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- PDB-4g6h: Crystal structure of NDH with NADH -

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Basic information

Entry
Database: PDB / ID: 4g6h
TitleCrystal structure of NDH with NADH
ComponentsRotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial
KeywordsOXIDOREDUCTASE / Rossmann fold / electron transfer / FAD / NADH
Function / homology
Function and homology information


NADH:quinone reductase (non-electrogenic) / NADH oxidation / mitochondrial electron transport, NADH to ubiquinone / NADH dehydrogenase (ubiquinone) activity / mitochondrial inner membrane / mitochondrial matrix / positive regulation of apoptotic process / mitochondrion / identical protein binding
Similarity search - Function
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 / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Rotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.262 Å
AuthorsLi, W. / Feng, Y. / Ge, J. / Yang, M.
CitationJournal: Nature / Year: 2012
Title: Structural insight into the type-II mitochondrial NADH dehydrogenases.
Authors: Feng, Y. / Li, W. / Li, J. / Wang, J. / Ge, J. / Xu, D. / Liu, Y. / Wu, K. / Zeng, Q. / Wu, J.W. / Tian, C. / Zhou, B. / Yang, M.
History
DepositionJul 19, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 24, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2012Group: Database references
Revision 1.2Nov 6, 2013Group: Non-polymer description
Revision 1.3Nov 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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_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)115,19612
Polymers112,1482
Non-polymers3,04810
Water9,818545
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10040 Å2
ΔGint-101 kcal/mol
Surface area38080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.187, 229.588, 111.870
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-722-

HOH

21A-791-

HOH

31A-855-

HOH

41B-793-

HOH

51B-820-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 42:513 OR RESSEQ 701:701 )
211CHAIN B AND (RESSEQ 42:513 OR RESSEQ 601:601 )

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Components

#1: Protein Rotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial / Internal NADH dehydrogenase


Mass: 56074.051 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's 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 / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH / Nicotinamide adenine dinucleotide


Mass: 665.441 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 545 / Source method: isolated from a natural source / Formula: H2O

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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: 3.61 Å3/Da / Density % sol: 65.95 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 3.8M potassium formate, 2% w/v Polyethylene glycol monomethyl ether 2000, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 24, 2012
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.25→50 Å / Num. all: 77170 / Num. obs: 75053 / % possible obs: 71.9 %
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.25-2.331100
2.33-2.421100
2.42-2.531100
2.53-2.671100
2.67-2.831100
2.83-3.051100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4G6G

4g6g


Resolution: 2.262→43.15 Å / SU ML: 0.32 / σ(F): 1.34 / Phase error: 23.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2251 3777 5.03 %
Rwork0.1933 --
obs0.1949 55454 98.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.583 Å2 / ksol: 0.378 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-10.3929 Å2-0 Å2-0 Å2
2---3.5793 Å20 Å2
3----6.8136 Å2
Refinement stepCycle: LAST / Resolution: 2.262→43.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7476 0 200 545 8221
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.018051
X-RAY DIFFRACTIONf_angle_d1.33610941
X-RAY DIFFRACTIONf_dihedral_angle_d19.8623172
X-RAY DIFFRACTIONf_chiral_restr0.0811219
X-RAY DIFFRACTIONf_plane_restr0.0051344
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A3738X-RAY DIFFRACTIONPOSITIONAL
12B3738X-RAY DIFFRACTIONPOSITIONAL0.058
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2621-2.29070.36341050.2887217082
2.2907-2.32090.33321170.273253396
2.3209-2.35270.34341270.2743261398
2.3527-2.38630.30311410.2735264599
2.3863-2.42190.30051540.26372629100
2.4219-2.45970.29671580.24782614100
2.4597-2.50.29651410.24882621100
2.5-2.54320.27291490.24692651100
2.5432-2.58940.27241370.23252631100
2.5894-2.63920.2561400.21212656100
2.6392-2.69310.23091150.21392676100
2.6931-2.75160.25851220.20532645100
2.7516-2.81560.25181700.21162652100
2.8156-2.8860.25391330.21022654100
2.886-2.9640.25871430.20422649100
2.964-3.05120.21321180.19472679100
3.0512-3.14970.21481540.19952643100
3.1497-3.26220.19571350.19622680100
3.2622-3.39280.21391470.18292656100
3.3928-3.54710.21041350.17512692100
3.5471-3.7340.19991470.15972680100
3.734-3.96780.20891210.15692683100
3.9678-4.27390.19111660.14582654100
4.2739-4.70350.16061460.14082693100
4.7035-5.38310.18441580.1571268199
5.3831-6.77780.22781560.2124269699
6.7778-43.15740.22471420.2064280098

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