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- EMDB-44329: Human endogenous FASN with 1,3-DBP - Class 1 focused condensing wing -

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Basic information

Entry
Database: EMDB / ID: EMD-44329
TitleHuman endogenous FASN with 1,3-DBP - Class 1 focused condensing wing
Map dataHuman endogenous FASN with 1,3-DBP - Class 1 focused condensing map
Sample
  • Complex: Human endogenous FASN with 1,3-DBP
    • Protein or peptide: Fatty acid synthase
KeywordsDe novo fatty acid synthesis Fatty acid synthase / BIOSYNTHETIC PROTEIN
Function / homology
Function and homology information


fatty-acid synthase system / ether lipid biosynthetic process / Vitamin B5 (pantothenate) metabolism / neutrophil differentiation / fatty-acyl-CoA biosynthetic process / enoyl-[acyl-carrier-protein] reductase (NADPH, Re-specific) / glandular epithelial cell development / establishment of endothelial intestinal barrier / [acyl-carrier-protein] S-acetyltransferase / [acyl-carrier-protein] S-acetyltransferase activity ...fatty-acid synthase system / ether lipid biosynthetic process / Vitamin B5 (pantothenate) metabolism / neutrophil differentiation / fatty-acyl-CoA biosynthetic process / enoyl-[acyl-carrier-protein] reductase (NADPH, Re-specific) / glandular epithelial cell development / establishment of endothelial intestinal barrier / [acyl-carrier-protein] S-acetyltransferase / [acyl-carrier-protein] S-acetyltransferase activity / glycogen granule / Fatty acyl-CoA biosynthesis / oleoyl-[acyl-carrier-protein] hydrolase / fatty acyl-[ACP] hydrolase activity / modulation by host of viral process / ChREBP activates metabolic gene expression / [acyl-carrier-protein] S-malonyltransferase / 3-hydroxyacyl-[acyl-carrier-protein] dehydratase / enoyl-[acyl-carrier-protein] reductase (NADPH) activity / [acyl-carrier-protein] S-malonyltransferase activity / beta-ketoacyl-[acyl-carrier-protein] synthase I / (3R)-hydroxyacyl-[acyl-carrier-protein] dehydratase activity / NR1H2 & NR1H3 regulate gene expression linked to lipogenesis / mammary gland development / 3-oxoacyl-[acyl-carrier-protein] reductase / 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / fatty acid synthase activity / monocyte differentiation / phosphopantetheine binding / 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 / cadherin binding / inflammatory response / 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 / : / Alcohol dehydrogenase-like, C-terminal / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Zinc-binding dehydrogenase / Acyl transferase domain superfamily / Acyl transferase/acyl hydrolase/lysophospholipase / Polyketide synthase, enoylreductase domain / Enoylreductase / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / PKS_KR / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Beta-ketoacyl synthase / Ketosynthase family 3 (KS3) domain profile. / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Polyketide synthase, beta-ketoacyl synthase domain / 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: 2.5 Å
AuthorsChoi W / Li C / Chen Y / Wang Y / Cheng Y
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM140847 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U54AI170792 United States
CitationJournal: Nature / Year: 2025
Title: Structural dynamics of human fatty acid synthase in the condensing cycle.
Authors: Wooyoung Choi / Chengmin Li / Yifei Chen / YongQiang Wang / Yifan Cheng /
Abstract: Long-chain fatty acids are the building blocks of fat in human bodies. In mammals, fatty acid synthase (FASN) contains multiple enzymatic domains to catalyse all chemical reactions needed for de novo ...Long-chain fatty acids are the building blocks of fat in human bodies. In mammals, fatty acid synthase (FASN) contains multiple enzymatic domains to catalyse all chemical reactions needed for de novo fatty acid synthesis. Although the chemical reactions carried out by these enzymatic domains are well defined, how the dimeric FASN with an open architecture continuously catalyses such reactions to synthesize a complete fatty acid remains elusive. Here, using a strategy of tagging and purifying endogenous FASN in HEK293T cells for single-particle cryo-electron microscopy studies, we characterized the structural dynamics of endogenous human FASN. We captured conformational snapshots of various functional substates in the condensing cycle and developed a procedure to analyse the particle distribution landscape of FASN with different orientations between its condensing and modifying wings. Together, our findings reveal that FASN function does not require a large rotational motion between its two main functional domains during the condensing cycle, and that the catalytic reactions in the condensing cycle carried out by the two monomers are unsynchronized. Our data thus provide a new composite view of FASN dynamics during the fatty acid synthesis condensing cycle.
History
DepositionMar 28, 2024-
Header (metadata) releaseFeb 26, 2025-
Map releaseFeb 26, 2025-
UpdateMay 21, 2025-
Current statusMay 21, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44329.png

Downloads & links

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Map

FileDownload / File: emd_44329.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHuman endogenous FASN with 1,3-DBP - Class 1 focused condensing map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 360 pix.
= 300.6 Å		0.84 Å/pix.
x 360 pix.
= 300.6 Å		0.84 Å/pix.
x 360 pix.
= 300.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.835 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0012
Minimum - Maximum-0.006217394 - 0.020843996
Average (Standard dev.)-0.00001279461 (±0.00054189656)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 300.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Human endogenous FASN with 1,3-DBP - Class 1...

Fileemd_44329_half_map_1.map
AnnotationHuman endogenous FASN with 1,3-DBP - Class 1 focused condensing half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Human endogenous FASN with 1,3-DBP - Class 1...

Fileemd_44329_half_map_2.map
AnnotationHuman endogenous FASN with 1,3-DBP - Class 1 focused condensing half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human endogenous FASN with 1,3-DBP

EntireName: Human endogenous FASN with 1,3-DBP
Components
  • Complex: Human endogenous FASN with 1,3-DBP
    • Protein or peptide: Fatty acid synthase

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Supramolecule #1: Human endogenous FASN with 1,3-DBP

SupramoleculeName: Human endogenous FASN with 1,3-DBP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Fatty acid synthase

MacromoleculeName: Fatty acid synthase / type: protein_or_peptide / ID: 1
Details: Phosphopantetheine (PNS)-modified acyl carrier protein domain
Number of copies: 2 / Enantiomer: LEVO / EC number: fatty-acid synthase system
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 92.515781 KDa
SequenceString: MEEVVIAGMS GKLPESENLQ EFWDNLIGGV DMVTDDDRRW KAGLYGLPRR SGKLKDLSRF DASFFGVHPK QAHTMDPQLR LLLEVTYEA IVDGGINPDS LRGTHTGVWV GVSGSETSEA LSRDPETLVG YSMVGCQRAM MANRLSFFFD FRGPSIALDT A CSSSLMAL ...String:
MEEVVIAGMS GKLPESENLQ EFWDNLIGGV DMVTDDDRRW KAGLYGLPRR SGKLKDLSRF DASFFGVHPK QAHTMDPQLR LLLEVTYEA IVDGGINPDS LRGTHTGVWV GVSGSETSEA LSRDPETLVG YSMVGCQRAM MANRLSFFFD FRGPSIALDT A CSSSLMAL QNAYQAIHSG QCPAAIVGGI NVLLKPNTSV QFLRLGMLSP EGTCKAFDTA GNGYCRSEGV VAVLLTKKSL AR RVYATIL NAGTNTDGFK EQGVTFPSGD IQEQLIRSLY QSAGVAPESF EYIEAHGTGT KVGDPQELNG ITRALCATRQ EPL LIGSTK SNMGHPEPAS GLAALAKVLL SLEHGLWAPN LHFHSPNPEI PALLDGRLQV VDQPLPVRGG NVGINSFGFG GSNV HIILR PNTQPPPAPA PHATLPRLLR ASGRTPEAVQ KLLEQGLRHS QDLAFLSMLN DIAAVPATAM PFRGYAVLGG ERGGP EVQQ VPAGERPLWF ICSGMGTQWR GMGLSLMRLD RFRDSILRSD EAVKPFGLKV SQLLLSTDES TFDDIVHSFV SLTAIQ IGL IDLLSCMGLR PDGIVGHSLG EVACGYADGC LSQEEAVLAA YWRGQCIKEA HLPPGAMAAV GLSWEECKQR CPPGVVP AC HNSKDTVTIS GPQAPVFEFV EQLRKEGVFA KEVRTGGMAF HSYFMEAIAP PLLQELKKVI REPKPRSARW LSTSIPEA Q WHSSLARTSS AEYNVNNLVS PVLFQEALWH VPEHAVVLEI APHALLQAVL KRGLKPSCTI IPLMKKDHRD NLEFFLAGI GRLHLSGIDA NPNALFPPVE FPAPRGTPLI SPLIKWDHSL AWDVPAAEDF PNGS

UniProtKB: Fatty acid synthase

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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

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 45.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 448162
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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