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- PDB-4ytm: Crystal structure of Mitochondrial rhodoquinol-fumarate reductase... -

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Basic information

Entry
Database: PDB / ID: 4ytm
TitleCrystal structure of Mitochondrial rhodoquinol-fumarate reductase from Ascaris suum with N-biphenyl-3-yl-2-(trifluoromethyl)benzamide
Components
  • (Succinate dehydrogenase [ubiquinone] ...) x 2
  • Cytochrome b-large subunit
  • Succinate dehydrogenase flavoprotein
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / OXIDOREDUCTASE / rhodoquinol-fumarate reductase / Complex II / Inhibitor / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
Function / homology
Function and homology information


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 / 2 iron, 2 sulfur cluster binding / mitochondrial membrane / 4 iron, 4 sulfur cluster binding ...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 / 2 iron, 2 sulfur cluster binding / mitochondrial membrane / 4 iron, 4 sulfur cluster binding / electron transfer activity / mitochondrial inner membrane / heme binding / metal ion binding
Similarity search - Function
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. / Fumarate reductase/succinate dehydrogenase, transmembrane subunit / Succinate dehydrogenase, cytochrome b556 subunit / Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal domain / Succinate dehydrogenase/fumarate reductase type B, transmembrane subunit ...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. / Fumarate reductase/succinate dehydrogenase, transmembrane subunit / Succinate dehydrogenase, cytochrome b556 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 / 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 / Succinate dehydogenase/fumarate reductase N-terminal / 2Fe-2S iron-sulfur cluster binding domain / Flavocytochrome C3; Chain A, domain 1 / Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain / Rhinovirus 14, subunit 4 / Alpha-helical ferredoxin / 2Fe-2S ferredoxin, iron-sulphur binding site / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / 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 / 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
Chem-EPH / FE3-S4 CLUSTER / N-biphenyl-3-yl-2-(trifluoromethyl)benzamide / FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / PROTOPORPHYRIN IX CONTAINING FE / MALONATE ION / IRON/SULFUR CLUSTER / Succinate dehydrogenase [ubiquinone] cytochrome b large subunit, mitochondrial / Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial ...Chem-EPH / FE3-S4 CLUSTER / N-biphenyl-3-yl-2-(trifluoromethyl)benzamide / FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / PROTOPORPHYRIN IX CONTAINING FE / MALONATE ION / IRON/SULFUR CLUSTER / Succinate dehydrogenase [ubiquinone] cytochrome b large subunit, mitochondrial / Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial / Succinate dehydrogenase [ubiquinone] cytochrome b large subunit, mitochondrial / Succinate dehydrogenase [ubiquinone] cytochrome b small subunit 1, mitochondrial / :
Similarity search - Component
Biological speciesAscaris suum (pig roundworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsHarada, S. / Shiba, T. / Sato, D. / Yamamoto, A. / Nagahama, M. / Yone, A. / Inaoka, D.K. / Sakamoto, K. / Inoue, M. / Honma, T. / Kita, K.
CitationJournal: Int J Mol Sci / Year: 2015
Title: Structural Insights into the Molecular Design of Flutolanil Derivatives Targeted for Fumarate Respiration of Parasite Mitochondria
Authors: Inaoka, D.K. / Shiba, T. / Sato, D. / Balogun, E.O. / Sasaki, T. / Nagahama, M. / Oda, M. / Matsuoka, S. / Ohmori, J. / Honma, T. / Inoue, M. / Kita, K. / Harada, S.
History
DepositionMar 18, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 5, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Succinate dehydrogenase flavoprotein
B: Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial
C: Cytochrome b-large subunit
D: Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial
E: Succinate dehydrogenase flavoprotein
F: Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial
G: Cytochrome b-large subunit
H: Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)288,54623
Polymers282,4988
Non-polymers6,04715
Water00
1
A: Succinate dehydrogenase flavoprotein
B: Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial
C: Cytochrome b-large subunit
D: Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,62812
Polymers141,2494
Non-polymers3,3798
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21850 Å2
ΔGint-185.6 kcal/mol
Surface area41760 Å2
MethodPISA
2
E: Succinate dehydrogenase flavoprotein
F: Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial
G: Cytochrome b-large subunit
H: Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,91811
Polymers141,2494
Non-polymers2,6697
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19960 Å2
ΔGint-179.3 kcal/mol
Surface area42640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.654, 126.426, 220.873
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21E
12B
22F
13C
23G
14D
24H

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1112A30 - 702
2112E30 - 702
1122B33 - 303
2122F33 - 303
1134C34 - 301
2134G34 - 301
1142D28 - 201
2142H28 - 201

NCS ensembles :
ID
1
2
3
4

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.995337, 0.015184, -0.095253), (0.040205, 0.962966, -0.26661), (0.087677, -0.269196, -0.959086)-37.30445, -18.81235, -141.47034

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Components

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Protein , 2 types, 4 molecules AECG

#1: Protein Succinate dehydrogenase flavoprotein / RHODOQUINOL-FUMARATE REDUCTASE FP SUBUNIT


Mass: 71392.203 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Ascaris suum (pig roundworm) / References: UniProt: U1LRQ3
#3: Protein Cytochrome b-large subunit / RHODOQUINOL-FUMARATE REDUCTASE CYBL SUBUNIT


Mass: 21168.160 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Ascaris suum (pig roundworm) / References: UniProt: P92506, UniProt: F1LC27*PLUS

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Succinate dehydrogenase [ubiquinone] ... , 2 types, 4 molecules BFDH

#2: Protein Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial / RHODOQUINOL-FUMARATE REDUCTASE IP SUBUNIT


Mass: 31673.951 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Ascaris suum (pig roundworm) / References: UniProt: O44074, succinate dehydrogenase
#4: Protein Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial / CybS / Cytochrome b558 small subunit / Succinate-ubiquinone reductase membrane anchor subunit


Mass: 17014.932 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Ascaris suum (pig roundworm) / References: UniProt: P92507

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Non-polymers , 8 types, 15 molecules

#5: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H2O4
#6: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#7: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#8: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#9: Chemical ChemComp-F3S / FE3-S4 CLUSTER


Mass: 295.795 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe3S4
#10: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#11: Chemical ChemComp-F6A / N-biphenyl-3-yl-2-(trifluoromethyl)benzamide


Mass: 341.326 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H14F3NO
#12: 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

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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: 3.06 Å3/Da / Density % sol: 59.74 %
Crystal growTemperature: 293 K / Method: microdialysis / pH: 8.4
Details: 15% (W/V) PEG 3350, 100MM TRIS-HCL, 200MM NACL, 1MM SODIUM MALONATE, 0.06% (W/V) C12E8, 0.04% (W/V) C12M

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: Bruker DIP-6040 / Detector: IMAGE PLATE / Date: Nov 28, 2007
RadiationMonochromator: double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3.4→50 Å / Num. obs: 49409 / % possible obs: 95.6 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.136 / Net I/σ(I): 11.1
Reflection shellResolution: 3.4→3.52 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 2.7 / % possible all: 93

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
HKL-2000data processing
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YSX

4ysx


Resolution: 3.4→20 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.886 / SU B: 23.895 / SU ML: 0.383 / Cross valid method: THROUGHOUT / ESU R Free: 0.559 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.245 2350 5.1 %RANDOM
Rwork0.178 ---
obs0.182 43572 94.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 78.59 Å2
Baniso -1Baniso -2Baniso -3
1--5.96 Å20 Å20 Å2
2--4.41 Å20 Å2
3---1.54 Å2
Refinement stepCycle: LAST / Resolution: 3.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17962 0 338 0 18300
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01918776
X-RAY DIFFRACTIONr_bond_other_d0.0010.0217892
X-RAY DIFFRACTIONr_angle_refined_deg1.271.98125490
X-RAY DIFFRACTIONr_angle_other_deg0.849341155
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.23952287
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.64123.241790
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.146153130
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.53515124
X-RAY DIFFRACTIONr_chiral_restr0.0680.22764
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02120974
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024346
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A5911medium positional0.310.5
2B2503medium positional0.320.5
3C2551medium positional0.360.5
4D1227medium positional0.560.5
1A3608tight thermal6.190.5
2B1473tight thermal4.290.5
4D755tight thermal7.340.5
1A5911medium thermal6.882
2B2503medium thermal5.012
3C2551medium thermal8.242
4D1227medium thermal8.132
LS refinement shellResolution: 3.4→3.49 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 166 -
Rwork0.241 2712 -
obs--84.25 %

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