[English] 日本語
Yorodumi
- EMDB-44330: Human endogenous FASN with 1,3-DBP - Class 1 focused modifying wing -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-44330
TitleHuman endogenous FASN with 1,3-DBP - Class 1 focused modifying wing
Map dataHuman endogenous FASN with 1,3-DBP - Class 1 focused modifying domain 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) / establishment of endothelial intestinal barrier / glycogen granule / [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) / establishment of endothelial intestinal barrier / glycogen granule / [acyl-carrier-protein] S-acetyltransferase / [acyl-carrier-protein] S-acetyltransferase activity / Fatty acyl-CoA biosynthesis / host-mediated perturbation of viral process / ChREBP activates metabolic gene expression / enoyl-[acyl-carrier-protein] reductase (NADPH) activity / [acyl-carrier-protein] S-malonyltransferase / [acyl-carrier-protein] S-malonyltransferase activity / 3-hydroxyacyl-[acyl-carrier-protein] dehydratase / (3R)-hydroxyacyl-[acyl-carrier-protein] dehydratase activity / beta-ketoacyl-[acyl-carrier-protein] synthase I / acetyl-CoA metabolic process / NR1H2 & NR1H3 regulate gene expression linked to lipogenesis / 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / 3-oxoacyl-[acyl-carrier-protein] reductase / mammary gland development / oleoyl-[acyl-carrier-protein] hydrolase / fatty acyl-[ACP] hydrolase activity / fatty acid synthase activity / monocyte differentiation / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / response to nutrient / cellular response to interleukin-4 / Activation of gene expression by SREBF (SREBP) / fatty acid metabolic process / osteoblast differentiation / fatty acid biosynthetic process / melanosome / cadherin binding / inflammatory response / Golgi apparatus / RNA binding / extracellular exosome / identical protein binding / membrane / plasma membrane / cytoplasm / cytosol
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 and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / Polyketide synthase, dehydratase domain superfamily / 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 / Zinc-binding dehydrogenase / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / 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 / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / 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: 2.7 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

-
Structure visualization

Supplemental images

emd_44330.png

Downloads & links

-
Map

FileDownload / File: emd_44330.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 modifying domain 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: 0.004
Minimum - Maximum-0.008200332 - 0.02325223
Average (Standard dev.)0.00003745745 (±0.0005934238)
SymmetrySpace group: 1
Details

EMDB XML:

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

-
Supplemental data

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

Fileemd_44330_half_map_1.map
AnnotationHuman endogenous FASN with 1,3-DBP - Class 1 focused modifying domain half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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

Fileemd_44330_half_map_2.map
AnnotationHuman endogenous FASN with 1,3-DBP - Class 1 focused modifying domain half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
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

-
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)

-
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: 181.078312 KDa
SequenceString: PSAAIYNIDT SSESPDHYLV DHTLDGRVLF PATGYLSIVW KTLARALGLG VEQLPVVFED VVLHQATILP KTGTVSLEVR LLEASRAFE VSENGNLVVS GKVYQWDDPD PRLFDHPESP TPNPTEPLFL AQAEVYKELR LRGYDYGPHF QGILEASLEG D SGRLLWKD ...String:
PSAAIYNIDT SSESPDHYLV DHTLDGRVLF PATGYLSIVW KTLARALGLG VEQLPVVFED VVLHQATILP KTGTVSLEVR LLEASRAFE VSENGNLVVS GKVYQWDDPD PRLFDHPESP TPNPTEPLFL AQAEVYKELR LRGYDYGPHF QGILEASLEG D SGRLLWKD NWVSFMDTML QMSILGSAKH GLYLPTRVTA IHIDPATHRQ KLYTLQDKAQ VADVVVSRWL RVTVAGGVHI SG LHTESAP RRQQEQQVPI LEKFCFTPHT EEGCLSERAA LQEELQLCKG LVQALQTKVT QQGLKMVVPG LDGAQIPRDP SQQ ELPRLL SAACRLQLNG NLQLELAQVL AQERPKLPED PLLSGLLDSP ALKACLDTAV ENMPSLKMKV VEVLAGHGHL YSRI PGLLS PHPLLQLSYT ATDRHPQALE AAQAELQQHD VAQGQWDPAD PAPSALGSAD LLVCNCAVAA LGDPASALSN MVAAL REGG FLLLHTLLRG HPLGDIVAFL TSTEPQYGQG ILSQDAWESL FSRVSLRLVG LKKSFYGSTL FLCRRPTPQD SPIFLP VDD TSFRWVESLK GILADEDSSR PVWLKAINCA TSGVVGLVNC LRREPGGNRL RCVLLSNLSS TSHVPEVDPG SAELQKV LQ GDLVMNVYRD GAWGAFRHFL LEEDKPEEPT AHAFVSTLTR GDLSSIRWVC SSLRHAQPTC PGAQLCTVYY ASLNFRDI M LATGKLSPDA IPGKWTSQDS LLGMEFSGRD ASGKRVMGLV PAKGLATSVL LSPDFLWDVP SNWTLEEAAS VPVVYSTAY YALVVRGRVR PGETLLIHSG SGGVGQAAIA IALSLGCRVF TTVGSAEKRA YLQARFPQLD STSFANSRDT SFEQHVLWHT GGKGVDLVL NSLAEEKLQA SVRCLATHGR FLEIGKFDLS QNHPLGMAIF LKNVTFHGVL LDAFFNESSA DWREVWALVQ A GIRDGVVR PLKCTVFHGA QVEDAFRYMA QGKHIGKVVV QVLAEEPEAV LKGAKPKLMS AISKTFCPAH KSYIIAGGLG GF GLELAQW LIQRGVQKLV LTSRSGIRTG YQAKQVRRWR RQGVQVQVST SNISSLEGAR GLIAEAAQLG PVGGVFNLAV VLR DGLLEN QTPEFFQDVC KPKYSGTLNL DRVTREACPE LDYFVVFSSV SCGRGNAGQS NYGFANSAME RICEKRRHEG LPGL AVQWG AIGDVGILVE TMSTNDTIVS GTLPQRMASC LEVLDLFLNQ PHMVLSSFVL AEKAAAYRDR DSQRDLVEAV AHILG IRDL AAVNLDSSLA DLGLDSLMSV EVRQTLEREL NLVLSVREVR QLTLRKLQEL SSKADEASEL ACPTPKEDGL AQQQTQ LNL RSLLVNPEGP TLMRLNSVQS SERPLFLVHP IEGSTTVFHS LASRLSIPTY GLQCTRAAPL DSIHSLAAYY IDCIRQV QP EGPYRVAGYS YGACVAFEMC SQLQAQQSPA PTHNSLFLFD GSPTYVLAYT QSYRAKLTPG CEAEAETEAI CFFVQQFT D MEHNRVLEAL LPLKGLEERV AAAVDLIIKS HQGLDRQELS FAARSFYYKL RAAEQYTPKA KYHGNVMLLR AKTGGAYGE DLGADYNLSQ VCDGKVSVHV IEGDHRTLLE GSGLESIISI IHSSLAEPRV SVREG

UniProtKB: Fatty acid synthase

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
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

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 448162
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
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