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- PDB-8dyd: Crystal structure of human SDHA-SDHAF2-SDHAF4 assembly intermediate -

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Basic information

Entry
Database: PDB / ID: 8dyd
TitleCrystal structure of human SDHA-SDHAF2-SDHAF4 assembly intermediate
Components
  • (Succinate dehydrogenase assembly factor ...) x 2
  • Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial
KeywordsFLAVOPROTEIN / SDHA / SDHAF2 / SDHAF4 / ASSEMBLY INTERMEDIATE / RESPIRATORY COMPLEX / OXIDOREDUCTASE / ELECTRON TRANSPORT
Function / homology
Function and homology information


protein-FAD linkage / mitochondrial respiratory chain complex II assembly / succinate metabolic process / : / mitochondrial electron transport, succinate to ubiquinone / succinate dehydrogenase / succinate dehydrogenase (quinone) activity / Citric acid cycle (TCA cycle) / Respiratory electron transport / negative regulation of epithelial to mesenchymal transition ...protein-FAD linkage / mitochondrial respiratory chain complex II assembly / succinate metabolic process / : / mitochondrial electron transport, succinate to ubiquinone / succinate dehydrogenase / succinate dehydrogenase (quinone) activity / Citric acid cycle (TCA cycle) / Respiratory electron transport / negative regulation of epithelial to mesenchymal transition / cellular respiration / anaerobic respiration / proton motive force-driven mitochondrial ATP synthesis / enzyme activator activity / tricarboxylic acid cycle / respiratory electron transport chain / protein dephosphorylation / negative regulation of canonical Wnt signaling pathway / nervous system development / flavin adenine dinucleotide binding / mitochondrial inner membrane / electron transfer activity / mitochondrial matrix / innate immune response / nucleolus / mitochondrion / cytosol
Similarity search - Function
Succinate dehydrogenase assembly factor 4 / Succinate dehydrogenase assembly factor 2, mitochondrial / Protein of unknown function (DUF1674) / 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 ...Succinate dehydrogenase assembly factor 4 / Succinate dehydrogenase assembly factor 2, mitochondrial / Protein of unknown function (DUF1674) / 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 / : / DI(HYDROXYETHYL)ETHER / Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial / Succinate dehydrogenase assembly factor 4, mitochondrial / Succinate dehydrogenase assembly factor 2, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 Å
AuthorsSharma, P. / Maklashina, E. / Cecchini, G. / Iverson, T.M.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM61606 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM61606 United States
American Heart Association19POST34450093 United States
CitationJournal: Nat Commun / Year: 2024
Title: Disordered-to-ordered transitions in assembly factors allow the complex II catalytic subunit to switch binding partners.
Authors: Sharma, P. / Maklashina, E. / Voehler, M. / Balintova, S. / Dvorakova, S. / Kraus, M. / Vanova, K.H. / Nahacka, Z. / Zobalova, R. / Boukalova, S. / Cunatova, K. / Mracek, T. / Ghayee, H.K. / ...Authors: Sharma, P. / Maklashina, E. / Voehler, M. / Balintova, S. / Dvorakova, S. / Kraus, M. / Vanova, K.H. / Nahacka, Z. / Zobalova, R. / Boukalova, S. / Cunatova, K. / Mracek, T. / Ghayee, H.K. / Pacak, K. / Rohlena, J. / Neuzil, J. / Cecchini, G. / Iverson, T.M.
History
DepositionAug 4, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 10, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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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 assembly factor 4, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,56040
Polymers97,2373
Non-polymers3,32337
Water9,350519
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15880 Å2
ΔGint48 kcal/mol
Surface area27080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.048, 103.206, 126.237
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 69416.406 Da / Num. of mol.: 1
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) / Strain (production host): K-12 / References: UniProt: P31040, succinate dehydrogenase

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Succinate dehydrogenase assembly factor ... , 2 types, 2 molecules BC

#2: Protein Succinate dehydrogenase assembly factor 2, mitochondrial / SDH assembly factor 2 / SDHAF2


Mass: 16592.828 Da / Num. of mol.: 1
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) / Strain (production host): K-12 / References: UniProt: Q9NX18
#3: Protein Succinate dehydrogenase assembly factor 4, mitochondrial / SDH assembly factor 4 / SDHAF4


Mass: 11227.444 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SDHAF4, C6orf57 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q5VUM1

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Non-polymers , 7 types, 556 molecules

#4: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 30 / Source method: obtained synthetically / Formula: C2H6O2
#9: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 519 / 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: 2.2 Å3/Da / Density % sol: 44.07 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 200 mM Ammonium citrate tribasic pH 7.0, 20% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.52→50 Å / Num. obs: 122221 / % possible obs: 91.7 % / Redundancy: 4.2 % / Biso Wilson estimate: 16.73 Å2 / CC1/2: 0.904 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.041 / Net I/σ(I): 24.4
Reflection shellResolution: 1.52→1.57 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 11699 / CC1/2: 0.648 / Rpim(I) all: 0.491 / % possible all: 89

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6VAX, 3SFD

6vax

3sfd


Resolution: 1.52→35.49 Å / SU ML: 0.1489 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.312
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1842 10884 4.85 %
Rwork0.1567 213341 -
obs0.1581 122221 86.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.06 Å2
Refinement stepCycle: LAST / Resolution: 1.52→35.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5962 0 212 519 6693
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00836412
X-RAY DIFFRACTIONf_angle_d1.02038637
X-RAY DIFFRACTIONf_chiral_restr0.0575911
X-RAY DIFFRACTIONf_plane_restr0.00681130
X-RAY DIFFRACTIONf_dihedral_angle_d16.83932378
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.52-1.530.31822950.30695950X-RAY DIFFRACTION72.5
1.53-1.550.31783540.29626830X-RAY DIFFRACTION83.86
1.55-1.570.27833520.2876896X-RAY DIFFRACTION83.86
1.57-1.590.28363840.2776931X-RAY DIFFRACTION85.73
1.59-1.610.28673510.26667121X-RAY DIFFRACTION86.01
1.61-1.630.24683900.25986973X-RAY DIFFRACTION86.6
1.63-1.660.25893450.25447152X-RAY DIFFRACTION86.87
1.66-1.680.26113450.24027125X-RAY DIFFRACTION87.03
1.68-1.710.24834030.22747092X-RAY DIFFRACTION87.34
1.71-1.740.25073320.21427171X-RAY DIFFRACTION87.16
1.74-1.770.2263680.21017173X-RAY DIFFRACTION88.06
1.77-1.80.20653310.19277249X-RAY DIFFRACTION88.07
1.8-1.830.21023090.18737289X-RAY DIFFRACTION87.78
1.83-1.870.19034070.17677189X-RAY DIFFRACTION88.71
1.87-1.910.19553310.16787255X-RAY DIFFRACTION88.52
1.91-1.960.19073900.16027259X-RAY DIFFRACTION88.82
1.96-2.010.15463470.14937329X-RAY DIFFRACTION89.05
2.01-2.060.16023450.14487268X-RAY DIFFRACTION88.95
2.06-2.120.17223990.13527328X-RAY DIFFRACTION89.32
2.12-2.190.14263850.1287282X-RAY DIFFRACTION89.65
2.19-2.270.17284010.1287276X-RAY DIFFRACTION89.5
2.27-2.360.15423640.12567356X-RAY DIFFRACTION89.5
2.36-2.460.16113470.12877383X-RAY DIFFRACTION89.88
2.46-2.590.15493980.12867287X-RAY DIFFRACTION89.9
2.59-2.760.16293910.12947265X-RAY DIFFRACTION88.96
2.76-2.970.16093480.13247285X-RAY DIFFRACTION88.85
2.97-3.270.14853460.1337188X-RAY DIFFRACTION87.76
3.27-3.740.16034160.13187076X-RAY DIFFRACTION86.93
3.74-4.710.16593410.12866872X-RAY DIFFRACTION84.05
4.71-35.490.22753690.18156491X-RAY DIFFRACTION79.87

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