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

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Basic information

Entry
Database: PDB / ID: 8dye
TitleCrystal structure of human SDHA-SDHAF4 assembly intermediate
Components(Succinate dehydrogenase ...) x 2
KeywordsFLAVOPROTEIN / SDHA / SDHAF4 / ASSEMBLY INTERMEDIATE / RESPIRATORY COMPLEX / OXIDOREDUCTASE
Function / homology
Function and homology information


mitochondrial respiratory chain complex II assembly / Oxidoreductases; Acting on the CH-OH group of donors; With a quinone or similar compound as acceptor / succinate metabolic process / respiratory chain complex II (succinate dehydrogenase) / mitochondrial electron transport, succinate to ubiquinone / Citric acid cycle (TCA cycle) / succinate dehydrogenase (quinone) activity / succinate dehydrogenase / Maturation of TCA enzymes and regulation of TCA cycle / Respiratory electron transport ...mitochondrial respiratory chain complex II assembly / Oxidoreductases; Acting on the CH-OH group of donors; With a quinone or similar compound as acceptor / succinate metabolic process / respiratory chain complex II (succinate dehydrogenase) / mitochondrial electron transport, succinate to ubiquinone / Citric acid cycle (TCA cycle) / succinate dehydrogenase (quinone) activity / succinate dehydrogenase / Maturation of TCA enzymes and regulation of TCA cycle / Respiratory electron transport / cellular respiration / proton motive force-driven mitochondrial ATP synthesis / tricarboxylic acid cycle / protein folding chaperone / respiratory electron transport chain / enzyme activator activity / flavin adenine dinucleotide binding / nervous system development / electron transfer activity / mitochondrial inner membrane / mitochondrial matrix / innate immune response / nucleolus / mitochondrion
Similarity search - Function
Succinate dehydrogenase assembly factor 4 / Protein of unknown function (DUF1674) / Succinate dehydrogenase, flavoprotein subunit / Succinate dehydrogenase/fumarate reductase, flavoprotein subunit / Fumarate reductase/succinate dehydrogenase, FAD-binding site / Fumarate reductase / succinate dehydrogenase FAD-binding site. / FAD-dependent oxidoreductase SdhA/FrdA/AprA / 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 assembly factor 4 / Protein of unknown function (DUF1674) / Succinate dehydrogenase, flavoprotein subunit / Succinate dehydrogenase/fumarate reductase, flavoprotein subunit / Fumarate reductase/succinate dehydrogenase, FAD-binding site / Fumarate reductase / succinate dehydrogenase FAD-binding site. / FAD-dependent oxidoreductase SdhA/FrdA/AprA / 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 / Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial / Succinate dehydrogenase assembly factor 4, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.44 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: 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
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial
B: Succinate dehydrogenase assembly factor 4, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,58125
Polymers78,3782
Non-polymers2,20323
Water7,602422
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7670 Å2
ΔGint-12 kcal/mol
Surface area24690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.049, 69.299, 72.657
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y,-z+1/2
#3: -x,y,-z
#4: -x+1/2,-y,z+1/2

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Components

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Succinate dehydrogenase ... , 2 types, 2 molecules AB

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


Mass: 67150.938 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
#2: 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 , 6 types, 445 molecules

#3: 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
#4: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 422 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.43 Å3/Da / Density % sol: 49.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.7
Details: 100 mM Sodium malonate, 12 % w/v PEG 3350, 1 mM DTT

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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: Jun 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.44→50 Å / Num. obs: 125714 / % possible obs: 99.8 % / Redundancy: 7 % / Biso Wilson estimate: 18.63 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.09 / Rsym value: 0.09 / Net I/σ(I): 35.61
Reflection shellResolution: 1.45→1.48 Å / Rmerge(I) obs: 1.39 / Mean I/σ(I) obs: 1.53 / Num. unique obs: 6190 / CC1/2: 0.548 / Rsym value: 1.39 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6VAX, 3SFD

6vax

3sfd


Resolution: 1.44→28.57 Å / SU ML: 0.1351 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.2603
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1728 6223 4.96 %
Rwork0.155 119247 -
obs0.1559 125470 99.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.09 Å2
Refinement stepCycle: LAST / Resolution: 1.44→28.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5034 0 144 422 5600
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00765426
X-RAY DIFFRACTIONf_angle_d0.97677347
X-RAY DIFFRACTIONf_chiral_restr0.0818782
X-RAY DIFFRACTIONf_plane_restr0.009967
X-RAY DIFFRACTIONf_dihedral_angle_d13.29951990
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.44-1.460.30971980.28013624X-RAY DIFFRACTION92.12
1.46-1.480.28071950.26144012X-RAY DIFFRACTION99.57
1.48-1.50.27081840.24363938X-RAY DIFFRACTION99.78
1.5-1.520.25632030.22673924X-RAY DIFFRACTION99.61
1.52-1.540.24721890.22513958X-RAY DIFFRACTION99.64
1.54-1.560.241910.21073953X-RAY DIFFRACTION99.71
1.56-1.580.20412080.20193960X-RAY DIFFRACTION99.76
1.58-1.60.22872220.19473914X-RAY DIFFRACTION99.64
1.6-1.630.20931910.18843955X-RAY DIFFRACTION99.74
1.63-1.650.20781990.18873976X-RAY DIFFRACTION99.74
1.65-1.680.23121870.18183981X-RAY DIFFRACTION99.76
1.68-1.710.18841970.16723953X-RAY DIFFRACTION99.76
1.71-1.750.18751860.16753990X-RAY DIFFRACTION99.83
1.75-1.780.18922210.15923960X-RAY DIFFRACTION99.83
1.78-1.820.1832370.15473956X-RAY DIFFRACTION99.88
1.82-1.860.17312150.15023957X-RAY DIFFRACTION99.9
1.86-1.910.16682290.14193924X-RAY DIFFRACTION99.83
1.91-1.960.15932050.143977X-RAY DIFFRACTION99.81
1.96-2.020.15452050.13984007X-RAY DIFFRACTION99.79
2.02-2.080.16641930.14133967X-RAY DIFFRACTION99.74
2.08-2.160.16011840.13724018X-RAY DIFFRACTION99.81
2.16-2.240.15162200.13513985X-RAY DIFFRACTION99.81
2.24-2.350.17821880.13534026X-RAY DIFFRACTION99.79
2.35-2.470.16371970.13763992X-RAY DIFFRACTION99.69
2.47-2.620.14572120.13954002X-RAY DIFFRACTION99.67
2.62-2.830.16952320.13984007X-RAY DIFFRACTION99.69
2.83-3.110.15252670.14313987X-RAY DIFFRACTION99.65
3.11-3.560.15032100.14144054X-RAY DIFFRACTION99.58
3.56-4.480.15162320.13924083X-RAY DIFFRACTION99.38
4.48-28.570.20162260.1874207X-RAY DIFFRACTION98.14
Refinement TLS params.Method: refined / Origin x: -22.185020435 Å / Origin y: 32.9800611895 Å / Origin z: -17.049469302 Å
111213212223313233
T0.117195865515 Å2-0.0247415130909 Å20.00918266911617 Å2-0.147855125317 Å2-0.0228735945845 Å2--0.118100472453 Å2
L0.838283721989 °20.084448066255 °20.0073079057559 °2-1.10999939076 °2-0.0911942644125 °2--0.453936256187 °2
S-0.0295236510587 Å °0.0737714202946 Å °-0.049111983321 Å °-0.185928791608 Å °0.0300855039904 Å °0.011748741997 Å °0.0229216017979 Å °-0.0168738472526 Å °0.0028788944847 Å °
Refinement TLS groupSelection details: all

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