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- PDB-2acz: Complex II (Succinate Dehydrogenase) From E. Coli with Atpenin A5... -

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Basic information

Entry
Database: PDB / ID: 2acz
TitleComplex II (Succinate Dehydrogenase) From E. Coli with Atpenin A5 inhibitor co-crystallized at the ubiquinone binding site
Components(Succinate dehydrogenase ...) x 4
KeywordsOxidoreductase/Electron transport / MEMBRANE PROTEIN / Aerobic reparatory Complex II / SQR / succinate:ubiquinone oxidoreductase / AA5 / AT5 / Atpenin A5 / SDH / succinate dehydrogenase / Oxidoreductase-Electron transport COMPLEX
Function / homology
Function and homology information


: / : / succinate dehydrogenase activity / succinate dehydrogenase / succinate dehydrogenase (quinone) activity / cytochrome complex assembly / oxidoreductase activity, acting on the CH-CH group of donors / aerobic electron transport chain / anaerobic respiration / 3 iron, 4 sulfur cluster binding ...: / : / succinate dehydrogenase activity / succinate dehydrogenase / succinate dehydrogenase (quinone) activity / cytochrome complex assembly / oxidoreductase activity, acting on the CH-CH group of donors / aerobic electron transport chain / anaerobic respiration / 3 iron, 4 sulfur cluster binding / iron-sulfur cluster binding / ubiquinone binding / tricarboxylic acid cycle / aerobic respiration / respiratory electron transport chain / electron transport chain / 2 iron, 2 sulfur cluster binding / flavin adenine dinucleotide binding / 4 iron, 4 sulfur cluster binding / membrane => GO:0016020 / electron transfer activity / heme binding / membrane / metal ion binding / plasma membrane
Similarity search - Function
Succinate dehydrogenase, hydrophobic membrane anchor / succinate dehydrogenase protein domain / Succinate dehydrogenase, cytochrome b556 subunit / Succinate dehydrogenase, cytochrome b subunit, conserved site / Succinate dehydrogenase cytochrome b subunit signature 1. / Succinate dehydrogenase cytochrome b subunit signature 2. / Succinate dehydrogenase, flavoprotein subunit / Fumarate reductase/succinate dehydrogenase, transmembrane subunit / Succinate dehydrogenase/fumarate reductase type B, transmembrane subunit / Succinate dehydrogenase/Fumarate reductase transmembrane subunit ...Succinate dehydrogenase, hydrophobic membrane anchor / succinate dehydrogenase protein domain / Succinate dehydrogenase, cytochrome b556 subunit / Succinate dehydrogenase, cytochrome b subunit, conserved site / Succinate dehydrogenase cytochrome b subunit signature 1. / Succinate dehydrogenase cytochrome b subunit signature 2. / Succinate dehydrogenase, flavoprotein subunit / Fumarate reductase/succinate dehydrogenase, transmembrane subunit / Succinate dehydrogenase/fumarate reductase type B, transmembrane subunit / Succinate dehydrogenase/Fumarate reductase transmembrane subunit / Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal domain / Alpha-helical ferredoxin / Fumarate Reductase Iron-sulfur Protein; Chain B, domain 2 / Fumarate reductase/succinate dehydrogenase, transmembrane subunit / Succinate dehydrogenase/fumarate reductase, flavoprotein subunit / Fumarate reductase/succinate dehydrogenase, FAD-binding site / FAD-dependent oxidoreductase SdhA/FrdA/AprA / Fumarate reductase / succinate dehydrogenase FAD-binding site. / 3 helical TM bundles of succinate and fumarate reductases / 4Fe-4S dicluster domain / Flavocytochrome C3; Chain A, domain 1 / Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain / Succinate dehydrogenase/fumarate reductase iron-sulphur protein / 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 / 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 / Alpha-helical ferredoxin / FAD binding domain / Rhinovirus 14, subunit 4 / Beta-grasp domain / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / FAD/NAD(P)-binding domain / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / FAD/NAD(P)-binding domain / 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 / Ubiquitin-like (UB roll) / Few Secondary Structures / Irregular / Roll / Alpha-Beta Complex / Up-down Bundle / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-AT5 / CARDIOLIPIN / FE3-S4 CLUSTER / FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / HEME B/C / OXALOACETATE ION / IRON/SULFUR CLUSTER / Succinate dehydrogenase iron-sulfur subunit / Succinate dehydrogenase flavoprotein subunit ...Chem-AT5 / CARDIOLIPIN / FE3-S4 CLUSTER / FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / HEME B/C / OXALOACETATE ION / IRON/SULFUR CLUSTER / Succinate dehydrogenase iron-sulfur subunit / Succinate dehydrogenase flavoprotein subunit / Succinate dehydrogenase hydrophobic membrane anchor 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 / FOURIER SYNTHESIS / Resolution: 3.1 Å
AuthorsHorsefield, R. / Yankovskaya, V. / Sexton, G. / Whittingham, W. / Shiomi, K. / Omura, S. / Byrne, B. / Cecchini, G. / Iwata, S.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Structural and computational analysis of the quinone-binding site of complex II (succinate-ubiquinone oxidoreductase): a mechanism of electron transfer and proton conduction during ubiquinone reduction.
Authors: Horsefield, R. / Yankovskaya, V. / Sexton, G. / Whittingham, W. / Shiomi, K. / Omura, S. / Byrne, B. / Cecchini, G. / Iwata, S.
History
DepositionJul 19, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 3, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_validate_chiral / struct_conn / 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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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 b556 subunit
D: Succinate dehydrogenase hydrophobic membrane anchor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,36712
Polymers118,4914
Non-polymers3,8768
Water00
1
A: Succinate dehydrogenase flavoprotein subunit
B: Succinate dehydrogenase iron-sulfur protein
C: Succinate dehydrogenase cytochrome b556 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 b556 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 b556 subunit
D: Succinate dehydrogenase hydrophobic membrane anchor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)367,10236
Polymers355,47412
Non-polymers11,62824
Water0
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 area63630 Å2
ΔGint-565 kcal/mol
Surface area110430 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)138.759, 138.759, 521.873
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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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) / Plasmid: pFAS / Production host: Escherichia coli (E. coli) / Strain (production host): DW35
References: UniProt: P10444, UniProt: P0AC41*PLUS, 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) / Plasmid: pFAS / Production host: Escherichia coli (E. coli) / Strain (production host): DW35 / References: UniProt: P07014, succinate dehydrogenase
#3: Protein Succinate dehydrogenase cytochrome b556 subunit / Cytochrome b-556


Mass: 14313.100 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pFAS / Production host: Escherichia coli (E. coli) / Strain (production host): DW35 / 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) / Plasmid: pFAS / Production host: Escherichia coli (E. coli) / Strain (production host): DW35 / References: UniProt: P10445, UniProt: P0AC44*PLUS

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Non-polymers , 8 types, 8 molecules

#5: Chemical ChemComp-OAA / OXALOACETATE ION


Mass: 131.064 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H3O5
#6: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


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


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


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


Mass: 295.795 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe3S4
#10: Chemical ChemComp-HEB / HEME B/C / HYBRID BETWEEN B AND C TYPE HEMES (PROTOPORPHYRIN IX CONTAINING FE)


Mass: 618.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#11: Chemical ChemComp-AT5 / 3-[(2S,4S,5R)-5,6-DICHLORO-2,4-DIMETHYL-1-OXOHEXYL]-4-HYDROXY-5,6-DIMETHOXY-2(1H)-PYRIDINONE / ATPENIN A5 / AA5


Mass: 366.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H21Cl2NO5
#12: Chemical ChemComp-CDN / CARDIOLIPIN


Mass: 1151.511 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C58H120O17P2

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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 Å3/Da / Density % sol: 68.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.2
Details: Tris-HCl, cacium chloride, Peg 400, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 170 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9393 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 10, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 3.1→40 Å / Num. all: 34954 / Num. obs: 34114 / % possible obs: 95.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.36 % / Rsym value: 0.078 / Net I/σ(I): 14.7
Reflection shellResolution: 3.1→3.16 Å / Mean I/σ(I) obs: 2 / Rsym value: 0.337 / % possible all: 86

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1NEK

1nek


Resolution: 3.1→40 Å / Cross valid method: THROUGHOUT / σ(F): -2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.308 966 Random
Rwork0.264 --
all-34954 -
obs-34114 -
Displacement parametersBiso mean: 73.7 Å2
Refinement stepCycle: LAST / Resolution: 3.1→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8297 0 224 0 8521
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcangle_it2.312
X-RAY DIFFRACTIONc_mcbond_it1.3071.5
X-RAY DIFFRACTIONc_scangle_it2.6552.5
X-RAY DIFFRACTIONc_scbond_it1.6612
LS refinement shellResolution: 3.1→3.16 Å / Rfactor Rfree: 0.429 / Rfactor Rwork: 0.376

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