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- PDB-4yt0: Crystal structure of Mitochondrial rhodoquinol-fumarate reductase... -

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Basic information

Entry
Database: PDB / ID: 4yt0
TitleCrystal structure of Mitochondrial rhodoquinol-fumarate reductase from Ascaris suum with 2-methyl-N-[3-(1-methylethoxy)phenyl]benzamide.
Components
  • (Succinate dehydrogenase [ubiquinone] ...) x 2
  • Cytochrome b-large subunit
  • Succinate dehydrogenase flavoprotein
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / rhodoquinol-fumarate reductase / Complex II / 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 / mitochondrial membrane / 2 iron, 2 sulfur cluster binding / 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 / mitochondrial membrane / 2 iron, 2 sulfur cluster binding / 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 / Fumarate reductase/succinate dehydrogenase, transmembrane subunit / : / 3 helical TM bundles of succinate and fumarate reductases / 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 / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / FAD/NAD(P)-binding domain / 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. / 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
FE3-S4 CLUSTER / FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / PROTOPORPHYRIN IX CONTAINING FE / MALONATE ION / 2-methyl-N-[3-(1-methylethoxy)phenyl]benzamide / 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 ...FE3-S4 CLUSTER / FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / PROTOPORPHYRIN IX CONTAINING FE / MALONATE ION / 2-methyl-N-[3-(1-methylethoxy)phenyl]benzamide / 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: 3.66 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 17, 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
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)287,69222
Polymers282,4988
Non-polymers5,19314
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)143,84611
Polymers141,2494
Non-polymers2,5977
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20500 Å2
ΔGint-180.4 kcal/mol
Surface area41630 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)143,84611
Polymers141,2494
Non-polymers2,5977
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20500 Å2
ΔGint-179.6 kcal/mol
Surface area41340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.803, 123.392, 219.001
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
1132C34 - 301
2132G34 - 301
1142D28 - 156
2142H28 - 156

NCS ensembles :
ID
1
2
3
4

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.971888, 0.016623, -0.234854), (-0.00053, -0.997348, -0.072785), (-0.235441, 0.070863, -0.969302)2.06923, -29.73427, 10.81901

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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 , 7 types, 14 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-MRN / 2-methyl-N-[3-(1-methylethoxy)phenyl]benzamide / 2-Methyl-N-(3-isopropoxy-phenyl)-benzamide


Mass: 269.338 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H19NO2

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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: 2.94 Å3/Da / Density % sol: 58.11 %
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: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 2, 2014
RadiationMonochromator: double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.65→50 Å / Num. obs: 37582 / % possible obs: 97.3 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.164 / Net I/σ(I): 4.5
Reflection shellResolution: 3.65→3.71 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.575 / Mean I/σ(I) obs: 2.4 / % possible all: 94.1

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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: 3.66→20 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.835 / SU B: 36.061 / SU ML: 0.513 / Cross valid method: THROUGHOUT / ESU R Free: 0.769 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26239 1652 4.9 %RANDOM
Rwork0.19308 ---
obs0.19655 31772 88.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 59.165 Å2
Baniso -1Baniso -2Baniso -3
1-1.12 Å20 Å2-0 Å2
2---0.89 Å20 Å2
3----0.23 Å2
Refinement stepCycle: LAST / Resolution: 3.66→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17952 0 284 0 18236
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01918711
X-RAY DIFFRACTIONr_bond_other_d0.0010.0217836
X-RAY DIFFRACTIONr_angle_refined_deg1.1441.97825409
X-RAY DIFFRACTIONr_angle_other_deg0.8123.00141021
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.22452285
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.19723.241790
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.646153129
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.34615124
X-RAY DIFFRACTIONr_chiral_restr0.0630.22761
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02120920
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024326
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
1A5913medium positional0.280.5
2B2506medium positional0.260.5
3C1657medium positional0.370.5
4D1227medium positional0.330.5
1A3608tight thermal5.690.5
2B1473tight thermal50.5
3C876tight thermal9.390.5
4D755tight thermal6.60.5
1A5913medium thermal6.142
2B2506medium thermal5.462
3C1657medium thermal9.252
4D1227medium thermal7.182
LS refinement shellResolution: 3.656→3.748 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 49 -
Rwork0.255 919 -
obs--36.45 %

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