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- PDB-1nek: Complex II (Succinate Dehydrogenase) From E. Coli with ubiquinone... -

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Basic information

Entry
Database: PDB / ID: 1nek
TitleComplex II (Succinate Dehydrogenase) From E. Coli with ubiquinone bound
Components(Succinate dehydrogenase ...) x 4
KeywordsOXIDOREDUCTASE/ELECTRON TRANSPORT / membrane protein / oxygen respiratory chain / OXIDOREDUCTASE-ELECTRON TRANSPORT COMPLEX
Function / homology
Function and homology information


succinate dehydrogenase activity / respiratory chain complex II (succinate dehydrogenase) / succinate dehydrogenase (quinone) activity / succinate dehydrogenase / cytochrome complex assembly / aerobic electron transport chain / anaerobic respiration / 3 iron, 4 sulfur cluster binding / ubiquinone binding / iron-sulfur cluster binding ...succinate dehydrogenase activity / respiratory chain complex II (succinate dehydrogenase) / succinate dehydrogenase (quinone) activity / succinate dehydrogenase / cytochrome complex assembly / aerobic electron transport chain / anaerobic respiration / 3 iron, 4 sulfur cluster binding / ubiquinone binding / iron-sulfur cluster binding / tricarboxylic acid cycle / aerobic respiration / respiratory electron transport chain / 2 iron, 2 sulfur cluster binding / flavin adenine dinucleotide binding / 4 iron, 4 sulfur cluster binding / electron transfer activity / heme binding / metal ion binding / membrane / plasma membrane
Similarity search - Function
Succinate dehydrogenase, hydrophobic membrane anchor / succinate dehydrogenase protein domain / Succinate dehydrogenase, cytochrome b subunit, conserved site / Succinate dehydrogenase cytochrome b subunit signature 1. / Succinate dehydrogenase cytochrome b subunit signature 2. / Fumarate reductase/succinate dehydrogenase, transmembrane subunit / Succinate dehydrogenase, cytochrome b556 subunit / Succinate dehydrogenase, flavoprotein subunit / Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal domain / Succinate dehydrogenase/fumarate reductase type B, transmembrane subunit ...Succinate dehydrogenase, hydrophobic membrane anchor / succinate dehydrogenase protein domain / Succinate dehydrogenase, cytochrome b subunit, conserved site / Succinate dehydrogenase cytochrome b subunit signature 1. / Succinate dehydrogenase cytochrome b subunit signature 2. / Fumarate reductase/succinate dehydrogenase, transmembrane subunit / Succinate dehydrogenase, cytochrome b556 subunit / Succinate dehydrogenase, flavoprotein subunit / Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal domain / Succinate dehydrogenase/fumarate reductase type B, transmembrane subunit / Succinate dehydrogenase/Fumarate reductase transmembrane subunit / Alpha-helical ferredoxin / Fumarate Reductase Iron-sulfur Protein; Chain B, domain 2 / Succinate dehydrogenase/fumarate reductase, flavoprotein subunit / Fumarate reductase/succinate dehydrogenase, FAD-binding site / Fumarate reductase / succinate dehydrogenase FAD-binding site. / 3 helical TM bundles of succinate and fumarate reductases / Fumarate reductase/succinate dehydrogenase, transmembrane subunit / : / 4Fe-4S dicluster domain / Succinate dehydrogenase/fumarate reductase iron-sulphur protein / FAD-dependent oxidoreductase SdhA/FrdA/AprA / Succinate dehydogenase/fumarate reductase N-terminal / 2Fe-2S iron-sulfur cluster binding domain / Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal / Fumarate reductase flavoprotein C-term / Flavocytochrome C3; Chain A, domain 1 / Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain / Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal domain superfamily / Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain superfamily / FAD-dependent oxidoreductase 2, FAD binding domain / Rhinovirus 14, subunit 4 / FAD binding domain / Alpha-helical ferredoxin / Beta-grasp domain / Beta-grasp domain superfamily / FAD/NAD(P)-binding domain / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / FAD/NAD(P)-binding domain / 2Fe-2S ferredoxin-like superfamily / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Few Secondary Structures / Irregular / Ubiquitin-like (UB roll) / Roll / Alpha-Beta Complex / Up-down Bundle / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
CARDIOLIPIN / Chem-EPH / FE3-S4 CLUSTER / FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / PROTOPORPHYRIN IX CONTAINING FE / OXALOACETATE ION / IRON/SULFUR CLUSTER / UBIQUINONE-2 / Succinate dehydrogenase iron-sulfur subunit ...CARDIOLIPIN / Chem-EPH / FE3-S4 CLUSTER / FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / PROTOPORPHYRIN IX CONTAINING FE / OXALOACETATE ION / IRON/SULFUR CLUSTER / UBIQUINONE-2 / Succinate dehydrogenase iron-sulfur subunit / Succinate dehydrogenase flavoprotein subunit / Succinate dehydrogenase hydrophobic membrane anchor subunit / Succinate dehydrogenase cytochrome b556 subunit
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 Å
AuthorsYankovskaya, V. / Horsefield, R. / Tornroth, S. / Luna-Chavez, C. / Miyoshi, H. / Leger, C. / Byrne, B. / Cecchini, G. / Iwata, S.
CitationJournal: Science / Year: 2003
Title: Architecture of succinate dehydrogenase and reactive oxygen species generation.
Authors: Yankovskaya, V. / Horsefield, R. / Tornroth, S. / Luna-Chavez, C. / Miyoshi, H. / Leger, C. / Byrne, B. / Cecchini, G. / Iwata, S.
History
DepositionDec 11, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 25, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 600HETEROGEN THE HET GROUP CDN WAS NAMED CARDIOLIPIN WHICH IS A GENERIC NAME FOR THIS TYPE OF LIPID. ...HETEROGEN THE HET GROUP CDN WAS NAMED CARDIOLIPIN WHICH IS A GENERIC NAME FOR THIS TYPE OF LIPID. THE 4 TAILS OF THE MOLECULE ARE DISORDERED IN THE STRUCTURE AND THEIR EXACT LENGTH CAN NOT ASCERTAINED MAKING IT DIFFICULT TO ASSIGN AN EXACT NAME.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Succinate dehydrogenase flavoprotein subunit
B: Succinate dehydrogenase iron-sulfur protein
C: Succinate dehydrogenase cytochrome b-556 subunit
D: Succinate dehydrogenase hydrophobic membrane anchor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,10815
Polymers118,4914
Non-polymers4,61611
Water2,522140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19390 Å2
ΔGint-193 kcal/mol
Surface area39860 Å2
MethodPISA
2
A: Succinate dehydrogenase flavoprotein subunit
B: Succinate dehydrogenase iron-sulfur protein
C: Succinate dehydrogenase cytochrome b-556 subunit
D: Succinate dehydrogenase hydrophobic membrane anchor protein
hetero molecules

A: Succinate dehydrogenase flavoprotein subunit
B: Succinate dehydrogenase iron-sulfur protein
C: Succinate dehydrogenase cytochrome b-556 subunit
D: Succinate dehydrogenase hydrophobic membrane anchor protein
hetero molecules

A: Succinate dehydrogenase flavoprotein subunit
B: Succinate dehydrogenase iron-sulfur protein
C: Succinate dehydrogenase cytochrome b-556 subunit
D: Succinate dehydrogenase hydrophobic membrane anchor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)369,32345
Polymers355,47412
Non-polymers13,84933
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-y+2,x-y+1,z1
crystal symmetry operation3_675-x+y+1,-x+2,z1
Buried area65760 Å2
ΔGint-624 kcal/mol
Surface area112010 Å2
MethodPISA
3
A: Succinate dehydrogenase flavoprotein subunit
B: Succinate dehydrogenase iron-sulfur protein
C: Succinate dehydrogenase cytochrome b-556 subunit
D: Succinate dehydrogenase hydrophobic membrane anchor protein
hetero molecules

A: Succinate dehydrogenase flavoprotein subunit
B: Succinate dehydrogenase iron-sulfur protein
C: Succinate dehydrogenase cytochrome b-556 subunit
D: Succinate dehydrogenase hydrophobic membrane anchor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)246,21530
Polymers236,9828
Non-polymers9,23322
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_565x-y+2/3,-y+4/3,-z+1/31
Buried area40260 Å2
ΔGint-402 kcal/mol
Surface area78260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.8, 138.8, 521.9
Angle α, β, γ (deg.)90.0, 90.0, 120.0
Int Tables number155
Space group name H-MH32
DetailsThe biological assembly is a trimer.

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Components

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Succinate dehydrogenase ... , 4 types, 4 molecules ABCD

#1: Protein Succinate dehydrogenase flavoprotein subunit


Mass: 64502.766 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: SDHA OR B0723 OR Z0877 OR ECS0748 / Plasmid: pfas / Production host: Escherichia coli (E. coli)
References: UniProt: P0AC41, EC: 1.3.99.1, succinate dehydrogenase
#2: Protein Succinate dehydrogenase iron-sulfur protein


Mass: 26800.912 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: SDHB OR B0724 / Plasmid: pfas / Production host: Escherichia coli (E. coli)
References: UniProt: P07014, EC: 1.3.99.1, succinate dehydrogenase
#3: Protein Succinate dehydrogenase cytochrome b-556 subunit


Mass: 14313.100 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: SDHC OR CYBA OR B0721 OR Z0875 OR ECS0746 / Plasmid: pfas / Production host: Escherichia coli (E. coli) / References: UniProt: P69054
#4: Protein Succinate dehydrogenase hydrophobic membrane anchor protein


Mass: 12874.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: SDHD OR B0722 / Plasmid: pfas / Production host: Escherichia coli (E. coli) / References: UniProt: P0AC44

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Non-polymers , 11 types, 151 molecules

#5: Chemical ChemComp-OAA / OXALOACETATE ION


Mass: 131.064 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H3O5
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#7: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#8: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2
#9: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#10: Chemical ChemComp-F3S / FE3-S4 CLUSTER


Mass: 295.795 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe3S4
#11: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#12: Chemical ChemComp-CDN / CARDIOLIPIN


Mass: 1151.511 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C58H120O17P2
#13: Chemical ChemComp-EPH / L-ALPHA-PHOSPHATIDYL-BETA-OLEOYL-GAMMA-PALMITOYL-PHOSPHATIDYLETHANOLAMINE


Mass: 709.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C39H68NO8P / Comment: phospholipid*YM
#14: Chemical ChemComp-UQ2 / UBIQUINONE-2


Mass: 318.407 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H26O4
#15: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.08 Å3/Da / Density % sol: 69.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.2
Details: Tris-HCl, CaCl2, PEG 400, BaCl2, ethylene glycol, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.0081 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 8, 2002
RadiationMonochromator: Si 111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0081 Å / Relative weight: 1
ReflectionResolution: 2.6→40 Å / Num. all: 59763 / Num. obs: 53727 / % possible obs: 89.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.9 % / Rsym value: 0.076
Reflection shellResolution: 2.6→2.69 Å / Rsym value: 0.408 / % possible all: 90

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
CNSrefinement
RefinementMethod to determine structure: MAD / Resolution: 2.6→40 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.289 504 random
Rwork0.247 --
obs0.247 53727 -
all-60059 -
Refinement stepCycle: LAST / Resolution: 2.6→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8297 0 261 140 8698
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d21.3
X-RAY DIFFRACTIONc_improper_angle_d1

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