[English] 日本語
Yorodumi
- EMDB-40783: MBP-tagged fusion fatty acid synthase from S. cerevisiae -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-40783
TitleMBP-tagged fusion fatty acid synthase from S. cerevisiae
Map data6xMBP fused FAS
Sample
  • Complex: MBP-tagged Fatty acid synthase
    • Protein or peptide: Fatty acid synthase
KeywordsFatty acid synthase / TRANSFERASE
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.21 Å
AuthorsMazhab-Jafari MT / Khalili Samani E
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: Commun Biol / Year: 2024
Title: Direct structural analysis of a single acyl carrier protein domain in fatty acid synthase from the fungus Saccharomyces cerevisiae.
Authors: Elnaz Khalili Samani / Amy C Chen / Jennifer W Lou / David L Dai / Alexander F A Keszei / Guihong Tan / Charles Boone / Martin Grininger / Mohammad T Mazhab-Jafari /
Abstract: Acyl carrier protein (ACP) is the work horse of polyketide (PKS) and fatty acid synthases (FAS) and acts as a substrate shuttling domain in these mega enzymes. In fungi, FAS forms a 2.6 MDa symmetric ...Acyl carrier protein (ACP) is the work horse of polyketide (PKS) and fatty acid synthases (FAS) and acts as a substrate shuttling domain in these mega enzymes. In fungi, FAS forms a 2.6 MDa symmetric assembly with six identical copies of FAS1 and FAS2 polypeptides. However, ACP spatial distribution is not restricted by symmetry owing to the long and flexible loops that tether the shuttling domain to its corresponding FAS2 polypeptide. This symmetry breaking has hampered experimental investigation of substrate shuttling route in fungal FAS. Here, we develop a protein engineering and expression method to isolate asymmetric fungal FAS proteins containing odd numbers of ACP domains. Electron cryomicroscopy (cryoEM) observation of the engineered complex reveals a non-uniform distribution of the substrate shuttling domain relative to its corresponding FAS2 polypeptide at 2.9 Å resolution. This work lays the methodological foundation for experimental study of ACP shuttling route in fungi.
History
DepositionMay 15, 2023-
Header (metadata) releaseJan 24, 2024-
Map releaseJan 24, 2024-
UpdateMay 8, 2024-
Current statusMay 8, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_40783.png

Downloads & links

-
Map

FileDownload / File: emd_40783.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation6xMBP fused FAS
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.03 Å/pix.
x 400 pix.
= 412. Å		1.03 Å/pix.
x 400 pix.
= 412. Å		1.03 Å/pix.
x 400 pix.
= 412. 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: 0.347
Minimum - Maximum-1.091563 - 2.2468886
Average (Standard dev.)0.004824593 (±0.1252819)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 412.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: Half map A

Fileemd_40783_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map B

Fileemd_40783_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : MBP-tagged Fatty acid synthase

EntireName: MBP-tagged Fatty acid synthase
Components
  • Complex: MBP-tagged Fatty acid synthase
    • Protein or peptide: Fatty acid synthase

-
Supramolecule #1: MBP-tagged Fatty acid synthase

SupramoleculeName: MBP-tagged Fatty acid synthase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 2.7 MDa

-
Macromolecule #1: Fatty acid synthase

MacromoleculeName: Fatty acid synthase / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MDAYSTRPLT LSHGSLEHVL LVPTASFFIA SQLQEQFNKI LPEPTEGFAA DDEPTTPAEL VGKFLGYVSS LVEPSKVGQF DQVLNLCLTE FENCYLEGND IHALAAKLLQ ENDTTLVKTK ELIKNYITAR IMAKRPFDKK SNSALFRAVG EGNAQLVAIF GGQGNTDDYF ...String:
MDAYSTRPLT LSHGSLEHVL LVPTASFFIA SQLQEQFNKI LPEPTEGFAA DDEPTTPAEL VGKFLGYVSS LVEPSKVGQF DQVLNLCLTE FENCYLEGND IHALAAKLLQ ENDTTLVKTK ELIKNYITAR IMAKRPFDKK SNSALFRAVG EGNAQLVAIF GGQGNTDDYF DELRDLYQTY HVLVGDLIKF SAETLSELIR TTLDAEKVFT QGLNILEWLE NPSNTPDKDY LLSIPISCPL IGVIQLAHYV VTAKLLGFTP GELRSYLKGA TGHSQGLVTA VAIAETDSWE SFFVSVRKAI TVLFFIGVRC YEAYPNTSLP PSILEDSLEN NEGVPSPMLS ISNLTQEQVQ DYVNKTNSHL PAGKQVEISL VNGAKNLVVS GPPQSLYGLN LTLRKAKAPS GLDQSRIPFS ERKLKFSNRF LPVASPFHSH LLVPASDLIN KDLVKNNVSF NAKDIQIPVY DTFDGSDLRV LSGSISERIV DCIIRLPVKW ETTTQFKATH ILDFGPGGAS GLGVLTHRNK DGTGVRVIVA GTLDINPDDD YGFKQEIFDV TSNGLKKNPN WLEEYHPKLI KNKSGKIFVE TKFSKLIGRP PLLVPGMTPC TVSPDFVAAT TNAGYTIELA GGGYFSAAGM TAAIDSVVSQ IEKGSTFGIN LIYVNPFMLQ WGIPLIKELR SKGYPIQFLT IGAGVPSLEV ASEYIETLGL KYLGLKPGSI DAISQVINIA KAHPNFPIAL QWTGGRGGGH HSFEDAHTPM LQMYSKIRRH PNIMLIFGSG FGSADDTYPY LTGEWSTKFD YPPMPFDGFL FGSRVMIAKE VKTSPDAKKC IAACTGVPDD KWEQTYKKPT GGIVTVRSEM GEPIHKIATR GVMLWKEFDE TIFNLPKNKL VPTLEAKRDY IISRLNADFQ KPWFATVNGQ ARDLATMTYE EVAKRLVELM FIRSTNSWFD VTWRTFTGDF LRRVEERFTK SKTLSLIQSY SLLDKPDEAI EKVFNAYPAA REQFLNAQDI DHFLSMCQNP MQKPVPFVPV LDRRFEIFFK KDSLWQSEHL EAVVDQDVQR TCILHGPVAA QFTKVIDEPI KSIMDGIHDG HIKKLLHQYY GDDESKIPAV EYFGGESPVD VQSQVDSSSV SEDSAVFKAT SSTDEESWFK ALAGSEINWR HASFLCSFIT QDKMFVSNPI RKVFKPSQGM VVEISNGNTS SKTVVTLSEP VQGGSGSGSG SMKIEEGKLV IWINGDKGYN GLAEVGKKFE KDTGIKVTVE HPDKLEEKFP QVAATGDGPD IIFWAHDRFG GYAQSGLLAE ITPDKAFQDK LYPFTWDAVR YNGKLIAYPI AVEALSLIYN KDLLPNPPKT WEEIPALDKE LKAKGKSALM FNLQEPYFTW PLIAADGGYA FKYENGKYDI KDVGVDNAGA KAGLTFLVDL IKNKHMNADT DYSIAEAAFN KGETAMTING PWAWSNIDTS KVNYGVTVLP TFKGQPSKPF VGVLSAGINA ASPNKELAKE FLENYLLTDE GLEAVNKDKP LGAVALKSYE EELAKDPRIA ATMENAQKGE IMPNIPQMSA FWYAVRTAVI NAASGRQTVD EALKDAQTGS GSGSGSELKP TVILKLLKEN IIQMEMIENR TMDGKPVSLP LLYNFNPDNG FAPISEVMED RNQRIKEMYW KLWIDEPFNL DFDPRDVIKG KDFEITAKEV YDFTHAVGNN CEDFVSRPDR TMLAPMDFAI VVGWRAIIKA IFPNTVDGDL LKLVHLSNGY KMIPGAKPLQ VGDVVSTTAV IESVVNQPTG KIVDVVGTLS RNGKPVMEVT SSFFYRGNYT DFENTFQKTV EPVYQMHIKT SKDIAVLRSK EWFQLDDEDF DLLNKTLTFE TETEVTFKNA NIFSSVKCFG PIKVELPTKE TVEIGIVDYE AGASHGNPVV DFLKRNGSTL EQKVNLENPI PIAVLDSYTP STNEPYARVS GDLNPIHVSR HFASYANLPG TITHGMFSSA SVRALIENWA ADSVSSRVRG YTCQFVDMVL PNTALKTSIQ HVGMINGRKL IKFETRNEDD VVVLTGEAEI EQPVTTFVFT GQGSQEQGMG MDLYKTSKAA QDVWNRADNH FKDTYGFSIL DIVINNPVNL TIHFGGEKGK RIRENYSAMI FETIVDGKLK TEKIFKEINE HSTSYTFRSE KGLLSATQFT QPALTLMEKA AFEDLKSKGL IPADATFAGH SLGEYAALAS LADVMSIESL VEVVFYRGMT MQVAVPRDEL GRSNYGMIAI NPGRVAASFS QEALQYVVER VGKRTGWLVE IVNYNVENQQ YVAAGDLRAL DTVTNVLNFI KLQKIDIIEL QKSLSLEEVE GHLFEIIDEA SKKSAVKPRP LKLERGFACI PLVGISVPFH STYLMNGVKP FKSFLKKNII KENVKVARLA GKYIPNLTAK PFQVTKEYFQ DVYDLTGSEP IKEIIDNWEK DEWGSPEVEQ ELAHILLTEL LAYQFASPVR WIETQDVFLK DFNTERVVEI GPSPTLAGMA QRTLKNKYES YDAALSLHRE ILCYSKDAKE IYYTPDPSEL AAKEEPAKEE APAPTPAASA PAPAAAAPAP VAAAAPAAAA AEIADEPVKA SLLLHVLVAH KLKKSLDSIP MSKTIKDLVG GKSTVQNEIL GDLGKEFGTT PEKPEETPLE ELAETFQDTF SGALGKQSSS LLSRLISSKM PGGFTITVAR KYLQTRWGLP SGRQDGVLLV ALSNEPAARL GSEADAKAFL DSMAQKYASI VGVDLSSAAS ASGAAGAGAA AGAAMIDAGA LEEITKDHKV LARQQLQVLA RYLKMDLDNG ERKFLKEKDT VAELQAQLDY LNAELGEFFV NGVATSFSRK KARTFDSSWN WAKQSLLSLY FEIIHGVLKN VDREVVSEAI NIMNRSNDAL IKFMEYHISN TDETKGENYQ LVKTLGEQLI ENCKQVLDVD PVYKDVAKPT GPKTAIDKNG NITYSEEPRE KVRKLSQYVQ EMALGGPITK ESQPTIEEDL TRVYKAISAQ ADKQDISSST RVEFEKLYSD LMKFLESSKE IDPSQTTQLA GMDVEDALDK DSTKEVASLP NKSTISKTVS STIPRETIPF LHLRKKTPAG DWKYDRQLSS LFLDGLEKAA FNGVTFKDKY VLITGAGKGS IGAEVLQGLL QGGAKVVVTT SRFSKQVTDY YQSIYAKYGA KGSTLIVVPF NQGSKQDVEA LIEFIYDTEK NGGLGWDLDA IIPFAAIPEQ GIELEHIDSK SEFAHRIMLT NILRMMGCVK KQKSARGIET RPAQVILPMS PNHGTFGGDG MYSESKLSLE TLFNRWHSES WANQLTVCGA IIGWTRGTGL MSANNIIAEG IEKMGVRTFS QKEMAFNLLG LLTPEVVELC QKSPVMADLN GGLQFVPELK EFTAKLRKEL VETSEVRKAV SIETALEHKV VNGNSADAAY AQVEIQPRAN IQLDFPELKP YKQVKQIAPA ELEGLLDLER VIVVTGFAEV GPWGSARTRW EMEAFGEFSL EGCVEMAWIM GFISYHNGNL KGRPYTGWVD SKTKEPVDDK DVKAKYETSI LEHSGIRLIE PELFNGYNPE KKEMIQEVIV EEDLEPFEAS KETAEQFKHQ HGDKVDIFEI PETGEYSVKL LKGATLYIPK ALRFDRLVAG QIPTGWNAKT YGISDDIISQ VDPITLFVLV SVVEAFIASG ITDPYEMYKY VHVSEVGNCS GSGMGGVSAL RGMFKDRFKD EPVQNDILQE SFINTMSAWV NMLLISSSGP IKTPVGACAT SVESVDIGVE TILSGKARIC IVGGYDDFQE EGSFEFGNMK ATSNTLEEFE HGRTPAEMSR PATTTRNGFM EAQGAGIQII MQADLALKMG VPIYGIVAMA ATATDKIGRS VPAPGKGILT TAREHHSSVK YASPNLNMKY RKRQLVTREA QIKDWVENEL EALKLEAEEI PSEDQNEFLL ERTREIHNEA ESQLRAAQQQ WGNDFYKRDP RIAPLRGALA TYGLTIDDLG VASFHGTSTK ANDKNESATI NEMMKHLGRS EGNPVIGVFQ KFLTGHPKGA AGAWMMNGAL QILNSGIIPG NRNADNVDKI LEQFEYVLYP SKTLKTDGVR AVSITSFGFG QKGGQAIVVH PDYLYGAITE DRYNEYVAKV SAREKSAYKF FHNGMIYNKL FVSKEHAPYT DELEEDVYLD PLARVSKDKK SGSLTFNSKN IQSKDSYINA NTIETAKMIE NMTKEKVSNG GVGVDVELIT SINVENDTFI ERNFTPQEIE YCSAQPSVQS SFAGTWSAKE AVFKSLGVKS LGGGAALKDI EIVRVNKNAP AVELHGNAKK AAEEAGVTDV KVSISHDDLQ AVAVAVSTKK HHHHHHHHHH

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration2 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. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 3974 / Average electron dose: 54.76 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

-
Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.21 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.0.2) / Number images used: 71932
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4)

+
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