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- EMDB-0011: Structure of Mycobacterium tuberculosis Fatty Acid Synthase - I -

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Basic information

Entry
Database: EMDB / ID: EMD-0011
TitleStructure of Mycobacterium tuberculosis Fatty Acid Synthase - I
Map data
Sample
  • Complex: Fatty Acid Synthase - I
    • Protein or peptide: Fatty acid synthase
  • Ligand: FLAVIN MONONUCLEOTIDE
Function / homology
Function and homology information


fatty acid synthase complex / beta-ketoacyl-[acyl-carrier-protein] synthase I / enoyl-[acyl-carrier-protein] reductase (NADH) activity / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / hydrolase activity
Similarity search - Function
Fatty acid synthase beta subunit AflB /Fas1-like, central domain / Fatty acid synthase subunit beta/Fas1-like, helical / Fatty acid synthase / Starter unit:ACP transacylase / Starter unit:ACP transacylase in aflatoxin biosynthesis / MaoC-like dehydratase domain / MaoC like domain / HotDog domain superfamily / Acyl transferase domain superfamily / Acyl transferase ...Fatty acid synthase beta subunit AflB /Fas1-like, central domain / Fatty acid synthase subunit beta/Fas1-like, helical / Fatty acid synthase / Starter unit:ACP transacylase / Starter unit:ACP transacylase in aflatoxin biosynthesis / MaoC-like dehydratase domain / MaoC like domain / HotDog domain superfamily / Acyl transferase domain superfamily / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase/acyl hydrolase/lysophospholipase / Beta-ketoacyl synthase / 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 / Thiolase-like / Aldolase-type TIM barrel / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Fatty acid synthase / Fatty acid synthase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsElad N / Baron S / Shakked Z / Zimhony O / Diskin R
CitationJournal: Nat Commun / Year: 2018
Title: Structure of Type-I Mycobacterium tuberculosis fatty acid synthase at 3.3 Å resolution.
Authors: Nadav Elad / Szilvia Baron / Yoav Peleg / Shira Albeck / Jacob Grunwald / Gal Raviv / Zippora Shakked / Oren Zimhony / Ron Diskin /
Abstract: Tuberculosis (TB) is a devastating and rapidly spreading disease caused by Mycobacterium tuberculosis (Mtb). Therapy requires prolonged treatment with a combination of multiple agents and ...Tuberculosis (TB) is a devastating and rapidly spreading disease caused by Mycobacterium tuberculosis (Mtb). Therapy requires prolonged treatment with a combination of multiple agents and interruptions in the treatment regimen result in emergence and spread of multi-drug resistant (MDR) Mtb strains. MDR Mtb poses a significant global health problem, calling for urgent development of novel drugs to combat TB. Here, we report the 3.3 Å resolution structure of the ~2 MDa type-I fatty acid synthase (FAS-I) from Mtb, determined by single particle cryo-EM. Mtb FAS-I is an essential enzymatic complex that contributes to the virulence of Mtb, and thus a prime target for anti-TB drugs. The structural information for Mtb FAS-I we have obtained enables computer-based drug discovery approaches, and the resolution achieved by cryo-EM is sufficient for elucidating inhibition mechanisms by putative small molecular weight inhibitors.
History
DepositionMay 16, 2018-
Header (metadata) releaseMay 23, 2018-
Map releaseSep 5, 2018-
UpdateDec 11, 2019-
Current statusDec 11, 2019Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.021
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.021
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6gjc
  • Surface level: 0.021
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0011.png

Downloads & links

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Map

FileDownload / File: emd_0011.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.054 Å
Density
Contour LevelBy AUTHOR: 0.021 / Movie #1: 0.021
Minimum - Maximum-0.06720291 - 0.15161994
Average (Standard dev.)0.00038904152 (±0.005205547)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 421.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0541.0541.054
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z421.600421.600421.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.0670.1520.000

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Supplemental data

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Mask #1

Fileemd_0011_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_0011_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_0011_half_map_2.map
Projections & Slices
AxesZYX

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Sample components

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Entire : Fatty Acid Synthase - I

EntireName: Fatty Acid Synthase - I
Components
  • Complex: Fatty Acid Synthase - I
    • Protein or peptide: Fatty acid synthase
  • Ligand: FLAVIN MONONUCLEOTIDE

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Supramolecule #1: Fatty Acid Synthase - I

SupramoleculeName: Fatty Acid Synthase - I / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Macromolecule #1: Fatty acid synthase

MacromoleculeName: Fatty acid synthase / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO / EC number: beta-ketoacyl-[acyl-carrier-protein] synthase I
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 329.35675 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKKWSHPQFE KGGSDYKDDD DKPICTIHEH DRVSADRGGD SPHTTHALVD RLMAGEPYAV AFGGQGSAWL ETLEELVSAT GIETELATL VGEAELLLDP VTDELIVVRP IGFEPLQWVR ALAAEDPVPS DKHLTSAAVS VPGVLLTQIA ATRALARQGM D LVATPPVA ...String:
MKKWSHPQFE KGGSDYKDDD DKPICTIHEH DRVSADRGGD SPHTTHALVD RLMAGEPYAV AFGGQGSAWL ETLEELVSAT GIETELATL VGEAELLLDP VTDELIVVRP IGFEPLQWVR ALAAEDPVPS DKHLTSAAVS VPGVLLTQIA ATRALARQGM D LVATPPVA MAGHSQGVLA VEALKAGGAR DVELFALAQL IGAAGTLVAR RRGISVLGDR PPMVSVTNAD PERIGRLLDE FA QDVRTVL PPVLSIRNGR RAVVITGTPE QLSRFELYCR QISEKEEADR KNKVRGGDVF SPVFEPVQVE VGFHTPRLSD GID IVAGWA EKAGLDVALA RELADAILIR KVDWVDEITR VHAAGARWIL DLGPGDILTR LTAPVIRGLG IGIVPAATRG GQRN LFTVG ATPEVARAWS SYAPTVVRLP DGRVKLSTKF TRLTGRSPIL LAGMTPTTVD AKIVAAAANA GHWAELAGGG QVTEE IFGN RIEQMAGLLE PGRTYQFNAL FLDPYLWKLQ VGGKRLVQKA RQSGAAIDGV VISAGIPDLD EAVELIDELG DIGISH VVF KPGTIEQIRS VIRIATEVPT KPVIMHVEGG RAGGHHSWED LDDLLLATYS ELRSRANITV CVGGGIGTPR RAAEYLS GR WAQAYGFPLM PIDGILVGTA AMATKESTTS PSVKRMLVDT QGTDQWISAG KAQGGMASSR SQLGADIHEI DNSASRCG R LLDEVAGDAE AVAERRDEII AAMAKTAKPY FGDVADMTYL QWLRRYVELA IGEGNSTADT ASVGSPWLAD TWRDRFEQM LQRAEARLHP QDFGPIQTLF TDAGLLDNPQ QAIAALLARY PDAETVQLHP ADVPFFVTLC KTLGKPVNFV PVIDQDVRRW WRSDSLWQA HDARYDADAV CIIPGTASVA GITRMDEPVG ELLDRFEQAA IDEVLGAGVE PKDVASRRLG RADVAGPLAV V LDAPDVRW AGRTVTNPVH RIADPAEWQV HDGPENPRAT HSSTGARLQT HGDDVALSVP VSGTWVDIRF TLPANTVDGG TP VIATEDA TSAMRTVLAI AAGVDSPEFL PAVANGTATL TVDWHPERVA DHTGVTATFG EPLAPSLTNV PDALVGPCWP AVF AAIGSA VTDTGEPVVE GLLSLVHLDH AARVVGQLPT VPAQLTVTAT AANATDTDMG RVVPVSVVVT GADGAVIATL EERF AILGR TGSAELADPA RAGGAVSANA TDTPRRRRRD VTITAPVDMR PFAVVSGDHN PIHTDRAAAL LAGLESPIVH GMWLS AAAQ HAVTATDGQA RPPARLVGWT ARFLGMVRPG DEVDFRVERV GIDQGAEIVD VAARVGSDLV MSASARLAAP KTVYAF PGQ GIQHKGMGME VRARSKAARK VWDTADKFTR DTLGFSVLHV VRDNPTSIIA SGVHYHHPDG VLYLTQFTQV AMATVAA AQ VAEMREQGAF VEGAIACGHS VGEYTALACV TGIYQLEALL EMVFHRGSKM HDIVPRDELG RSNYRLAAIR PSQIDLDD A DVPAFVAGIA ESTGEFLEIV NFNLRGSQYA IAGTVRGLEA LEAEVERRRE LTGGRRSFIL VPGIDVPFHS RVLRVGVAE FRRSLDRVMP RDADPDLIIG RYIPNLVPRL FTLDRDFIQE IRDLVPAEPL DEILADYDTW LRERPREMAR TVFIELLAWQ FASPVRWIE TQDLLFIEEA AGGLGVERFV EIGVKSSPTV AGLATNTLKL PEYAHSTVEV LNAERDAAVL FATDTDPEPE P EEDEPVAE SPAPDVVSEA APVAPAASSA GPRPDDLVFD AADATLALIA LSAKMRIDQI EELDSIESIT DGASSRRNQL LV DLGSELN LGAIDGAAES DLAGLRSQVT KLARTYKPYG PVLSDAINDQ LRTVLGPSGK RPGAIAERVK KTWELGEGWA KHV TVEVAL GTREGSSVRG GAMGHLHEGA LADAASVDKV IDAAVASVAA RQGVSVALPS AGSGGGATID AAALSEFTDQ ITGR EGVLA SAARLVLGQL GLDDPVNALP AAPDSELIDL VTAELGADWP RLVAPVFDPK KAVVFDDRWA SAREDLVKLW LTDEG DIDA DWPRLAERFE GAGHVVATQA TWWQGKSLAA GRQIHASLYG RIAAGAENPE PGRYGGEVAV VTGASKGSIA ASVVAR LLD GGATVIATTS KLDEERLAFY RTLYRDHARY GAALWLVAAN MASYSDVDAL VEWIGTEQTE SLGPQSIHIK DAQTPTL LF PFAAPRVVGD LSEAGSRAEM EMKVLLWAVQ RLIGGLSTIG AERDIASRLH VVLPGSPNRG MFGGDGAYGE AKSALDAV V SRWHAESSWA ARVSLAHALI GWTRGTGLMG HNDAIVAAVE EAGVTTYSTD EMAALLLDLC DAESKVAAAR SPIKADLTG GLAEANLDMA ELAAKAREQM SAAAAVDEDA EAPGAIAALP SPPRGFTPAP PPQWDDLDVD PADLVVIVGG AEIGPYGSSR TRFEMEVEN ELSAAGVLEL AWTTGLIRWE DDPQPGWYDT ESGEMVDESE LVQRYHDAVV QRVGIREFVD DGAIDPDHAS P LLVSVFLE KDFAFVVSSE ADARAFVEFD PEHTVIRPVP DSTDWQVIRK AGTEIRVPRK TKLSRVVGGQ IPTGFDPTVW GI SADMAGS IDRLAVWNMV ATVDAFLSSG FSPAEVMRYV HPSLVANTQG TGMGGGTSMQ TMYHGNLLGR NKPNDIFQEV LPN IIAAHV VQSYVGSYGA MIHPVAACAT AAVSVEEGVD KIRLGKAQLV VAGGLDDLTL EGIIGFGDMA ATADTSMMCG RGIH DSKFS RPNDRRRLGF VEAQGGGTIL LARGDLALRM GLPVLAVVAF AQSFGDGVHT SIPAPGLGAL GAGRGGKDSP LARAL AKLG VAADDVAVIS KHDTSTLAND PNETELHERL ADALGRSEGA PLFVVSQKSL TGHAKGGAAV FQMMGLCQIL RDGVIP PNR SLDCVDDELA GSAHFVWVRD TLRLGGKFPL KAGMLTSLGF GHVSGLVALV HPQAFIASLD PAQRADYQRR ADARLLA GQ RRLASAIAGG APMYQRPGDR RFDHHAPERP QEASMLLNPA ARLGDGEAYI

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Macromolecule #2: FLAVIN MONONUCLEOTIDE

MacromoleculeName: FLAVIN MONONUCLEOTIDE / type: ligand / ID: 2 / Number of copies: 6 / Formula: FMN
Molecular weightTheoretical: 456.344 Da
Chemical component information

ChemComp-FMN:
FLAVIN MONONUCLEOTIDE / Flavin mononucleotide

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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: 7.2
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 4.49 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: Gctf
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4v8l

Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final reconstructionApplied symmetry - Point group: D3 (2x3 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 40160
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: FLEXIBLE FIT
Output model

PDB-6gjc:
Structure of Mycobacterium tuberculosis Fatty Acid Synthase - I

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