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- EMDB-44378: Human endogenous FASN - combined class1 condensing wing with clas... -

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Basic information

Entry
Database: EMDB / ID: EMD-44378
TitleHuman endogenous FASN - combined class1 condensing wing with classification
Map dataHuman endogenous FASN - Combined class 1 focused condensing domain map
Sample
  • Complex: Human endogenous FASN with 1,3-DBP
    • Protein or peptide: Human fatty acid synthase
KeywordsDe novo fatty acid synthesis Fatty acid synthase / BIOSYNTHETIC PROTEIN / TRANSFERASE
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: 2.9 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
DepositionApr 1, 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_44378.png

Downloads & links

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Map

FileDownload / File: emd_44378.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHuman endogenous FASN - Combined class 1 focused condensing domain map
Projections & slices

Image control

Size
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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

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.835 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.001
Minimum - Maximum-0.00540991 - 0.019333344
Average (Standard dev.)-0.0000091937345 (±0.0005194397)
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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Additional map: Human endogenous FASN - Combined class 1 focused...

Fileemd_44378_additional_1.map
AnnotationHuman endogenous FASN - Combined class 1 focused condensing domain ACP-MAT
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Additional map: Human endogenous FASN - Combined class 1 focused...

Fileemd_44378_additional_10.map
AnnotationHuman endogenous FASN - Combined class 1 focused condensing domain ACP-KS class 2
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Additional map: Human endogenous FASN - Combined class 1 focused...

Fileemd_44378_additional_11.map
AnnotationHuman endogenous FASN - Combined class 1 focused condensing domain ACP-KS class 1
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Additional map: Human endogenous FASN - Combined class 1 focused...

Fileemd_44378_additional_12.map
AnnotationHuman endogenous FASN - Combined class 1 focused condensing domain No-ACP class 5
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Additional map: Human endogenous FASN - Combined class 1 focused...

Fileemd_44378_additional_2.map
AnnotationHuman endogenous FASN - Combined class 1 focused condensing domain dynamic MAT class 1
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Additional map: Human endogenous FASN - Combined class 1 focused...

Fileemd_44378_additional_3.map
AnnotationHuman endogenous FASN - Combined class 1 focused condensing domain No-ACP class 1
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Additional map: Human endogenous FASN - Combined class 1 focused...

Fileemd_44378_additional_4.map
AnnotationHuman endogenous FASN - Combined class 1 focused condensing domain No-ACP class 3
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Additional map: Human endogenous FASN - Combined class 1 focused...

Fileemd_44378_additional_5.map
AnnotationHuman endogenous FASN - Combined class 1 focused condensing domain junk class
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Additional map: Human endogenous FASN - Combined class 1 focused...

Fileemd_44378_additional_6.map
AnnotationHuman endogenous FASN - Combined class 1 focused condensing domain floating ACP class
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Additional map: Human endogenous FASN - Combined class 1 focused...

Fileemd_44378_additional_7.map
AnnotationHuman endogenous FASN - Combined class 1 focused condensing domain No-ACP class 2
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Additional map: Human endogenous FASN - Combined class 1 focused...

Fileemd_44378_additional_8.map
AnnotationHuman endogenous FASN - Combined class 1 focused condensing domain No-ACP class 4
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Additional map: Human endogenous FASN - Combined class 1 focused...

Fileemd_44378_additional_9.map
AnnotationHuman endogenous FASN - Combined class 1 focused condensing domain dynamic MAT class 2
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Half map: Human endogenous FASN - Combined class 1 focused...

Fileemd_44378_half_map_1.map
AnnotationHuman endogenous FASN - Combined class 1 focused condensing domain half map 1
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Half map: Human endogenous FASN - Combined class 1 focused...

Fileemd_44378_half_map_2.map
AnnotationHuman endogenous FASN - Combined class 1 focused condensing domain half map 2
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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: Human 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: Human fatty acid synthase

MacromoleculeName: Human fatty acid synthase / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString: MEEVVIAGMS GKLPESENLQ EFWDNLIGGV DMVTDDDRRW KAGLYGLPRR SGKLKDLSRF DASFFGVHP KQAHTMDPQL RLLLEVTYEA IVDGGINPDS LRGTHTGVWV GVSGSETSEA L SRDPETLV GYSMVGCQRA MMANRLSFFF DFRGPSIALD TACSSSLMAL ...String:
MEEVVIAGMS GKLPESENLQ EFWDNLIGGV DMVTDDDRRW KAGLYGLPRR SGKLKDLSRF DASFFGVHP KQAHTMDPQL RLLLEVTYEA IVDGGINPDS LRGTHTGVWV GVSGSETSEA L SRDPETLV GYSMVGCQRA MMANRLSFFF DFRGPSIALD TACSSSLMAL QNAYQAIHSG QC PAAIVGG INVLLKPNTS VQFLRLGMLS PEGTCKAFDT AGNGYCRSEG VVAVLLTKKS LAR RVYATI LNAGTNTDGF KEQGVTFPSG DIQEQLIRSL YQSAGVAPES FEYIEAHGTG TKVG DPQEL NGITRALCAT RQEPLLIGST KSNMGHPEPA SGLAALAKVL LSLEHGLWAP NLHFH SPNP EIPALLDGRL QVVDQPLPVR GGNVGINSFG FGGSNVHIIL RPNTQPPPAP APHATL PRL LRASGRTPEA VQKLLEQGLR HSQDLAFLSM LNDIAAVPAT AMPFRGYAVL GGERGGP EV QQVPAGERPL WFICSGMGTQ WRGMGLSLMR LDRFRDSILR SDEAVKPFGL KVSQLLLS T DESTFDDIVH SFVSLTAIQI GLIDLLSCMG LRPDGIVGHS LGEVACGYAD GCLSQEEAV LAAYWRGQCI KEAHLPPGAM AAVGLSWEEC KQRCPPGVVP ACHNSKDTVT ISGPQAPVFE FVEQLRKEG VFAKEVRTGG MAFHSYFMEA IAPPLLQELK KVIREPKPRS ARWLSTSIPE A QWHSSLAR TSSAEYNVNN LVSPVLFQEA LWHVPEHAVV LEIAPHALLQ AVLKRGLKPS CT IIPLMKK DHRDNLEFFL AGIGRLHLSG IDANPNALFP PVEFPAPRGT PLISPLIKWD HSL AWDVPA AEDFPNGSGS PSAAIYNIDT SSESPDHYLV DHTLDGRVLF PATGYLSIVW KTLA RALGL GVEQLPVVFE DVVLHQATIL PKTGTVSLEV RLLEASRAFE VSENGNLVVS GKVYQ WDDP DPRLFDHPES PTPNPTEPLF LAQAEVYKEL RLRGYDYGPH FQGILEASLE GDSGRL LWK DNWVSFMDTM LQMSILGSAK HGLYLPTRVT AIHIDPATHR QKLYTLQDKA QVADVVV SR WLRVTVAGGV HISGLHTESA PRRQQEQQVP ILEKFCFTPH TEEGCLSERA ALQEELQL C KGLVQALQTK VTQQGLKMVV PGLDGAQIPR DPSQQELPRL LSAACRLQLN GNLQLELAQ VLAQERPKLP EDPLLSGLLD SPALKACLDT AVENMPSLKM KVVEVLAGHG HLYSRIPGLL SPHPLLQLS YTATDRHPQA LEAAQAELQQ HDVAQGQWDP ADPAPSALGS ADLLVCNCAV A ALGDPASA LSNMVAALRE GGFLLLHTLL RGHPLGDIVA FLTSTEPQYG QGILSQDAWE SL FSRVSLR LVGLKKSFYG STLFLCRRPT PQDSPIFLPV DDTSFRWVES LKGILADEDS SRP VWLKAI NCATSGVVGL VNCLRREPGG NRLRCVLLSN LSSTSHVPEV DPGSAELQKV LQGD LVMNV YRDGAWGAFR HFLLEEDKPE EPTAHAFVST LTRGDLSSIR WVCSSLRHAQ PTCPG AQLC TVYYASLNFR DIMLATGKLS PDAIPGKWTS QDSLLGMEFS GRDASGKRVM GLVPAK GLA TSVLLSPDFL WDVPSNWTLE EAASVPVVYS TAYYALVVRG RVRPGETLLI HSGSGGV GQ AAIAIALSLG CRVFTTVGSA EKRAYLQARF PQLDSTSFAN SRDTSFEQHV LWHTGGKG V DLVLNSLAEE KLQASVRCLA THGRFLEIGK FDLSQNHPLG MAIFLKNVTF HGVLLDAFF NESSADWREV WALVQAGIRD GVVRPLKCTV FHGAQVEDAF RYMAQGKHIG KVVVQVLAEE PEAVLKGAK PKLMSAISKT FCPAHKSYII AGGLGGFGLE LAQWLIQRGV QKLVLTSRSG I RTGYQAKQ VRRWRRQGVQ VQVSTSNISS LEGARGLIAE AAQLGPVGGV FNLAVVLRDG LL ENQTPEF FQDVCKPKYS GTLNLDRVTR EACPELDYFV VFSSVSCGRG NAGQSNYGFA NSA MERICE KRRHEGLPGL AVQWGAIGDV GILVETMSTN DTIVSGTLPQ RMASCLEVLD LFLN QPHMV LSSFVLAEKA AAYRDRDSQR DLVEAVAHIL GIRDLAAVNL DSSLADLGLD SLMSV EVRQ TLERELNLVL SVREVRQLTL RKLQELSSKA DEASELACPT PKEDGLAQQQ TQLNLR SLL VNPEGPTLMR LNSVQSSERP LFLVHPIEGS TTVFHSLASR LSIPTYGLQC TRAAPLD SI HSLAAYYIDC IRQVQPEGPY RVAGYSYGAC VAFEMCSQLQ AQQSPAPTHN SLFLFDGS P TYVLAYTQSY RAKLTPGCEA EAETEAICFF VQQFTDMEHN RVLEALLPLK GLEERVAAA VDLIIKSHQG LDRQELSFAA RSFYYKLRAA EQYTPKAKYH GNVMLLRAKT GGAYGEDLGA DYNLSQVCD GKVSVHVIEG DHRTLLEGSG LESIISIIHS SLAEPRVSVR EG

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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

MicroscopeFEI TITAN 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: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 752729
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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