubMed Abstract: 

    • Mitochondrial Complex II (succinate:ubiquinone oxidoreductase) is purified in a partially inactivated state, which can be activated by removal of tightly bound oxaloacetate (E.B. Kearney, et al., Biochem. Biophys. Res. Commun. 49 1115-1121). We crystallized Complex II in the presence of oxaloacetate or with the endogenous inhibitor bound ...

    Mitochondrial Complex II (succinate:ubiquinone oxidoreductase) is purified in a partially inactivated state, which can be activated by removal of tightly bound oxaloacetate (E.B. Kearney, et al., Biochem. Biophys. Res. Commun. 49 1115-1121). We crystallized Complex II in the presence of oxaloacetate or with the endogenous inhibitor bound. The structure showed a ligand essentially identical to the "malate-like intermediate" found in Shewanella Flavocytochrome c crystallized with fumarate (P. Taylor, et al., Nat. Struct. Biol. 6 1108-1112) Crystallization of Complex II in the presence of excess fumarate also gave the malate-like intermediate or a mixture of that and fumarate at the active site. In order to more conveniently monitor the occupation state of the dicarboxylate site, we are developing a library of UV/Vis spectral effects induced by binding different ligands to the site. Treatment with fumarate results in rapid development of the fumarate difference spectrum and then a very slow conversion into a species spectrally similar to the OAA-liganded complex. Complex II is known to be capable of oxidizing malate to the enol form of oxaloacetate (Y.O. Belikova, et al., Biochim. Biophys. Acta 936 1-9). The observations above suggest it may also be capable of interconverting fumarate and malate. It may be useful for understanding the mechanism and regulation of the enzyme to identify the malate-like intermediate and its pathway of formation from oxaloacetate or fumarate.

    Related Citations: 
    • 3-nitropropionic acid is a suicide inhibitor of mitochondrial respiration that, upon oxidation by complex II, forms a covalent adduct with a catalytic base arginine in the active site of the enzyme.
      Huang, L.S., Sun, G., Cobessi, D., Wang, A.C., Shen, J.T., Tung, E.Y., Anderson, V.E., Berry, E.A.
      (2006) J Biol Chem 281: 5965
    • Crystallization of mitochondrial respiratory complex II from chicken heart: a membrane-protein complex diffracting to 2.0 A
      Huang, L.S., Borders, T.M., Shen, J.T., Wang, C.J., Berry, E.A.
      (2005) Acta Crystallogr D Biol Crystallogr 61: 380
    • Crystal structure of mitochondrial respiratory membrane protein complex II.
      Sun, F., Huo, X., Zhai, Y., Wang, A., Xu, J., Su, D., Bartlam, M., Rao, Z.
      (2005) Cell 121: 1043
    Organizational Affiliation: 

    Physical Biosciences Division, Lawrence Berkeley National Lab., MS 64-0121, 1 Cyclotron Road, Berkeley CA 94720, USA.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SUCCINATE DEHYDROGENASE FLAVOPROTEIN SUBUNITA,
E [auth N]		621Gallus gallusMutation(s): 0 
Gene Names: SDHA
EC: 1.3.5.1
Membrane Entity: Yes 
UniProt
Find proteins for Q9YHT1 (Gallus gallus)
Explore Q9YHT1 
Go to UniProtKB:  Q9YHT1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9YHT1
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Succinate dehydrogenase Ip subunitB,
F [auth O]		252Gallus gallusMutation(s): 0 
Gene Names: SDHB
EC: 1.3.5.1
Membrane Entity: Yes 
UniProt
Find proteins for Q9YHT2 (Gallus gallus)
Explore Q9YHT2 
Go to UniProtKB:  Q9YHT2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9YHT2
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
SUCCINATE DEHYDROGENASE CYTOCHROME B, LARGE SUBUNITC,
G [auth P]		140Gallus gallusMutation(s): 0 
EC: 1.3.5.1
Membrane Entity: Yes 
UniProt
Find proteins for D0VWW3 (Gallus gallus)
Explore D0VWW3 
Go to UniProtKB:  D0VWW3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD0VWW3
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Succinate dehydrogenase cytochrome B, small subunitD,
H [auth Q]		103Gallus gallusMutation(s): 0 
Gene Names: SDHD, RCJMB04_23p7
EC: 1.3.5.1
Membrane Entity: Yes 
UniProt
Find proteins for Q5ZIS0 (Gallus gallus)
Explore Q5ZIS0 
Go to UniProtKB:  Q5ZIS0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5ZIS0
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 11 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD
Download Ideal Coordinates CCD File 
K [auth A],
ZA [auth N]		FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N		 Ligand Interaction
HEM
Query on HEM
Download Ideal Coordinates CCD File 
CA [auth C],
VB [auth P]		PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L		 Ligand Interaction
SF4
Query on SF4
Download Ideal Coordinates CCD File 
NB [auth O],
U [auth B]		IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC		 Ligand Interaction
F3S
Query on F3S
Download Ideal Coordinates CCD File 
OB [auth O],
V [auth B]		FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-MZMDZPPWAW		 Ligand Interaction
BHG
Query on BHG
Download Ideal Coordinates CCD File 
BA [auth C],
UB [auth P]		hexyl beta-D-galactopyranoside
C12 H24 O6
JVAZJLFFSJARQM-YBXAARCKSA-N		 Ligand Interaction
FES
Query on FES
Download Ideal Coordinates CCD File 
MB [auth O],
T [auth B]		FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N		 Ligand Interaction
TEO
Query on TEO
Download Ideal Coordinates CCD File 
AB [auth N],
L [auth A]		MALATE LIKE INTERMEDIATE
C4 H4 O5
QFBHYOKSQPPXHZ-UWTATZPHSA-L		 Ligand Interaction
GOL
Query on GOL
Download Ideal Coordinates CCD File 
AA [auth B],
TB [auth O]		GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
AZI
Query on AZI
Download Ideal Coordinates CCD File 
J [auth A],
YA [auth N]		AZIDE ION
N3
IVRMZWNICZWHMI-UHFFFAOYSA-N		 Ligand Interaction
K
Query on K
Download Ideal Coordinates CCD File 
I [auth A],
LB [auth O],
S [auth B],
XA [auth N]		POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N		 Ligand Interaction
UNL
Query on UNL
Download Ideal Coordinates CCD File 
AC [auth P]
BB [auth N]
BC [auth P]
CB [auth N]
CC [auth P]
AC [auth P],
BB [auth N],
BC [auth P],
CB [auth N],
CC [auth P],
DA [auth C],
DB [auth N],
DC [auth P],
EA [auth C],
EB [auth N],
EC [auth P],
FA [auth C],
FB [auth N],
FC [auth P],
GA [auth C],
GB [auth N],
GC [auth P],
HA [auth C],
HB [auth N],
HC [auth P],
IA [auth C],
IB [auth N],
IC [auth P],
JA [auth C],
JB [auth N],
JC [auth P],
KA [auth C],
KB [auth N],
KC [auth Q],
LA [auth C],
LC [auth Q],
M [auth A],
MA [auth D],
MC [auth Q],
N [auth A],
NA [auth D],
NC [auth Q],
O [auth A],
OA [auth D],
OC [auth Q],
P [auth A],
PA [auth D],
PB [auth O],
PC [auth Q],
Q [auth A],
QA [auth D],
QB [auth O],
R [auth A],
RA [auth D],
RB [auth O],
SA [auth D],
SB [auth O],
TA [auth D],
UA [auth D],
VA [auth D],
W [auth B],
WA [auth D],
WB [auth P],
X [auth B],
XB [auth P],
Y [auth B],
YB [auth P],
Z [auth B],
ZB [auth P]
Unknown ligand
NPYPAHLBTDXSSS-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.179 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 119.972α = 90
b = 199.391β = 90.35
c = 68.063γ = 90
Software Package:
Software NamePurpose
CNSrefinement
BOSdata collection
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-06-20
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Database references, Derived calculations, Structure summary
  • Version 1.5: 2023-08-30
    Changes: Data collection, Database references, Refinement description, Structure summary