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- EMDB-41495: Crosslinked 6-deoxyerythronolide B synthase (DEBS) Module 3 in co... -

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Basic information

Entry
Database: EMDB / ID: EMD-41495
TitleCrosslinked 6-deoxyerythronolide B synthase (DEBS) Module 3 in complex with antibody fragment 1B2: cis-oriented 1B2 and ACP
Map data
Sample
  • Complex: Crosslinked DEBS Module 3 in complex with Antibody Fragment 1B2
    • Protein or peptide: EryAII,EryAII,EryAII,EryAII,6-deoxyerythronolide-B synthase EryA3, modules 5 and 6
    • Protein or peptide: Antibody Fragment 1B2, Heavy Chain
    • Protein or peptide: Antibody Fragment 1B2, Light Chain
Keywordspolyketide synthase / antibody / BIOSYNTHETIC PROTEIN
Function / homology
Function and homology information


6-deoxyerythronolide-B synthase / macrolide biosynthetic process / fatty acid synthase activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / oxidoreductase activity
Similarity search - Function
Erythronolide synthase, docking / Erythronolide synthase, docking domain superfamily / Erythronolide synthase, docking / : / Polyketide synthase extender module SpnB, Rossmann fold domain / Polyketide synthase, docking domain / Erythronolide synthase docking domain / Zinc-binding dehydrogenase / : / Polyketide synthase dehydratase N-terminal domain ...Erythronolide synthase, docking / Erythronolide synthase, docking domain superfamily / Erythronolide synthase, docking / : / Polyketide synthase extender module SpnB, Rossmann fold domain / Polyketide synthase, docking domain / Erythronolide synthase docking domain / Zinc-binding dehydrogenase / : / Polyketide synthase dehydratase N-terminal domain / Polyketide synthase, dehydratase domain / PKS_DH / PKS_PP_betabranch / : / 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 / : / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase domain superfamily / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase / Acyl transferase/acyl hydrolase/lysophospholipase / 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 / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
6-deoxyerythronolide-B synthase
Similarity search - Component
Biological speciesSaccharopolyspora erythraea (bacteria) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.46 Å
AuthorsCogan DP / Soohoo AM / Chen M / Brodsky KL / Liu Y / Khosla C
Funding support United States, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM141799 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM136039 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM129541 United States
National Science Foundation (NSF, United States)DGE-1656518 United States
CitationJournal: Nat Chem Biol / Year: 2025
Title: Structural basis for intermodular communication in assembly-line polyketide biosynthesis.
Authors: Dillon P Cogan / Alexander M Soohoo / Muyuan Chen / Yan Liu / Krystal L Brodsky / Chaitan Khosla /
Abstract: Assembly-line polyketide synthases (PKSs) are modular multi-enzyme systems with considerable potential for genetic reprogramming. Understanding how they selectively transport biosynthetic ...Assembly-line polyketide synthases (PKSs) are modular multi-enzyme systems with considerable potential for genetic reprogramming. Understanding how they selectively transport biosynthetic intermediates along a defined sequence of active sites could be harnessed to rationally alter PKS product structures. To investigate functional interactions between PKS catalytic and substrate acyl carrier protein (ACP) domains, we employed a bifunctional reagent to crosslink transient domain-domain interfaces of a prototypical assembly line, the 6-deoxyerythronolide B synthase, and resolved their structures by single-particle cryogenic electron microscopy (cryo-EM). Together with statistical per-particle image analysis of cryo-EM data, we uncovered interactions between ketosynthase (KS) and ACP domains that discriminate between intra-modular and inter-modular communication while reinforcing the relevance of conformational asymmetry during the catalytic cycle. Our findings provide a foundation for the structure-based design of hybrid PKSs comprising biosynthetic modules from different naturally occurring assembly lines.
History
DepositionAug 5, 2023-
Header (metadata) releaseAug 7, 2024-
Map releaseAug 7, 2024-
UpdateJun 11, 2025-
Current statusJun 11, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41495.png

Downloads & links

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Map

FileDownload / File: emd_41495.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.26 Å/pix.
x 448 pix.
= 563.136 Å		1.26 Å/pix.
x 448 pix.
= 563.136 Å		1.26 Å/pix.
x 448 pix.
= 563.136 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.257 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.745
Minimum - Maximum-0.62858427 - 2.3664465
Average (Standard dev.)0.00012603885 (±0.043365337)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 563.136 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_41495_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_41495_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Crosslinked DEBS Module 3 in complex with Antibody Fragment 1B2

EntireName: Crosslinked DEBS Module 3 in complex with Antibody Fragment 1B2
Components
  • Complex: Crosslinked DEBS Module 3 in complex with Antibody Fragment 1B2
    • Protein or peptide: EryAII,EryAII,EryAII,EryAII,6-deoxyerythronolide-B synthase EryA3, modules 5 and 6
    • Protein or peptide: Antibody Fragment 1B2, Heavy Chain
    • Protein or peptide: Antibody Fragment 1B2, Light Chain

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Supramolecule #1: Crosslinked DEBS Module 3 in complex with Antibody Fragment 1B2

SupramoleculeName: Crosslinked DEBS Module 3 in complex with Antibody Fragment 1B2
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharopolyspora erythraea (bacteria)
Molecular weightTheoretical: 420 KDa

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Macromolecule #1: EryAII,EryAII,EryAII,EryAII,6-deoxyerythronolide-B synthase EryA3...

MacromoleculeName: EryAII,EryAII,EryAII,EryAII,6-deoxyerythronolide-B synthase EryA3, modules 5 and 6
type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO / EC number: 6-deoxyerythronolide-B synthase
Source (natural)Organism: Saccharopolyspora erythraea (bacteria)
Molecular weightTheoretical: 186.489578 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MASTDSEKVA EYLRRATLDL RAARQRIREL ESDPIAIVSM ACRLPGGVNT PQRLWELLRE GGETLSGFPT DRGWDLARLH HPDPDNPGT SYVDKGGFLD DAAGFDAEFF GVSPREAAAM DPQQRLLLET SWELVENAGI DPHSLRGTAT GVFLGVAKFG Y GEDTAAAE ...String:
MASTDSEKVA EYLRRATLDL RAARQRIREL ESDPIAIVSM ACRLPGGVNT PQRLWELLRE GGETLSGFPT DRGWDLARLH HPDPDNPGT SYVDKGGFLD DAAGFDAEFF GVSPREAAAM DPQQRLLLET SWELVENAGI DPHSLRGTAT GVFLGVAKFG Y GEDTAAAE DVEGYSVTGV APAVASGRIS YTMGLEGPSI SVDTACSSSL VALHLAVESL RKGESSMAVV GGAAVMATPG VF VDFSRQR ALAADGRSKA FGAGADGFGF SEGVTLVLLE RLSEARRNGH EVLAVVRGSA LNQDGASNGL SAPSGPAQRR VIR QALESC GLEPGDVDAV EAHGTGTALG DPIEANALLD TYGRDRDADR PLWLGSVKSN IGHTQAAAGV TGLLKVVLAL RNGE LPATL HVEEPTPHVD WSSGGVALLA GNQPWRRGER TRRAAVSAFG ISGTNAHVIV EEAPEREHRE TTAHDGRPVP LVVSA RTTA ALRAQAAQIA ELLERPDADL AGVGLGLATT RARHEHRAAV VASTREEAVR GLREIAAGAA TADAVVEGVT EVDGRN VVF LFPGQGSQWA GMGAELLSSS PVFAGKIRAC DESMAPMQDW KVSDVLRQAP GAPGLDRVDV VQPVLFAVMV SLAELWR SY GVEPAAVVGH SQGEIAAAHV AGALTLEDAA KLVVGRSRLM RSLSGEGGMA AVALGEAAVR ERLRPWQDRL SVAAVNGP R SVVVSGEPGA LRAFSEDCAA EGIRVRDIDV DYASHSPQIE RVREELLETT GDIAPRPARV TFHSTVESRS MDGTELDAR YWYRNLRETV RFADAVTRLA ESGYDAFIEV SPHPVVVQAV EEAVEEADGA EDAVVVGSLH RDGGDLSAFL RSMATAHVSG VDIRWDVAL PGAAPFALPT YPFQRKRYWL QPAAPAAASD ELAYRVSWTP IEKPESGNLD GDWLVVTPLI SPEWTEMLCE A INANGGRA LRCEVDTSAS RTEMAQAVAQ AGTGFRGVLS LLSSDESACR PGVPAGAVGL LTLVQALGDA GVDAPVWCLT QG AVRTPAD DDLARPAQTT AHGFAQVAGL ELPGRWGGVV DLPESVDDAA LRLLVAVLRG GGRAEDHLAV RDGRLHGRRV VRA SLPQSG SRSWTPHGTV LVTGAASPVG DQLVRWLADR GAERLVLAGA CPGDDLLAAV EEAGASAVVC AQDAAALREA LGDE PVTAL VHAGTLTNFG SISEVAPEEF AETIAAKTAL LAVLDEVLGD RAVEREVYCS SVAGIWGGAG MAAYAAGSAY LDALA EHHR ARGRSCTSVA WTPWALPGGA VDDGYLRERG LRSLSADRAM RTWERVLAAG PVSVAVADVD WPVLSEGFAA TRPTAL FAE LAGRGGQAEA EPDSGPTGEP AQRLAGLSPD EQQENLLELV ANAVAEVLGH ESAAEINVRR AFSELGLD(4HH)L NAM ALRKRL SASTGLRLPA SLVFDHPTVT ALAQHTSQLD SGTPAREASS ALRDGYRQAG VSGRVRSYLD LLAGLSDFRE HFDG SDGFS LDLVDMADGP GEVTVICCAG TAAISGPHEF TRLAGALRGI APVRAVPQPG YEEGEPLPSS MAAVAAVQAD AVIRT QGDK PFVVAGHSAG ALMAYALATE LLDRGHPPRG VVLIDVYPPG HQDAMNAWLE ELTATLFDRE TVRMDDTRLT ALGAYD RLT GQWRPRETGL PTLLVSAGEP MGPWPDDSWK PTWPFEHDTV AVPGDHFTMV QEHADAIARH IDAWLGGGNS SSVDKLA AA LEHHHHHH

UniProtKB: 6-deoxyerythronolide-B synthase

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Macromolecule #2: Antibody Fragment 1B2, Heavy Chain

MacromoleculeName: Antibody Fragment 1B2, Heavy Chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 26.447611 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MAEVQLVQSG GGLVQPGRSL RLSCTASGFT FGDYAMSWVR QAPGKGLEWV GFIRSKAYGG TTEYAASVKG RFTISRDDSK SIAYLQMNS LKTEDTAVYY CTRGGTLFDY WGQGTLVTVS SASTKGPSVF PLAPSSKSTS GGTAALGCLV KDYFPEPVTV S WNSGALTS ...String:
MAEVQLVQSG GGLVQPGRSL RLSCTASGFT FGDYAMSWVR QAPGKGLEWV GFIRSKAYGG TTEYAASVKG RFTISRDDSK SIAYLQMNS LKTEDTAVYY CTRGGTLFDY WGQGTLVTVS SASTKGPSVF PLAPSSKSTS GGTAALGCLV KDYFPEPVTV S WNSGALTS GVHTFPAVLQ SSGLYSLSSV VTVPSSSLGT QTYICNVNHK PSNTKVDKKV EPKSCAALVP RGSAHHHHHH AA DYKDDDD KA

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Macromolecule #3: Antibody Fragment 1B2, Light Chain

MacromoleculeName: Antibody Fragment 1B2, Light Chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.715832 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: LFAIPLVVPF YSHSALDVVM TQSPLSLPVT PGEPASISCR SSQSLLHSNG YNYLDWYLQK PGQSPQLLIY LGSNRASGVP DRFSGSGSG TDFTLKISRV EAEDVGVYYC MQSLQTPRLT FGPGTKVDIK RTVAAPSVFI FPPSDEQLKS GTASVVCLLN N FYPRGAKV ...String:
LFAIPLVVPF YSHSALDVVM TQSPLSLPVT PGEPASISCR SSQSLLHSNG YNYLDWYLQK PGQSPQLLIY LGSNRASGVP DRFSGSGSG TDFTLKISRV EAEDVGVYYC MQSLQTPRLT FGPGTKVDIK RTVAAPSVFI FPPSDEQLKS GTASVVCLLN N FYPRGAKV QWKVDNALQS GNSQESVTEQ DSKDSTYSLS STLTLSKADY EKHKVYACEV THQGLSSPVT KSFNRGEC

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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

Concentration8 mg/mL
BufferpH: 7.2
Component:
ConcentrationFormulaName
100.0 mMC6H8O7citric acid
100.0 mMNaClsodium chloride
10.0 mMC8H18N2O4SHEPES
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 11 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Details: 30 s glow, 10 s hold, 15 mA
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 10480 / Average exposure time: 2.79 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 150.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 81000
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: 573745
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.46 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 59205
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: OTHER
Final 3D classificationNumber classes: 8 / Avg.num./class: 40000

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Atomic model buiding 1

Initial modelPDB ID:

6c9u


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-8tpw:
Crosslinked 6-deoxyerythronolide B synthase (DEBS) Module 3 in complex with antibody fragment 1B2: cis-oriented 1B2 and ACP

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