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- EMDB-46507: Cryo-EM structure of mycocerosic acid synthase with KS-ACP' cross... -

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Basic information

Entry
Database: EMDB / ID: EMD-46507
TitleCryo-EM structure of mycocerosic acid synthase with KS-ACP' crosslink and DH-ACP crosslink using C16 alpha-bromoamide. Complex D
Map datamain map
Sample
  • Complex: Homodimeric MAS doubly crosslinked between ACP'=KS domains and ACP=DH domains
    • Protein or peptide: Mycocerosic acid synthase
Keywordspolyketide / crosslinked / ketosynthase / dehydratase BIOSYNTHETIC PROTEIN / BIOSYNTHETIC PROTEIN
Biological speciesMycobacterium tuberculosis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.15 Å
AuthorsHeberlig GW / Jiang Z / Burkart MD
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM095970 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)K12 HL141956 United States
National Science Foundation (NSF, United States)DMR-2011924 United States
CitationJournal: To Be Published
Title: Visualizing Acyl Carrier Protein Interactions within a Crosslinked Type I Polyketide Synthase
Authors: Jiang Z / Heberlig GW / Chen JA / Huynh J / La Clair JJ / Burkart MD
History
DepositionAug 9, 2024-
Header (metadata) releaseAug 13, 2025-
Map releaseAug 13, 2025-
UpdateAug 13, 2025-
Current statusAug 13, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_46507.png

Downloads & links

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Map

FileDownload / File: emd_46507.map.gz / Format: CCP4 / Size: 209.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmain map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.89 Å/pix.
x 380 pix.
= 337.82 Å		0.89 Å/pix.
x 380 pix.
= 337.82 Å		0.89 Å/pix.
x 380 pix.
= 337.82 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.889 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.11188056 - 0.2983258
Average (Standard dev.)0.00082359085 (±0.012491196)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions380380380
Spacing380380380
CellA=B=C: 337.82 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half A

Fileemd_46507_half_map_1.map
Annotationhalf A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half B

Fileemd_46507_half_map_2.map
Annotationhalf B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Homodimeric MAS doubly crosslinked between ACP'=KS domains and AC...

EntireName: Homodimeric MAS doubly crosslinked between ACP'=KS domains and ACP=DH domains
Components
  • Complex: Homodimeric MAS doubly crosslinked between ACP'=KS domains and ACP=DH domains
    • Protein or peptide: Mycocerosic acid synthase

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Supramolecule #1: Homodimeric MAS doubly crosslinked between ACP'=KS domains and AC...

SupramoleculeName: Homodimeric MAS doubly crosslinked between ACP'=KS domains and ACP=DH domains
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)

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Macromolecule #1: Mycocerosic acid synthase

MacromoleculeName: Mycocerosic acid synthase / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO / EC number: mycocerosate synthase
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MESRVTPVAV IGMGCRLPGG INSPDKLWES LLRGDDLVTE IPPDRWDADD YYDPEPGVPG RSVSRWGGFL DDVAGFDAEF FGISEREATS IDPQQRLLLE TSWEAIEHAG LDPASLAGSS TAVFTGLTHE DYLVLTTTAG GLASPYVVTG LNNSVASGRI AHTLGLHGPA ...String:
MESRVTPVAV IGMGCRLPGG INSPDKLWES LLRGDDLVTE IPPDRWDADD YYDPEPGVPG RSVSRWGGFL DDVAGFDAEF FGISEREATS IDPQQRLLLE TSWEAIEHAG LDPASLAGSS TAVFTGLTHE DYLVLTTTAG GLASPYVVTG LNNSVASGRI AHTLGLHGPA MTFDTACSSG LMAVHLACRS LHDGEADLAL AGGCAVLLEP HASVAASAQG MLSSTGRCHS FDADADGFVR SEGCAMVLLK RLPDALRDGN RIFAVVRGTA TNQDGRTETL TMPSEDAQVA VYRAALAAAG VQPETVGVVE AHGTGTPIGD PIEYRSLARV YGAGTPCALG SAKSNMGHST ASAGTVGLIK AILSLRHGVV PPLLHFNRLP DELSDVETGL FVPQAVTPWP NGNDHTPKRV AVSSFGMSGT NVHAIVEEAP AEASAPESSP GDAEVGPRLF MLSSTSSDAL RQTARQLATW VEEHQDCVAA SDLAYTLARG RAHRPVRTAV VAANLPELVE GLREVADGDA LYDAAVGHGD RGPVWVFSGQ GSQWAAMGTQ LLASEPVFAA TIAKLEPVIA AESGFSVTEA ITAQQTVTGI DKVQPAVFAV QVALAATMEQ TYGVRPGAVV GHSMGESAAA VVAGALSLED AARVICRRSK LMTRIAGAGA MGSVELPAKQ VNSELMARGI DDVVVSVVAS PQSTVIGGTS DTVRDLIARW EQRDVMAREV AVDVASHSPQ VDPILDDLAA ALADIAPMTP KVPYYSATLF DPREQPVCDG AYWVDNLRNT VQFAAAVQAA MEDGYRVFAE LSPHPLLTHA VEQTGRSLDM SVAALAGMRR EQPLPHGLRG LLTELHRAGA ALDYSALYPA GRLVDAPLPA WTHARLFIDD DGQEQRAQGA CTITVHPLLG SHVRLTEEPE RHVWQGDVGT SVLSWLSDHQ VHNVAALPGA AYCEMALAAA AEVFGEAAEV RDITFEQMLL LDEQTPIDAV ASIDAPGVVN FTVETNRDGE TTRHATAALR AAEDDCPPPG YDITALLQAH PHAVNGTAMR ESFAERGVTL GAAFGGLTTA HTAEAGAATV LAEVALPASI RFQQGAYRIH PALLDACFQS VGAGVQAGTA TGGLLLPLGV RSLRAYGPTR NARYCYTRLT KAFNDGTRGG EADLDVLDEH GTVLLAVRGL RMGTGTSERD ERDRLVSERL LTLGWQQRAL PEVGDGEAGS WLLIDTSNAV DTPDMLASTL TDALKSHGPQ GTECASLSWS VQDTPPNDQA GLEKLGSQLR GRDGVVIVYG PRVGDPDEHS LLAGREQVRH LVRITRELAE FEGELPRLFV VTRQAQIVKP HDSGERANLE QAGLRGLLRV ISSEHPMLRT TLIDVDEHTD VERVAQQLLS GSEEDETAWR NGDWYVARLT PSPLGHEERR TAVLDPDHDG MRVQVRRPGD LQTLEFVASD RVPPGPGQIE VAVSMSSINF ADVLIAFGRF PIIDDREPQL GMDFVGVVTA VGEGVTGHQV GDRVGGFSEG GCWRTFLTCD ANLAVTLPPG LTDEQAITAA TAHATAWYGL NDLAQIKAGD KVLIHSATGG VGQAAISIAR AKGAEIFATA GNPAKRAMLR DMGVEHVYDS RSVEFAEQIR RDTDGYGVDI VLNSLTGAAQ RAGLELLAFG GRFVEIGKAD VYGNTRLGLF PFRRGLTFYY LDLALMSVTQ PDRVRELLAT VFKLTADGVL TAPQCTHYPL AEAADAIRAM SNAEHTGKLV LDVPRSGRRS VAVTPEQAPL YRRDGSYIIT GGLGGLGLFF ASKLAAAGCG RIVLTARSQP NPKARQTIEG LRAAGADIVV ECGNIAEPDT ADRLVSAATA TGLPLRGVLH SAAVVEDATL TNITDELIDR DWSPKVFGSW NLHRATLGQP LDWFCLFSSG AALLGSPGQG AYAAANSWVD VFAHWRRAQG LPVSAIAWGA WGEVGRATFL AEGGEIMITP EEGAYAFETL VRHDRAYSGY IPILGAPWLA DLVRRSPWGE MFASTGQRSR GPSKFRMELL SLPQDEWAGR LRRLLVEQAS VILRRTIDAD RSFIEYGLDS LGMLEMRTHV ETETGIRLTP KVIATNNTAR ALAQYLADTL AEEQAAAPAA SKLAAALEHH HHHH

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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

Concentration1.0 mg/mL
BufferpH: 7.4
Component:
ConcentrationName
50.0 mMTris HCl
150.0 mMSodium chloride
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 3135 / Average electron dose: 55.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1055614
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 6.15 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 19622
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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