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

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Basic information

Entry
Database: PDB / ID: 5yjy
TitleStructure of the Ndi1 protein from Saccharomyces cerevisiae in complex with AC0-12.
Components(Rotenone-insensitive NADH-ubiquinone oxidoreductase, ...) x 2
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
2-dodecyl-1-oxidanidyl-quinolin-1-ium-4-ol / FLAVIN-ADENINE DINUCLEOTIDE / Rotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 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
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
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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_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)111,18616
Polymers108,3712
Non-polymers2,81514
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8000 Å2
ΔGint-104 kcal/mol
Surface area39100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.854, 115.795, 166.499
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Rotenone-insensitive NADH-ubiquinone oxidoreductase, ... , 2 types, 2 molecules AB

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


Mass: 54134.973 Da / Num. of mol.: 1 / Fragment: UNP residues 29-513
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: Protein Rotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial / Internal NADH dehydrogenase / NADH:ubiquinone reductase (non-electrogenic)


Mass: 54236.074 Da / Num. of mol.: 1 / 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)

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Non-polymers , 4 types, 14 molecules

#3: 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
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-8WF / 2-dodecyl-1-oxidanidyl-quinolin-1-ium-4-ol / 2-dodecyl -4-HYDROXY QUINOLINE N-OXIDE


Mass: 329.476 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H31NO2
#6: 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

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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: 3.11 Å3/Da / Density % sol: 60.41 %
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: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jun 28, 2014
RadiationMonochromator: 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: 18371 / % possible obs: 97.3 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 7.9
Reflection shellResolution: 3.4→3.46 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.773 / Mean I/σ(I) obs: 1.3 / % possible all: 98.6

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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: 3.4→20 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.822 / SU B: 30.628 / SU ML: 0.507 / Cross valid method: THROUGHOUT / ESU R Free: 0.78 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29865 807 5.1 %RANDOM
Rwork0.20709 ---
obs0.2118 15012 82.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 62.912 Å2
Baniso -1Baniso -2Baniso -3
1-7.37 Å20 Å2-0 Å2
2---3.17 Å2-0 Å2
3----4.2 Å2
Refinement stepCycle: 1 / Resolution: 3.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7280 0 176 0 7456
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0197682
X-RAY DIFFRACTIONr_bond_other_d0.0020.027469
X-RAY DIFFRACTIONr_angle_refined_deg1.6091.99510420
X-RAY DIFFRACTIONr_angle_other_deg0.838317217
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1915936
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.54624.164317
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.583151314
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7411537
X-RAY DIFFRACTIONr_chiral_restr0.0780.21153
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0218526
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021729
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: 3.4→3.486 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.394 28 -
Rwork0.252 529 -
obs--40.96 %

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