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- PDB-6vax: Crystal structure of human SDHA-SDHAF2 assembly intermediate -

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Basic information

Entry
Database: PDB / ID: 6vax
TitleCrystal structure of human SDHA-SDHAF2 assembly intermediate
Components(Succinate dehydrogenase ...) x 2
KeywordsOXIDOREDUCTASE / SDHA / FLAVOPROTEIN / SDHAF2 / ASSEMBLY INTERMEDIATE / RESPIRATORY COMPLEX
Function / homology
Function and homology information


protein-FAD linkage / mitochondrial respiratory chain complex II assembly / succinate metabolic process / mitochondrial electron transport, succinate to ubiquinone / mitochondrial respiratory chain complex II, succinate dehydrogenase complex (ubiquinone) / succinate dehydrogenase (quinone) activity / : / succinate dehydrogenase / Citric acid cycle (TCA cycle) / Respiratory electron transport ...protein-FAD linkage / mitochondrial respiratory chain complex II assembly / succinate metabolic process / mitochondrial electron transport, succinate to ubiquinone / mitochondrial respiratory chain complex II, succinate dehydrogenase complex (ubiquinone) / succinate dehydrogenase (quinone) activity / : / succinate dehydrogenase / Citric acid cycle (TCA cycle) / Respiratory electron transport / negative regulation of epithelial to mesenchymal transition / proton motive force-driven mitochondrial ATP synthesis / tricarboxylic acid cycle / respiratory electron transport chain / protein dephosphorylation / negative regulation of canonical Wnt signaling pathway / flavin adenine dinucleotide binding / nervous system development / mitochondrial inner membrane / electron transfer activity / mitochondrial matrix / nucleolus / mitochondrion / cytosol
Similarity search - Function
Succinate dehydrogenase assembly factor 2, mitochondrial / Flavinator of succinate dehydrogenase / Flavinator of succinate dehydrogenase superfamily / Flavinator of succinate dehydrogenase / Succinate dehydrogenase, flavoprotein subunit / Succinate dehydrogenase/fumarate reductase, flavoprotein subunit / Fumarate reductase/succinate dehydrogenase, FAD-binding site / FAD-dependent oxidoreductase SdhA/FrdA/AprA / Fumarate reductase / succinate dehydrogenase FAD-binding site. / Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal ...Succinate dehydrogenase assembly factor 2, mitochondrial / Flavinator of succinate dehydrogenase / Flavinator of succinate dehydrogenase superfamily / Flavinator of succinate dehydrogenase / Succinate dehydrogenase, flavoprotein subunit / Succinate dehydrogenase/fumarate reductase, flavoprotein subunit / Fumarate reductase/succinate dehydrogenase, FAD-binding site / FAD-dependent oxidoreductase SdhA/FrdA/AprA / Fumarate reductase / succinate dehydrogenase FAD-binding site. / Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal / Fumarate reductase flavoprotein C-term / Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal domain superfamily / Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain superfamily / FAD-dependent oxidoreductase 2, FAD binding domain / FAD binding domain / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / : / MALONATE ION / OXALOACETATE ION / Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial / Succinate dehydrogenase assembly factor 2, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsSharma, P. / Maklashina, E. / Cecchini, G. / Iverson, T.M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM61606 United States
American Heart Association19POST34450093 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: The roles of SDHAF2 and dicarboxylate in covalent flavinylation of SDHA, the human complex II flavoprotein.
Authors: Sharma, P. / Maklashina, E. / Cecchini, G. / Iverson, T.M.
History
DepositionDec 18, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 7, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Mar 8, 2023Group: Database references / Structure summary / Category: database_2 / struct
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct.title
Revision 1.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial
B: Succinate dehydrogenase assembly factor 2, mitochondrial
C: Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial
D: Succinate dehydrogenase assembly factor 2, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,84222
Polymers178,0864
Non-polymers2,75618
Water1,78399
1
A: Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial
B: Succinate dehydrogenase assembly factor 2, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,44111
Polymers89,0432
Non-polymers1,3989
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7270 Å2
ΔGint-18 kcal/mol
Surface area25930 Å2
MethodPISA
2
C: Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial
D: Succinate dehydrogenase assembly factor 2, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,40111
Polymers89,0432
Non-polymers1,3589
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7260 Å2
ΔGint-18 kcal/mol
Surface area26270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)210.558, 68.782, 126.578
Angle α, β, γ (deg.)90.000, 93.160, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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Succinate dehydrogenase ... , 2 types, 4 molecules ACBD

#1: Protein Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial / Flavoprotein subunit of complex II / Fp


Mass: 69416.406 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SDHA, SDH2, SDHF / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P31040, succinate dehydrogenase
#2: Protein Succinate dehydrogenase assembly factor 2, mitochondrial / SDHAF2


Mass: 19626.445 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SDHAF2, C11orf79, PGL2, SDH5 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q9NX18

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Non-polymers , 7 types, 117 molecules

#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / 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-OAA / OXALOACETATE ION / Oxaloacetic acid


Mass: 131.064 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H3O5 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MLI / MALONATE ION / Malonic acid


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#8: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.67 Å3/Da / Density % sol: 53.87 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 100 mM Sodium malonate, 12 % w/v PEG 3350, 10 mM Oxaloacetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 2.59→50 Å / Num. obs: 56205 / % possible obs: 99.7 % / Redundancy: 6.8 % / Biso Wilson estimate: 66.11 Å2 / CC1/2: 0.991 / Net I/σ(I): 24.7
Reflection shellResolution: 2.59→2.64 Å / Redundancy: 6.8 % / Num. unique obs: 2855 / CC1/2: 0.951 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3B58, 1ZOY

3b58

1zoy


Resolution: 2.59→45.05 Å / SU ML: 0.3592 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 34.0475
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2489 2818 5.05 %
Rwork0.1991 52981 -
obs0.2015 55799 98.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 93.32 Å2
Refinement stepCycle: LAST / Resolution: 2.59→45.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11214 0 181 99 11494
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001711635
X-RAY DIFFRACTIONf_angle_d0.436115761
X-RAY DIFFRACTIONf_chiral_restr0.03861698
X-RAY DIFFRACTIONf_plane_restr0.00292058
X-RAY DIFFRACTIONf_dihedral_angle_d15.7394227
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.59-2.640.45161080.33422548X-RAY DIFFRACTION92.71
2.64-2.690.37231490.32312576X-RAY DIFFRACTION99.05
2.69-2.740.33881440.29472644X-RAY DIFFRACTION99.22
2.74-2.790.35941440.27892643X-RAY DIFFRACTION99.36
2.79-2.850.30421240.2662636X-RAY DIFFRACTION98.75
2.85-2.920.30851540.26082653X-RAY DIFFRACTION99.4
2.92-2.990.33321550.27482652X-RAY DIFFRACTION99.43
2.99-3.070.31781230.26542661X-RAY DIFFRACTION99.15
3.07-3.160.32441270.25422645X-RAY DIFFRACTION99.11
3.16-3.270.35611510.24962674X-RAY DIFFRACTION99.33
3.27-3.380.28681440.2372606X-RAY DIFFRACTION99.06
3.38-3.520.24861470.22472669X-RAY DIFFRACTION99.22
3.52-3.680.25241380.20792673X-RAY DIFFRACTION99.57
3.68-3.870.25891460.20142644X-RAY DIFFRACTION99.18
3.87-4.110.23341470.18172658X-RAY DIFFRACTION98.84
4.11-4.430.22271500.16372640X-RAY DIFFRACTION98.59
4.43-4.880.17041310.16232662X-RAY DIFFRACTION98.14
4.88-5.580.22691370.16682671X-RAY DIFFRACTION98.84
5.58-7.030.23331650.18562714X-RAY DIFFRACTION99.76
7.03-45.050.20061340.15372712X-RAY DIFFRACTION96.38
Refinement TLS params.Method: refined / Origin x: 50.7755476619 Å / Origin y: 32.0873630009 Å / Origin z: 31.5716434814 Å
111213212223313233
T0.377931389173 Å20.0620624309892 Å2-0.068451079219 Å2-0.473663947115 Å20.0270009987618 Å2--0.681079555779 Å2
L0.582197347096 °20.106187884165 °2-1.07366342654 °2-0.277809614063 °2-0.00786936620887 °2--3.63372906505 °2
S-0.0927462260162 Å °-0.202438189125 Å °-0.0508563814157 Å °-0.038780072267 Å °0.00367132562334 Å °-0.0323361343326 Å °0.1670480319 Å °0.440822903917 Å °0.059317222083 Å °
Refinement TLS groupSelection details: all

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