[English] 日本語
Yorodumi
- PDB-8dyd: Crystal structure of human SDHA-SDHAF2-SDHAF4 assembly intermediate -

+
Open data


ID or keywords:

Loading...

-
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 / 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 ...protein-FAD linkage / 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 / negative regulation of epithelial to mesenchymal transition / proton motive force-driven mitochondrial ATP synthesis / protein dephosphorylation / tricarboxylic acid cycle / protein folding chaperone / respiratory electron transport chain / enzyme activator activity / negative regulation of canonical Wnt signaling pathway / flavin adenine dinucleotide binding / nervous system development / electron transfer activity / mitochondrial inner membrane / 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 / Fumarate reductase / succinate dehydrogenase FAD-binding site. ...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 / 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 / : / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
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

-
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

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more