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- PDB-4g6g: Crystal structure of NDH with TRT -

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Basic information

Entry
Database: PDB / ID: 4g6g
TitleCrystal structure of NDH with TRT
ComponentsRotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial
KeywordsOXIDOREDUCTASE / Rossmann fold / electron transfer / TRT
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 / Rotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.39 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 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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)116,07720
Polymers112,1482
Non-polymers3,92918
Water8,359464
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11500 Å2
ΔGint-129 kcal/mol
Surface area38240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.921, 230.598, 112.250
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-714-

HOH

21A-857-

HOH

31B-725-

HOH

41B-880-

HOH

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

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 36:417 OR RESSEQ 426:513 OR RESSEQ 601:601 OR RESSEQ 701:704 )
211CHAIN B AND (RESSEQ 42:419 OR RESSEQ 429:513 OR RESSEQ 601:601 OR RESSEQ 701:704 )

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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-TRT / FRAGMENT OF TRITON X-100 / 1-{2-[2-(2-METHOXYETHOXY)ETHOXY]ETHOXY}-4-(1,1,3,3-TETRAMETHYLBUTYL)BENZENE


Mass: 352.508 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H36O4 / Comment: detergent*YM
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 464 / 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: 3.83 Å3/Da / Density % sol: 67.93 %
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: MAR CCD 165 mm / Detector: CCD / Date: Oct 10, 2010
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.39→35.59 Å / Num. all: 66303 / Num. obs: 65729 / % possible obs: 99.13 %
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.39-2.48183.7
2.48-2.57190.2
2.57-2.67197.8
2.69-2.83199.8
2.83-3.01199.9
3.01-3.24199.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHELXSphasing
PHENIX(phenix.refine: 1.6.3_473)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.39→35.59 Å / SU ML: 0.37 / σ(F): 0 / Phase error: 24.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2342 3252 5.2 %
Rwork0.1926 --
obs0.1948 62479 91.33 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.152 Å2 / ksol: 0.347 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-11.3592 Å2-0 Å2-0 Å2
2---7.6705 Å20 Å2
3----3.6887 Å2
Refinement stepCycle: LAST / Resolution: 2.39→35.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7371 0 232 464 8067
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087779
X-RAY DIFFRACTIONf_angle_d1.33910563
X-RAY DIFFRACTIONf_dihedral_angle_d17.2452882
X-RAY DIFFRACTIONf_chiral_restr0.1031170
X-RAY DIFFRACTIONf_plane_restr0.0051318
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A3696X-RAY DIFFRACTIONPOSITIONAL
12B3696X-RAY DIFFRACTIONPOSITIONAL0.059
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3902-2.42590.34213790.29421633X-RAY DIFFRACTION68
2.4259-2.46380.27442143X-RAY DIFFRACTION73
2.4638-2.50420.25192201X-RAY DIFFRACTION75
2.5042-2.54740.24682317X-RAY DIFFRACTION78
2.5474-2.59370.29954480.23431980X-RAY DIFFRACTION83
2.5937-2.64350.24132479X-RAY DIFFRACTION85
2.6435-2.69750.23382608X-RAY DIFFRACTION89
2.6975-2.75610.21632714X-RAY DIFFRACTION91
2.7561-2.82020.2964800.22252251X-RAY DIFFRACTION92
2.8202-2.89070.22892765X-RAY DIFFRACTION94
2.8907-2.96880.21862808X-RAY DIFFRACTION95
2.9688-3.05610.29714040.21732426X-RAY DIFFRACTION96
3.0561-3.15470.21272846X-RAY DIFFRACTION96
3.1547-3.26740.21472865X-RAY DIFFRACTION97
3.2674-3.39810.23144160.20332496X-RAY DIFFRACTION98
3.3981-3.55260.17872927X-RAY DIFFRACTION99
3.5526-3.73980.16332925X-RAY DIFFRACTION99
3.7398-3.97380.18743940.14412555X-RAY DIFFRACTION99
3.9738-4.28010.13952964X-RAY DIFFRACTION99
4.2801-4.710.16793150.1332644X-RAY DIFFRACTION99
4.71-5.38950.1612981X-RAY DIFFRACTION99
5.3895-6.78250.27262720.21752746X-RAY DIFFRACTION99
6.7825-35.59350.18311440.21222953X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.3505-0.23760.25710.8390.0121.1047-0.0162-0.02260.03730.15-0.0271-0.12730.22240.06890.03980.09220.01490.01140.05180.00480.112540.010927.38173.4509
21.3506-0.58350.37951.0001-0.38670.30860.16220.44180.0705-0.4104-0.2776-0.0870.15750.09740.04210.20340.10190.06270.18990.06240.03426.665837.7433-32.46
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESID 36:513
2X-RAY DIFFRACTION2CHAIN B AND RESID 42:513

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