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- PDB-5yjx: Structure of the Ndi1 protein from Saccharomyces cerevisiae in co... -

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Basic information

Entry
Database: PDB / ID: 5yjx
TitleStructure of the Ndi1 protein from Saccharomyces cerevisiae in complex with myxothiazol.
ComponentsRotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial
KeywordsOXIDOREDUCTASE / monotopic membrane protein / NUCLEOTIDE-BINDING DOMAIN
Function / homology
Function and homology information


NADH:quinone reductase (non-electrogenic) / NADH dehydrogenase (quinone) (non-electrogenic) activity / mitochondrial electron transport, NADH to ubiquinone / NADH dehydrogenase (ubiquinone) activity / oxidoreductase activity / mitochondrial inner membrane / positive regulation of apoptotic process / mitochondrial matrix / mitochondrion / identical protein binding
Similarity search - Function
: / NDH2 C-terminal domain / Alternative NADH dehydrogenase / FAD/NAD(P)-binding domain - #100 / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Chem-MYX / Rotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.21 Å
AuthorsYamasita, T. / Inaoka, D.K. / Shiba, T. / Oohashi, T. / Iwata, S. / Yagi, T. / Kosaka, H. / Harada, S. / Kita, K. / Hirano, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
JSPS KAKENHI15K07005 Japan
CitationJournal: Sci Rep / Year: 2018
Title: Ubiquinone binding site of yeast NADH dehydrogenase revealed by structures binding novel competitive- and mixed-type inhibitors
Authors: Yamashita, T. / Inaoka, D.K. / Shiba, T. / Oohashi, T. / Iwata, S. / Yagi, T. / Kosaka, H. / Miyoshi, H. / Harada, S. / Kita, K. / Hirano, K.
History
DepositionOct 11, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 14, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2018Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation_author.name
Revision 1.2Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.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_seq_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Rotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial
B: Rotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,60416
Polymers108,4722
Non-polymers3,13114
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10700 Å2
ΔGint-109 kcal/mol
Surface area38580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.336, 116.401, 166.619
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Rotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial / Internal NADH dehydrogenase / NADH:ubiquinone reductase (non-electrogenic)


Mass: 54236.074 Da / Num. of mol.: 2 / Fragment: UNP residues 28-513
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: NDI1, YML120C, YM7056.06C / Production host: Escherichia coli (E. coli)
References: UniProt: P32340, NADH:quinone reductase (non-electrogenic)
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Chemical ChemComp-MYX / (2Z,6E)-7-{2'-[(2E,4E)-1,6-DIMETHYLHEPTA-2,4-DIENYL]-2,4'-BI-1,3-THIAZOL-4-YL}-3,5-DIMETHOXY-4-METHYLHEPTA-2,6-DIENAMID E / 7-[2'-(1,6-DIMETHYL-HEPTA-2,4-DIENYL)-[2,4']BITHIAZOLYL-4-YL]-3,5-DIMETHOXY-4-METHYL-HEPTA-2,6-DIENOIC ACID AMIDE / MYXOTHIAZOL


Mass: 487.678 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H33N3O3S2

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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: 3.14 Å3/Da / Density % sol: 60.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 50mM Mes(pH 6.0), 34%(v/v) PEG 400, 100mM NaCl, 2%(v/v) ethylene glycol, 5%(v/v) glycerol
PH range: 6.0-6.6

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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: May 17, 2014
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 22984 / % possible obs: 98.1 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.125 / Net I/σ(I): 7.1
Reflection shellResolution: 3.2→3.26 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.609 / Mean I/σ(I) obs: 2.7 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4G9K

4g9k


Resolution: 3.21→20 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.857 / SU B: 23.808 / SU ML: 0.404 / Cross valid method: THROUGHOUT / ESU R Free: 0.603 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28458 1045 5.1 %RANDOM
Rwork0.21958 ---
obs0.22281 19430 88.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 87.365 Å2
Baniso -1Baniso -2Baniso -3
1-3.21 Å20 Å2-0 Å2
2---2.31 Å20 Å2
3----0.91 Å2
Refinement stepCycle: 1 / Resolution: 3.21→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7310 0 204 0 7514
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0197742
X-RAY DIFFRACTIONr_bond_other_d0.0010.027515
X-RAY DIFFRACTIONr_angle_refined_deg1.4311.99910505
X-RAY DIFFRACTIONr_angle_other_deg0.809317323
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8285936
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.37324.286322
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.661151324
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.111536
X-RAY DIFFRACTIONr_chiral_restr0.0670.21169
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0218597
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021753
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
LS refinement shellResolution: 3.211→3.292 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.385 53 -
Rwork0.28 926 -
obs--61.15 %

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