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- EMDB-50185: KS + AT di-domain of polyketide synthase 13 in Mycobacterium tube... -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-50185
TitleKS + AT di-domain of polyketide synthase 13 in Mycobacterium tuberculosis
Map dataFinal map for Pks13 from M. tuberculosis
Sample
  • Complex: Subunit of Pks13
    • Protein or peptide: Polyketide synthase Pks13
KeywordsMycolic acid synthesis / Claisen condensation / cell wall synthesis / BIOSYNTHETIC PROTEIN
Function / homology
Function and homology information


DIM/DIP cell wall layer assembly / fatty acid synthase activity / secondary metabolite biosynthetic process / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / fatty acid biosynthetic process / plasma membrane / cytoplasm
Similarity search - Function
Thioesterase / Thioesterase domain / Malonyl-CoA ACP transacylase, ACP-binding / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Acyl transferase domain superfamily / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase/acyl hydrolase/lysophospholipase ...Thioesterase / Thioesterase domain / Malonyl-CoA ACP transacylase, ACP-binding / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Acyl transferase domain superfamily / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase/acyl hydrolase/lysophospholipase / Ketosynthase family 3 (KS3) domain profile. / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / 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 / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
Polyketide synthase Pks13
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria) / Mycobacterium tuberculosis H37Rv (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsJohnston HE / Futterer K
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/S000542/1 United Kingdom
Medical Research Council (MRC, United Kingdom)MR/R001154/1 United Kingdom
CitationJournal: To be published
Title: CryoEM structure of the di-domain core of Mycobacterium tuberculosis polyketide synthase 13, essential for mycobacterial mycolic acid synthesis
Authors: Johnston HE / Batt SM / Brown AK / Savva CG / Besra GS / Futterer K
History
DepositionApr 26, 2024-
Header (metadata) releaseMay 22, 2024-
Map releaseMay 22, 2024-
UpdateMay 22, 2024-
Current statusMay 22, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50185.png

Downloads & links

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Map

FileDownload / File: emd_50185.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFinal map for Pks13 from M. tuberculosis
Voxel sizeX=Y=Z: 1.09 Å
Density
Contour LevelBy AUTHOR: 0.000747
Minimum - Maximum-0.058972042 - 0.115474425
Average (Standard dev.)0.00008320585 (±0.0017154444)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 392.40002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map 1

Fileemd_50185_half_map_1.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2

Fileemd_50185_half_map_2.map
AnnotationHalf 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 : Subunit of Pks13

EntireName: Subunit of Pks13
Components
  • Complex: Subunit of Pks13
    • Protein or peptide: Polyketide synthase Pks13

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Supramolecule #1: Subunit of Pks13

SupramoleculeName: Subunit of Pks13 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mycobacterium tuberculosis (bacteria) / Strain: H37Rv
Molecular weightTheoretical: 187 KDa

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Macromolecule #1: Polyketide synthase Pks13

MacromoleculeName: Polyketide synthase Pks13 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
EC number: Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
Source (natural)Organism: Mycobacterium tuberculosis H37Rv (bacteria)
Molecular weightTheoretical: 186.642188 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MADVAESQEN APAERAELTV PEMRQWLRNW VGKAVGKAPD SIDESVPMVE LGLSSRDAVA MAADIEDLTG VTLSVAVAFA HPTIESLAT RIIEGEPETD LAGDDAEDWS RTGPAERVDI AIVGLSTRFP GEMNTPEQTW QALLEGRDGI TDLPDGRWSE F LEEPRLAA ...String:
MADVAESQEN APAERAELTV PEMRQWLRNW VGKAVGKAPD SIDESVPMVE LGLSSRDAVA MAADIEDLTG VTLSVAVAFA HPTIESLAT RIIEGEPETD LAGDDAEDWS RTGPAERVDI AIVGLSTRFP GEMNTPEQTW QALLEGRDGI TDLPDGRWSE F LEEPRLAA RVAGARTRGG YLKDIKGFDS EFFAVAKTEA DNIDPQQRMA LELTWEALEH ARIPASSLRG QAVGVYIGSS TN DYSFLAV SDPTVAHPYA ITGTSSSIIA NRVSYFYDFH GPSVTIDTAC SSSLVAIHQG VQALRNGEAD VVVAGGVNAL ITP MVTLGF DEIGAVLAPD GRIKSFSADA DGYTRSEGGG MLVLKRVDDA RRDGDAILAV IAGSAVNHDG RSNGLIAPNQ DAQA DVLRR AYKDAGIDPR TVDYIEAHGT GTILGDPIEA EALGRVVGRG RPADRPALLG AVKTNVGHLE SAAGAASMAK VVLAL QHDK LPPSINFAGP SPYIDFDAMR LKMITTPTDW PRYGGYALAG VSSFGFGGAN AHVVVREVLP RDVVEKEPEP EPEPKA AAE PAEAPTLAGH ALRFDEFGNI ITDSAVAEEP EPELPGVTEE ALRLKEAALE ELAAQEVTAP LVPLAVSAFL TSRKKAA AA ELADWMQSPE GQASSLESIG RSLSRRNHGR SRAVVLAHDH DEAIKGLRAV AAGKQAPNVF SVDGPVTTGP VWVLAGFG A QHRKMGKSLY LRNEVFAAWI EKVDALVQDE LGYSVLELIL DDAQDYGIET TQVTIFAIQI ALGELLRHHG AKPAAVIGQ SLGEAASAYF AGGLSLRDAT RAICSRSHLM GEGEAMLFGE YIRLMALVEY SADEIREVFS DFPDLEVCVY AAPTQTVIGG PPEQVDAIL ARAEAEGKFA RKFATKGASH TSQMDPLLGE LTAELQGIKP TSPTCGIFST VHEGRYIKPG GEPIHDVEYW K KGLRHSVY FTHGIRNAVD SGHTTFLELA PNPVALMQVA LTTADAGLHD AQLIPTLARK QDEVSSMVST MAQLYVYGHD LD IRTLFSR ASGPQDYANI PPTRFKRKEH WLPAHFSGDG STYMPGTHVA LPDGRHVWEY APRDGNVDLA ALVRAAAAHV LPD AQLTAA EQRAVPGDGA RLVTTMTRHP GGASVQVHAR IDESFTLVYD ALVSRAGSES VLPTAVGAAT AIAVADGAPV APET PAEDA DAETLSDSLT TRYMPSGMTR WSPDSGETIA ERLGLIVGSA MGYEPEDLPW EVPLIELGLD SLMAVRIKNR VEYDF DLPP IQLTAVRDAN LYNVEKLIEY AVEHRDEVQQ LHEHQKTQTA EEIARAQAEL LHGKVGKTEP VDSEAGVALP SPQNGE QPN PTGPALNVDV PPRDAAERVT FATWAIVTGK SPGGIFNELP RLDDEAAAKI AQRLSERAEG PITAEDVLTS SNIEALA DK VRTYLEAGQI DGFVRTLRAR PEAGGKVPVF VFHPAGGSTV VYEPLLGRLP ADTPMYGFER VEGSIEERAQ QYVPKLIE M QGDGPYVLVG WSLGGVLAYA CAIGLRRLGK DVRFVGLIDA VRAGEEIPQT KEEIRKRWDR YAAFAEKTFN VTIPAIPYE QLEELDDEGQ VRFVLDAVSQ SGVQIPAGII EHQRTSYLDN RAIDTAQIQP YDGHVTLYMA DRYHDDAIMF EPRYAVRQPD GGWGEYVSD LEVVPIGGEH IQAIDEPIIA KVGEHMSRAL GQIEADRTSE VGKQ

UniProtKB: Polyketide synthase Pks13

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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

Concentration0.9 mg/mL
BufferpH: 7.9 / Component - Concentration: 20.0 mM / Component - Formula: C4H11NO3 / Component - Name: Tris
Details: 20 mM Tris-HCl pH 7.9, 50 mM NaCl, 2.5 mM beta-mercaptoethanol
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 291 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 1412 / Average exposure time: 3.0 sec. / Average electron dose: 16.5 e/Å2 / Details: movie mode
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: OTHER / Cs: 2.7 mm / Nominal defocus max: 2.7 µm / Nominal defocus min: 1.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 310055
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: OTHER / Number images used: 168566
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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