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- EMDB-28691: Atomic model of the core modifying region of human fatty acid syn... -

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Basic information

Entry
Database: EMDB / ID: EMD-28691
TitleAtomic model of the core modifying region of human fatty acid synthase in complex with TVB-2640
Map data
Sample
  • Complex: Fatty acid synthase
    • Protein or peptide: Fatty acid synthase
  • Ligand: denifanstat
  • Ligand: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
KeywordsFatty acid synthase / TRANSFERASE / TRANSFERASE-INHIBITOR complex
Function / homology
Function and homology information


fatty-acid synthase system / : / : / : / ether lipid biosynthetic process / Vitamin B5 (pantothenate) metabolism / : / neutrophil differentiation / enoyl-[acyl-carrier-protein] reductase (NADPH, Re-specific) / glandular epithelial cell development ...fatty-acid synthase system / : / : / : / ether lipid biosynthetic process / Vitamin B5 (pantothenate) metabolism / : / neutrophil differentiation / enoyl-[acyl-carrier-protein] reductase (NADPH, Re-specific) / glandular epithelial cell development / glycogen granule / establishment of endothelial intestinal barrier / [acyl-carrier-protein] S-acetyltransferase / [acyl-carrier-protein] S-acetyltransferase activity / : / oleoyl-[acyl-carrier-protein] hydrolase / Fatty acyl-CoA biosynthesis / fatty acyl-[ACP] hydrolase activity / modulation by host of viral process / enoyl-[acyl-carrier-protein] reductase (NADPH) activity / ChREBP activates metabolic gene expression / [acyl-carrier-protein] S-malonyltransferase / [acyl-carrier-protein] S-malonyltransferase activity / 3-hydroxyacyl-[acyl-carrier-protein] dehydratase / beta-ketoacyl-[acyl-carrier-protein] synthase I / mammary gland development / NR1H2 & NR1H3 regulate gene expression linked to lipogenesis / 3-oxoacyl-[acyl-carrier-protein] reductase / 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / fatty acid synthase activity / phosphopantetheine binding / monocyte differentiation / 3-oxoacyl-[acyl-carrier-protein] synthase activity / cellular response to interleukin-4 / Activation of gene expression by SREBF (SREBP) / fatty acid metabolic process / fatty acid biosynthetic process / osteoblast differentiation / melanosome / inflammatory response / cadherin binding / Golgi apparatus / RNA binding / extracellular exosome / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
: / Fatty acid synthase, pseudo-KR domain / Methyltransferase type 12 / Methyltransferase domain / Thioesterase / Thioesterase domain / Polyketide synthase, dehydratase domain / PKS_DH / : / Polyketide synthase dehydratase domain ...: / Fatty acid synthase, pseudo-KR domain / Methyltransferase type 12 / Methyltransferase domain / Thioesterase / Thioesterase domain / Polyketide synthase, dehydratase domain / PKS_DH / : / Polyketide synthase dehydratase domain / Polyketide synthase, dehydratase domain superfamily / : / Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Polyketide synthase, ketoreductase domain / KR domain / Malonyl-CoA ACP transacylase, ACP-binding / : / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase domain superfamily / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Acyl transferase/acyl hydrolase/lysophospholipase / Polyketide synthase, enoylreductase domain / Enoylreductase / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / PKS_KR / Ketosynthase family 3 (KS3) domain profile. / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / GroES-like superfamily / Thiolase-like / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Alpha/Beta hydrolase fold / NAD(P)-binding domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsHasan SMN / Keszei A / Mazhab-Jafari MT
Funding support Canada, 2 items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)419240 Canada
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2018-06070 Canada
CitationJournal: Nat Commun / Year: 2023
Title: Atomic model for core modifying region of human fatty acid synthase in complex with Denifanstat.
Authors: S M Naimul Hasan / Jennifer W Lou / Alexander F A Keszei / David L Dai / Mohammad T Mazhab-Jafari /
Abstract: Fatty acid synthase (FASN) catalyzes the de novo synthesis of palmitate, a 16-carbon chain fatty acid that is the primary precursor of lipid metabolism and an important intracellular signaling ...Fatty acid synthase (FASN) catalyzes the de novo synthesis of palmitate, a 16-carbon chain fatty acid that is the primary precursor of lipid metabolism and an important intracellular signaling molecule. FASN is an attractive drug target in diabetes, cancer, fatty liver diseases, and viral infections. Here, we develop an engineered full-length human FASN (hFASN) that enables isolation of the condensing and modifying regions of the protein post-translation. The engineered protein enables electron cryo-microscopy (cryoEM) structure determination of the core modifying region of hFASN to 2.7 Å resolution. Examination of the dehydratase dimer within this region reveals that unlike its close homolog, porcine FASN, the catalytic cavity is close-ended and is accessible only through one opening in the vicinity of the active site. The core modifying region exhibits two major global conformational variabilities that describe long-range bending and twisting motions of the complex in solution. Finally, we solved the structure of this region bound to an anti-cancer drug, Denifanstat (i.e., TVB-2640), demonstrating the utility of our approach as a platform for structure guided design of future hFASN small molecule inhibitors.
History
DepositionOct 27, 2022-
Header (metadata) releaseMay 24, 2023-
Map releaseMay 24, 2023-
UpdateJun 19, 2024-
Current statusJun 19, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28691.png

Downloads & links

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Map

FileDownload / File: emd_28691.map.gz / Format: CCP4 / Size: 59.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.03 Å/pix.
x 250 pix.
= 257.5 Å		1.03 Å/pix.
x 250 pix.
= 257.5 Å		1.03 Å/pix.
x 250 pix.
= 257.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.03 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.341
Minimum - Maximum-3.7249131 - 6.1678295
Average (Standard dev.)0.00030850552 (±0.17612787)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions250250250
Spacing250250250
CellA=B=C: 257.5 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_28691_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_28691_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : Fatty acid synthase

EntireName: Fatty acid synthase
Components
  • Complex: Fatty acid synthase
    • Protein or peptide: Fatty acid synthase
  • Ligand: denifanstat
  • Ligand: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

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Supramolecule #1: Fatty acid synthase

SupramoleculeName: Fatty acid synthase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 340 KDa

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Macromolecule #1: Fatty acid synthase

MacromoleculeName: Fatty acid synthase / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: fatty-acid synthase system
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 182.749016 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GGSPSAAIYN IDTSSESPDH YLVDHTLDGR VLFPATGYLS IVWKTLARAL GLGVEQLPVV FEDVVLHQAT ILPKTGTVSL EVRLLEASR AFEVSENGNL VVSGKVYQWD DPDPRLFDHP ESPTPNPTEP LFLAQAEVYK ELRLRGYDYG PHFQGILEAS L EGDSGRLL ...String:
GGSPSAAIYN IDTSSESPDH YLVDHTLDGR VLFPATGYLS IVWKTLARAL GLGVEQLPVV FEDVVLHQAT ILPKTGTVSL EVRLLEASR AFEVSENGNL VVSGKVYQWD DPDPRLFDHP ESPTPNPTEP LFLAQAEVYK ELRLRGYDYG PHFQGILEAS L EGDSGRLL WKDNWVSFMD TMLQMSILGS AKHGLYLPTR VTAIHIDPAT HRQKLYTLQD KAQVADVVVS RWLRVTVAGG VH ISGLHTE SAPRRQQEQQ VPILEKFCFT PHTEEGCLSE RAALQEELQL CKGLVQALQT KVTQQGLKMV VPGLDGAQIP RDP SQQELP RLLSAACRLQ LNGNLQLELA QVLAQERPKL PEDPLLSGLL DSPALKACLD TAVENMPSLK MKVVEVLAGH GHLY SRIPG LLSPHPLLQL SYTATDRHPQ ALEAAQAELQ QHDVAQGQWD PADPAPSALG SADLLVCNCA VAALGDPASA LSNMV AALR EGGFLLLHTL LRGHPLGDIV AFLTSTEPQY GQGILSQDAW ESLFSRVSLR LVGLKKSFYG STLFLCRRPT PQDSPI FLP VDDTSFRWVE SLKGILADED SSRPVWLKAI NCATSGVVGL VNCLRREPGG NRLRCVLLSN LSSTSHVPEV DPGSAEL QK VLQGDLVMNV YRDGAWGAFR HFLLEEDKPE EPTAHAFVST LTRGDLSSIR WVCSSLRHAQ PTCPGAQLCT VYYASLNF R DIMLATGKLS PDAIPGKWTS QDSLLGMEFS GRDASGKRVM GLVPAKGLAT SVLLSPDFLW DVPSNWTLEE AASVPVVYS TAYYALVVRG RVRPGETLLI HSGSGGVGQA AIAIALSLGC RVFTTVGSAE KRAYLQARFP QLDSTSFANS RDTSFEQHVL WHTGGKGVD LVLNSLAEEK LQASVRCLAT HGRFLEIGKF DLSQNHPLGM AIFLKNVTFH GVLLDAFFNE SSADWREVWA L VQAGIRDG VVRPLKCTVF HGAQVEDAFR YMAQGKHIGK VVVQVLAEEP EAVLKGAKPK LMSAISKTFC PAHKSYIIAG GL GGFGLEL AQWLIQRGVQ KLVLTSRSGI RTGYQAKQVR RWRRQGVQVQ VSTSNISSLE GARGLIAEAA QLGPVGGVFN LAV VLRDGL LENQTPEFFQ DVCKPKYSGT LNLDRVTREA CPELDYFVVF SSVSCGRGNA GQSNYGFANS AMERICEKRR HEGL PGLAV QWGAIGDVGI LVETMSTNDT IVSGTLPQRM ASCLEVLDLF LNQPHMVLSS FVLAEKAAAY RDRDSQRDLV EAVAH ILGI RDLAAVNLDS SLADLGLDSL MSVEVRQTLE RELNLVLSVR EVRQLTLRKL QELSSKADEA SELACPTPKE DGLAQQ QTQ LNLRSLLVNP EGPTLMRLNS VQSSERPLFL VHPIEGSTTV FHSLASRLSI PTYGLQCTRA APLDSIHSLA AYYIDCI RQ VQPEGPYRVA GYSYGACVAF EMCSQLQAQQ SPAPTHNSLF LFDGSPTYVL AYTQSYRAKL TPGCEAEAET EAICFFVQ Q FTDMEHNRVL EALLPLKGLE ERVAAAVDLI IKSHQGLDRQ ELSFAARSFY YKLRAAEQYT PKAKYHGNVM LLRAKTGGA YGEDLGADYN LSQVCDGKVS VHVIEGDHRT LLEGSGLESI ISIIHSSLAE PRVSVREGLE SRGPHHHHHH

UniProtKB: Fatty acid synthase

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Macromolecule #2: denifanstat

MacromoleculeName: denifanstat / type: ligand / ID: 2 / Number of copies: 2 / Formula: X5O
Molecular weightTheoretical: 439.552 Da
Chemical component information

ChemComp-X5O:
denifanstat

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Macromolecule #3: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

MacromoleculeName: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
type: ligand / ID: 3 / Number of copies: 4 / Formula: NDP
Molecular weightTheoretical: 745.421 Da
Chemical component information

ChemComp-NDP:
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.8 mg/mL
BufferpH: 7.4
GridModel: Homemade / Material: COPPER/RHODIUM / Mesh: 400 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 25 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 4801 / Average electron dose: 50.76 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3) / Number images used: 311983
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-8eyk:
Atomic model of the core modifying region of human fatty acid synthase in complex with TVB-2640

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