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- PDB-7q5s: Protein community member fatty acid synthase complex from C. ther... -

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Basic information

Entry
Database: PDB / ID: 7q5s
TitleProtein community member fatty acid synthase complex from C. thermophilum
Components
  • 3-hydroxyacyl-[acyl-carrier-protein] dehydratase
  • 3-oxoacyl-[acyl-carrier-protein] reductase
KeywordsTRANSFERASE / Fatty Acid Synthase / complex / chaetomium / thermophilum / fatty / acid / synthesis
Function / homology
Function and homology information


fatty acid synthase complex / holo-[acyl-carrier-protein] synthase activity / long-chain fatty acid biosynthetic process / fatty acid synthase activity / enoyl-[acyl-carrier-protein] reductase (NADH) activity / fatty acid biosynthetic process / magnesium ion binding
Similarity search - Function
: / Fatty acid synthase beta subunit AflB /Fas1-like, fungi / Fatty acid synthase beta subunit AflB /Fas1-like, central domain / Fatty acid synthase alpha subunit, yeast / Fatty acid synthase subunit beta/Fas1-like, helical / Fatty acid synthase / Starter unit:ACP transacylase / Starter unit:ACP transacylase in aflatoxin biosynthesis / Holo-[acyl carrier protein] synthase / Phosphopantetheine-protein transferase domain ...: / Fatty acid synthase beta subunit AflB /Fas1-like, fungi / Fatty acid synthase beta subunit AflB /Fas1-like, central domain / Fatty acid synthase alpha subunit, yeast / Fatty acid synthase subunit beta/Fas1-like, helical / Fatty acid synthase / Starter unit:ACP transacylase / Starter unit:ACP transacylase in aflatoxin biosynthesis / Holo-[acyl carrier protein] synthase / Phosphopantetheine-protein transferase domain / MaoC-like dehydratase domain / MaoC like domain / 4'-phosphopantetheinyl transferase domain / 4'-phosphopantetheinyl transferase domain superfamily / 4'-phosphopantetheinyl transferase superfamily / HotDog domain superfamily / Acyl transferase domain superfamily / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase/acyl hydrolase/lysophospholipase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / Thiolase-like / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Aldolase-type TIM barrel / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Fatty acid synthase alpha subunit-like protein / Malonyltransferase-like protein
Similarity search - Component
Biological speciesChaetomium thermophilum var. thermophilum DSM 1495 (fungus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.47 Å
AuthorsChojnowski, G. / Skalidis, I. / Kyrilis, F.L. / Tueting, C. / Hamdi, F. / Kastritis, P.L.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Structure / Year: 2022
Title: Cryo-EM and artificial intelligence visualize endogenous protein community members.
Authors: Ioannis Skalidis / Fotis L Kyrilis / Christian Tüting / Farzad Hamdi / Grzegorz Chojnowski / Panagiotis L Kastritis /
Abstract: Cellular function is underlined by megadalton assemblies organizing in proximity, forming communities. Metabolons are protein communities involving metabolic pathways such as protein, fatty acid, and ...Cellular function is underlined by megadalton assemblies organizing in proximity, forming communities. Metabolons are protein communities involving metabolic pathways such as protein, fatty acid, and thioesters of coenzyme-A synthesis. Metabolons are highly heterogeneous due to their function, making their analysis particularly challenging. Here, we simultaneously characterize metabolon-embedded architectures of a 60S pre-ribosome, fatty acid synthase, and pyruvate/oxoglutarate dehydrogenase complex E2 cores de novo. Cryo-electron microscopy (cryo-EM) 3D reconstructions are resolved at 3.84-4.52 Å resolution by collecting <3,000 micrographs of a single cellular fraction. After combining cryo-EM with artificial intelligence-based atomic modeling and de novo sequence identification methods, at this resolution range, polypeptide hydrogen bonding patterns are discernible. Residing molecular components resemble their purified counterparts from other eukaryotes but also exhibit substantial conformational variation with potential functional implications. Our results propose an integrated tool, boosted by machine learning, that opens doors for structural systems biology spearheaded by cryo-EM characterization of native cell extracts.
History
DepositionNov 4, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 2, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 9, 2022Group: 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_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Apr 20, 2022Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Dec 13, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Assembly

Deposited unit
B: 3-hydroxyacyl-[acyl-carrier-protein] dehydratase
A: 3-oxoacyl-[acyl-carrier-protein] reductase
C: 3-hydroxyacyl-[acyl-carrier-protein] dehydratase
D: 3-oxoacyl-[acyl-carrier-protein] reductase
E: 3-hydroxyacyl-[acyl-carrier-protein] dehydratase
F: 3-oxoacyl-[acyl-carrier-protein] reductase
G: 3-hydroxyacyl-[acyl-carrier-protein] dehydratase
H: 3-oxoacyl-[acyl-carrier-protein] reductase
I: 3-hydroxyacyl-[acyl-carrier-protein] dehydratase
J: 3-oxoacyl-[acyl-carrier-protein] reductase
K: 3-hydroxyacyl-[acyl-carrier-protein] dehydratase
L: 3-oxoacyl-[acyl-carrier-protein] reductase


Theoretical massNumber of molelcules
Total (without water)2,643,10612
Polymers2,643,10612
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "J"
d_2ens_1chain "D"
d_3ens_1chain "F"
d_4ens_1chain "H"
d_5ens_1chain "L"
d_6ens_1chain "A"
d_1ens_2chain "I"
d_2ens_2chain "B"
d_3ens_2chain "E"
d_4ens_2chain "G"
d_5ens_2chain "C"
d_6ens_2chain "K"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1METLEUJ1 - 1550
d_21ens_1METLEUD1 - 1550
d_31ens_1METLEUF1 - 1550
d_41ens_1METLEUH1 - 1550
d_51ens_1METLEUL1 - 1550
d_61ens_1METLEUB1 - 1550
d_11ens_2SERASPI1 - 2039
d_21ens_2SERASPA1 - 2039
d_31ens_2SERASPE1 - 2039
d_41ens_2SERASPG1 - 2039
d_51ens_2SERASPC1 - 2039
d_61ens_2SERASPK1 - 2039

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.999991664017, -0.00190938082744, 0.00360917751765), (-0.00191132080072, 0.999998030773, -0.000534138466777), (-0.00360815053661, -0.00054103231027, -0.999993344245)278.909298274, 0.109338248889, 285.765413156
2given(0.499582188032, -0.866266313552, -0.000558037717784), (-0.86626646686, -0.499582228266, -7.4792557618E-5), (-0.000213995453338, 0.000520774391743, -0.9999998415)207.044771592, 358.32788104, 285.266409749
3given(-0.500406799982, -0.865790343746, -0.00033942261852), (0.865790383669, -0.500406648946, -0.000444114538628), (0.000214660743952, -0.000516106774214, 0.999999843777)346.470235283, 116.818190436, 0.0727157918342
4given(-0.499581938528, 0.866266458213, 0.00055684059573), (-0.866266610684, -0.499581979028, -7.37876121908E-5), (0.000214267793345, -0.000519235373892, 0.999999842242)72.0326281253, 358.331323089, 0.0731629427096
5given(0.499585023681, 0.866260501523, -0.00274729216075), (0.866263958169, -0.499586563372, 0.000143091930674), (-0.00124855536154, -0.002451366767, -0.999996215948)-67.1398146339, 116.623271352, 285.849100809
6given(0.500010510814, 0.866019335255, 6.36102917171E-6), (0.866019335267, -0.500010510831, 1.40523241405E-6), (4.39753988665E-6, 4.80614327774E-6, -0.999999999979)-67.3713910373, 116.679331191, 285.338566466
7given(0.500100333014, -0.865967467803, 4.03275465976E-5), (-0.865967468393, -0.500100333592, -5.09392817571E-6), (2.45789955899E-5, -3.23748682566E-5, -0.999999999174)206.885950742, 358.383135047, 285.342688478
8given(-0.498093748577, -0.867120439912, -0.00218181452869), (0.867122812311, -0.498089625654, -0.00218018006431), (0.000803739514615, -0.00297783521087, 0.999995243239)346.574751114, 116.416680668, 0.392164901295
9given(-0.999993081442, 0.00228090480523, 0.00293845911074), (0.00229130840108, 0.999991102011, 0.00354200564544), (-0.00293035398667, 0.00354871405592, -0.999989409771)278.558081882, -0.384773820462, 285.035485449
10given(-0.499977928639, 0.866038146316, -9.01491159021E-8), (-0.866038146316, -0.499977928639, -6.72978629622E-8), (-1.03355084728E-7, 4.44251271022E-8, 1)72.1679467297, 358.373486314, 1.53734981012E-6

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Components

#1: Protein
3-hydroxyacyl-[acyl-carrier-protein] dehydratase / Enoyl-[acyl-carrier-protein] reductase [NADH] / S-acyl fatty acid synthase thioesterase / [Acyl- ...Enoyl-[acyl-carrier-protein] reductase [NADH] / S-acyl fatty acid synthase thioesterase / [Acyl-carrier-protein] acetyltransferase / [Acyl-carrier-protein] malonyltransferase


Mass: 235450.672 Da / Num. of mol.: 6 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
References: UniProt: G0S867
#2: Protein
3-oxoacyl-[acyl-carrier-protein] reductase / 3-oxoacyl-[acyl-carrier-protein] synthase / Acyl carrier / Beta-ketoacyl reductase / Beta-ketoacyl ...3-oxoacyl-[acyl-carrier-protein] synthase / Acyl carrier / Beta-ketoacyl reductase / Beta-ketoacyl synthase / Fatty acid synthase subunit alpha


Mass: 205066.922 Da / Num. of mol.: 6 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
References: UniProt: G0S866

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Fatty Acid Synthase Complex from Chaetomium thermophilum
Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightUnits: MEGADALTONS / Experimental value: NO
Source (natural)Organism: Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Buffer solutionpH: 7.4
Buffer componentConc.: 200 mM / Name: Ammonium acetate / Formula: NH4CH2COOH
SpecimenConc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277 K
Details: For plunging, blot force 2 and blotting time of 6 sec were applied.

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal magnification: 92000 X / Calibrated magnification: 95675 X / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: OTHER / Temperature (max): 103.15 K / Temperature (min): 77.15 K / Residual tilt: 14.7 mradians
Image recordingElectron dose: 30 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of real images: 2808

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Processing

Software
NameVersionClassificationNB
phenix.real_space_refine1.18.2_3874refinement
PHENIX1.18.2_3874refinement
EM software
IDNameVersionCategoryDetails
1cryoSPARC3.1particle selectionBlob Picker
4cryoSPARC3.1CTF correctionPatch CTF
7Coot0.9.2-premodel fitting
9cryoSPARC3.1initial Euler assignmentAb-Initio Reconstruction
10cryoSPARC3.1final Euler assignment
11cryoSPARC3.1classification2D Classification
12cryoSPARC3.13D reconstructionHomogeneous Refinement
13Coot0.9.2-premodel refinement
14PHENIX1.18.2model refinementphenix.real_space_refine
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.47 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 5231 / Algorithm: SIMULTANEOUS ITERATIVE (SIRT) / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Details: Initial models were predicted using AlphaFold v2.0.1, fitted into reconstructions using COOT and finally refined in real space using COOT and phenix.real_space_refine
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 244.94 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0054172272
ELECTRON MICROSCOPYf_angle_d0.8933233568
ELECTRON MICROSCOPYf_chiral_restr0.050925962
ELECTRON MICROSCOPYf_plane_restr0.006430354
ELECTRON MICROSCOPYf_dihedral_angle_d26.369163984
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2JELECTRON MICROSCOPYNCS constraints0.033116786264
ens_1d_3JELECTRON MICROSCOPYNCS constraints0.033419085142
ens_1d_4JELECTRON MICROSCOPYNCS constraints0.000701616506773
ens_1d_5JELECTRON MICROSCOPYNCS constraints0.000706431306184
ens_1d_6JELECTRON MICROSCOPYNCS constraints0.0331128170036
ens_2d_2IELECTRON MICROSCOPYNCS constraints0.02887809096
ens_2d_3IELECTRON MICROSCOPYNCS constraints0.00070474578071
ens_2d_4IELECTRON MICROSCOPYNCS constraints0.000707430627256
ens_2d_5IELECTRON MICROSCOPYNCS constraints0.0382715185447
ens_2d_6IELECTRON MICROSCOPYNCS constraints0.000577671192073

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