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- PDB-4g73: Crystal structure of NDH with NADH and Quinone -

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Basic information

Entry
Database: PDB / ID: 4g73
TitleCrystal structure of NDH with NADH and Quinone
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 / NADH:ubiquinone reductase (non-electrogenic) activity / mitochondrial electron transport, NADH to ubiquinone / NADH dehydrogenase (ubiquinone) activity / mitochondrial inner membrane / oxidoreductase activity / mitochondrial matrix / positive regulation of apoptotic process / mitochondrion / identical protein binding
Similarity search - Function
Alternative NADH dehydrogenase / NDH2 C-terminal domain / 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 / Chem-UQ5 / Rotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.522 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)117,93122
Polymers112,1482
Non-polymers5,78320
Water6,972387
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13630 Å2
ΔGint-169 kcal/mol
Surface area37460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.406, 230.186, 112.921
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
11B-830-

HOH

21B-880-

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 701:704 )
211CHAIN B AND (RESSEQ 42:513 OR RESSEQ 701:704 )

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Components

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Protein , 1 types, 2 molecules AB

#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)

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Non-polymers , 5 types, 407 molecules

#2: Chemical
ChemComp-UQ5 / 2,3-DIMETHOXY-5-METHYL-6-(3,11,15,19-TETRAMETHYL-EICOSA-2,6,10,14,18-PENTAENYL)-[1,4]BENZOQUINONE


Mass: 522.758 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C34H50O4
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


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


Mass: 665.441 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 387 / 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: 3.69 Å3/Da / Density % sol: 66.68 %
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 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 19, 2012
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 55609 / % possible obs: 99.9 % / Rmerge(I) obs: 0.114
Reflection shell
Resolution (Å)Rmerge(I) obsDiffraction-ID% possible all
2.5-2.590.753199.9
2.59-2.690.584199.9
2.69-2.820.461199.9
2.82-2.960.331199.9
2.96-3.150.227199.9
3.15-3.390.134199.9

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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: 2.522→38.364 Å / SU ML: 0.32 / σ(F): 1.34 / Phase error: 21.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2175 2821 5.08 %
Rwork0.189 --
obs0.1904 55582 98.95 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.052 Å2 / ksol: 0.34 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-7.5845 Å2-0 Å2-0 Å2
2---4.8864 Å20 Å2
3----2.698 Å2
Refinement stepCycle: LAST / Resolution: 2.522→38.364 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7476 0 307 387 8170
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0118079
X-RAY DIFFRACTIONf_angle_d1.41610981
X-RAY DIFFRACTIONf_dihedral_angle_d21.4783196
X-RAY DIFFRACTIONf_chiral_restr0.0851219
X-RAY DIFFRACTIONf_plane_restr0.0051345
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A3733X-RAY DIFFRACTIONPOSITIONAL
12B3733X-RAY DIFFRACTIONPOSITIONAL0.065
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5223-2.56580.28831070.2817215881
2.5658-2.61250.30371340.26312637100
2.6125-2.66270.31371490.24782629100
2.6627-2.7170.3271480.25742616100
2.717-2.77610.2861390.24562626100
2.7761-2.84070.2731440.24152677100
2.8407-2.91170.26871310.22142633100
2.9117-2.99040.24761350.21172659100
2.9904-3.07830.24851200.20532634100
3.0783-3.17760.23031370.22648100
3.1776-3.29120.24151340.20672680100
3.2912-3.42290.20571470.17732643100
3.4229-3.57850.2091430.17472644100
3.5785-3.7670.17271700.16542661100
3.767-4.00280.19591370.15562638100
4.0028-4.31150.1591490.14712677100
4.3115-4.74470.17191330.14132704100
4.7447-5.42960.20561360.16732704100
5.4296-6.83440.2071590.2032693100
6.8344-38.36880.2171690.1938280099

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