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Basic information

Entry
Database: PDB / ID: 3aeg
TitleCrystal structure of porcine heart mitochondrial complex II bound with N-Biphenyl-3-yl-2-iodo-benzamide
Components
  • (Succinate dehydrogenase [ubiquinone] ...) x 3
  • Succinate dehydrogenase cytochrome b560 subunit, mitochondrial
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / respiratory complex II / inhibitors / Electron transport / Iron / Iron-sulfur / Metal-binding / Mitochondrion / Mitochondrion inner membrane / Oxidoreductase / Transit peptide / Transport / Tricarboxylic acid cycle / Heme / Transmembrane / FAD-binding protein / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
Function / homology
Function and homology information


Maturation of TCA enzymes and regulation of TCA cycle / Citric acid cycle (TCA cycle) / Oxidoreductases; Acting on the CH-OH group of donors; With a quinone or similar compound as acceptor / respiratory chain complex II (succinate dehydrogenase) / : / mitochondrial electron transport, succinate to ubiquinone / succinate dehydrogenase (quinone) activity / succinate dehydrogenase / 3 iron, 4 sulfur cluster binding / ubiquinone binding ...Maturation of TCA enzymes and regulation of TCA cycle / Citric acid cycle (TCA cycle) / Oxidoreductases; Acting on the CH-OH group of donors; With a quinone or similar compound as acceptor / respiratory chain complex II (succinate dehydrogenase) / : / mitochondrial electron transport, succinate to ubiquinone / succinate dehydrogenase (quinone) activity / succinate dehydrogenase / 3 iron, 4 sulfur cluster binding / ubiquinone binding / tricarboxylic acid cycle / aerobic respiration / respiratory electron transport chain / mitochondrial membrane / 2 iron, 2 sulfur cluster binding / flavin adenine dinucleotide binding / 4 iron, 4 sulfur cluster binding / mitochondrial inner membrane / electron transfer activity / heme binding / metal ion binding
Similarity search - Function
Single helix bin / Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, CybS / CybS, succinate dehydrogenase cytochrome B small subunit / 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. / Succinate dehydrogenase, cytochrome b556 subunit / Succinate dehydrogenase, flavoprotein subunit / Fumarate reductase/succinate dehydrogenase, transmembrane subunit ...Single helix bin / Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, CybS / CybS, succinate dehydrogenase cytochrome B small subunit / 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. / Succinate dehydrogenase, cytochrome b556 subunit / 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 / Fumarate reductase / succinate dehydrogenase FAD-binding site. / FAD-dependent oxidoreductase SdhA/FrdA/AprA / 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 / 2Fe-2S ferredoxin, iron-sulphur binding site / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / 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 / FAD/NAD(P)-binding domain / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / 3-Layer(bba) Sandwich / Ubiquitin-like (UB roll) / FAD/NAD(P)-binding domain superfamily / Few Secondary Structures / Irregular / Roll / Alpha-Beta Complex / Up-down Bundle / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
N-biphenyl-3-yl-2-iodobenzamide / FE3-S4 CLUSTER / FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / PROTOPORPHYRIN IX CONTAINING FE / IRON/SULFUR CLUSTER / Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial / Succinate dehydrogenase cytochrome b560 subunit, mitochondrial / Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial / Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.27 Å
AuthorsHarada, S. / Sasaki, T. / Shindo, M. / Kido, Y. / Inaoka, D.K. / Omori, J. / Osanai, A. / Sakamoto, K. / Mao, J. / Matsuoka, S. ...Harada, S. / Sasaki, T. / Shindo, M. / Kido, Y. / Inaoka, D.K. / Omori, J. / Osanai, A. / Sakamoto, K. / Mao, J. / Matsuoka, S. / Inoue, M. / Honma, T. / Tanaka, A. / Kita, K.
CitationJournal: To be Published
Title: Crystal structure of porcine heart mitochondrial complex II bound with N-Biphenyl-3-yl-2-iodo-benzamide
Authors: Harada, S. / Sasaki, T. / Shindo, M. / Kido, Y. / Inaoka, D.K. / Omori, J. / Osanai, A. / Sakamoto, K. / Mao, J. / Matsuoka, S. / Inoue, M. / Honma, T. / Tanaka, A. / Kita, K.
History
DepositionFeb 4, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 11, 2017Group: Refinement description / Category: software
Revision 1.3Nov 1, 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 / 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
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial
B: Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial
C: Succinate dehydrogenase cytochrome b560 subunit, mitochondrial
D: Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,94310
Polymers123,3184
Non-polymers2,6256
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13020 Å2
ΔGint-51 kcal/mol
Surface area42410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.862, 83.874, 294.862
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Succinate dehydrogenase [ubiquinone] ... , 3 types, 3 molecules ABD

#1: Protein Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial / Flavoprotein subunit of complex II / Fp


Mass: 68313.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: heart / Tissue: muscle / References: UniProt: Q0QF01, succinate dehydrogenase
#2: Protein Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial / Iron-sulfur subunit of complex II / Ip


Mass: 28764.217 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: heart / Tissue: muscle / References: UniProt: Q007T0, succinate dehydrogenase
#4: Protein Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial / Succinate-ubiquinone oxidoreductase cytochrome b small subunit / CybS / Succinate-ubiquinone ...Succinate-ubiquinone oxidoreductase cytochrome b small subunit / CybS / Succinate-ubiquinone reductase membrane anchor subunit / QPs3 / CII-4 / Succinate dehydrogenase complex subunit D


Mass: 10936.758 Da / Num. of mol.: 1 / Fragment: residues 57-159 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: heart / Tissue: muscle / References: UniProt: A5GZW8

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Protein , 1 types, 1 molecules C

#3: Protein Succinate dehydrogenase cytochrome b560 subunit, mitochondrial / Succinate-ubiquinone oxidoreductase cytochrome B large subunit / CYBL


Mass: 15304.081 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: heart / Tissue: muscle / References: UniProt: D0VWV4

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Non-polymers , 6 types, 6 molecules

#5: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


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


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


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


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


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#10: Chemical ChemComp-11J / N-biphenyl-3-yl-2-iodobenzamide


Mass: 399.225 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H14INO

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Details

Compound detailsTHESE COMPLEX FORMS MITOCHONDRIAL RESPIRATORY COMPLEX II.
Has protein modificationY
Sequence detailsTHE SEQUENCE OF CHAIN D IS REFERRED IN REF 2 IN A5GZW8, UNIPROT.

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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: 3.6 Å3/Da / Density % sol: 65.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 25mM HEPES-NAOH, 7% PEG 4000, 200mM Sucrose, 100mM NaCl, 10mM CaCl2, 0.5mM EDTA, 3% 1,6-haxanediol, 0.5% n-decyl-beta-D-maltoside, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: MAC Science DIP-2040B / Detector: IMAGE PLATE / Date: Jul 1, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3.27→50 Å / Num. obs: 22430 / % possible obs: 78.8 % / Redundancy: 4 % / Rmerge(I) obs: 0.096 / Χ2: 0.977 / Net I/σ(I): 9.728
Reflection shellResolution: 3.27→3.39 Å / Redundancy: 4 % / Rmerge(I) obs: 0.581 / Mean I/σ(I) obs: 1.46 / Num. unique all: 2268 / Χ2: 1.054 / % possible all: 81.6

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4 Å49.15 Å
Translation4 Å49.15 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ZOY

1zoy


Resolution: 3.27→49.14 Å / Cor.coef. Fo:Fc: 0.904 / Cor.coef. Fo:Fc free: 0.834 / WRfactor Rfree: 0.317 / WRfactor Rwork: 0.255 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.755 / SU B: 59.185 / SU ML: 0.49 / SU R Cruickshank DPI: 0.548 / SU Rfree: 0.716 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.716 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.312 1148 5.1 %RANDOM
Rwork0.244 ---
obs0.248 22368 78.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 120.04 Å2 / Biso mean: 114.014 Å2 / Biso min: 54.8 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 3.27→49.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8480 0 137 0 8617
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0228824
X-RAY DIFFRACTIONr_angle_refined_deg0.911.98811974
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.26651088
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.80723.413375
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.512151469
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.5321559
X-RAY DIFFRACTIONr_chiral_restr0.060.21303
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0216651
X-RAY DIFFRACTIONr_mcbond_it0.1351.55411
X-RAY DIFFRACTIONr_mcangle_it0.24528676
X-RAY DIFFRACTIONr_scbond_it0.14633413
X-RAY DIFFRACTIONr_scangle_it0.2554.53281
LS refinement shellResolution: 3.272→3.357 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.422 92 -
Rwork0.362 1584 -
all-1676 -
obs-1676 81.6 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.7114-0.1496-0.53190.7756-0.08562.60320.0009-0.0763-0.0269-0.083-0.02690.0356-0.26090.11330.02590.1903-0.04890.00660.33760.03410.4033-17.0405-17.963517.8625
22.1718-0.2174-0.6870.8857-1.04771.66510.2336-0.09790.70320.5910.11380.0824-0.8685-0.0547-0.34740.8924-0.11470.01980.0940.04010.602-19.61298.32825.183
31.597-0.1608-0.10210.8938-0.46822.75570.018-0.04480.0898-0.1148-0.0297-0.1259-0.37640.37540.01170.2112-0.14810.02750.35890.07780.3683-4.2321-10.951911.3041
42.22890.2336-0.66041.78631.2581.3949-0.0316-0.50360.3139-0.00270.1396-0.15-0.1320.6524-0.10810.1661-0.2333-0.0680.74580.09260.3873-3.033-11.545946.0061
51.3275-0.5261-1.03660.5661-0.14894.0786-0.09330.20970.04850.1022-0.04730.19470.2472-0.33790.14070.2035-0.00720.03590.3052-0.01890.4857-29.5822-24.505640.1976
62.86950.02170.24760.7987-0.75261.1657-0.2550.18950.19090.1893-0.257-0.30310.30390.61950.5120.72540.24220.09580.3830.19390.4056-16.5434-28.027853.2439
71.73210.3593-1.19482.8293-0.09953.76460.1184-0.2628-0.11650.4116-0.1752-0.21-0.3716-0.00440.05680.43630.0010.11010.2439-0.02130.52-34.5285-21.714177.2879
81.99961.17621.41822.43320.01691.4843-0.2326-0.1171-0.04690.27120.09790.0833-0.4582-0.28080.13470.70110.08970.17060.3511-0.10860.5381-43.1387-31.200466.9851
94.4603-0.2475-2.8070.11780.27879.6358-0.2338-0.1589-0.6705-0.0536-0.143-0.0251-0.3839-0.0350.37670.5784-0.00430.23330.14830.09810.5714-35.6359-37.756875.3607
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 255
2X-RAY DIFFRACTION2A256 - 353
3X-RAY DIFFRACTION3A354 - 622
4X-RAY DIFFRACTION4B9 - 105
5X-RAY DIFFRACTION5B106 - 247
6X-RAY DIFFRACTION6C6 - 52
7X-RAY DIFFRACTION7C53 - 143
8X-RAY DIFFRACTION8D35 - 87
9X-RAY DIFFRACTION9D88 - 136

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