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- EMDB-23711: 6-Deoxyerythronolide B synthase (DEBS) module 1 in complex with a... -

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Basic information

Entry
Database: EMDB / ID: EMD-23711
Title6-Deoxyerythronolide B synthase (DEBS) module 1 in complex with antibody fragment 1B2: State 1
Map data
Sample
  • Complex: Complex between DEBS (3)M1TE and antibody fragment 1B2
    • Protein or peptide: EryAI,6-deoxyerythronolide-B synthase EryA3, modules 5 and 6 chimera
    • Protein or peptide: 1B2 (heavy chain)
    • Protein or peptide: 1B2 (light chain)
  • Ligand: N~3~-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-N-(2-sulfanylethyl)-beta-alaninamide
Keywordspolyketide synthase / antibody fragment / BIOSYNTHETIC PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


6-deoxyerythronolide-B synthase / erythronolide synthase activity / macrolide biosynthetic process / DIM/DIP cell wall layer assembly / fatty acid synthase activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / antibiotic biosynthetic process / fatty acid biosynthetic process / plasma membrane / cytoplasm
Similarity search - Function
Polyketide synthase, docking domain superfmaily / Polyketide synthase, thioesterase domain / Thioesterase / CurL-like, PKS C-terminal / Polyketide synthase, docking domain / Erythronolide synthase docking domain / Thioesterase / Thioesterase domain / PKS_PP_betabranch / Polyketide synthase, C-terminal extension ...Polyketide synthase, docking domain superfmaily / Polyketide synthase, thioesterase domain / Thioesterase / CurL-like, PKS C-terminal / Polyketide synthase, docking domain / Erythronolide synthase docking domain / Thioesterase / Thioesterase domain / PKS_PP_betabranch / 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 / Acyl transferase/acyl hydrolase/lysophospholipase / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / PKS_KR / 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 / Thiolase-like / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Alpha/Beta hydrolase fold / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
6-deoxyerythronolide-B synthase EryA3, modules 5 and 6 / EryAI
Similarity search - Component
Biological speciesSaccharopolyspora erythraea (bacteria) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsCogan DP / Zhang K
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM079429 United States
CitationJournal: Science / Year: 2021
Title: Mapping the catalytic conformations of an assembly-line polyketide synthase module.
Authors: Dillon P Cogan / Kaiming Zhang / Xiuyuan Li / Shanshan Li / Grigore D Pintilie / Soung-Hun Roh / Charles S Craik / Wah Chiu / Chaitan Khosla /
Abstract: Assembly-line polyketide synthases, such as the 6-deoxyerythronolide B synthase (DEBS), are large enzyme factories prized for their ability to produce specific and complex polyketide products. By ...Assembly-line polyketide synthases, such as the 6-deoxyerythronolide B synthase (DEBS), are large enzyme factories prized for their ability to produce specific and complex polyketide products. By channeling protein-tethered substrates across multiple active sites in a defined linear sequence, these enzymes facilitate programmed small-molecule syntheses that could theoretically be harnessed to access countless polyketide product structures. Using cryogenic electron microscopy to study DEBS module 1, we present a structural model describing this substrate-channeling phenomenon. Our 3.2- to 4.3-angstrom-resolution structures of the intact module reveal key domain-domain interfaces and highlight an unexpected module asymmetry. We also present the structure of a product-bound module that shines light on a recently described “turnstile” mechanism for transient gating of active sites along the assembly line.
History
DepositionMar 28, 2021-
Header (metadata) releaseNov 17, 2021-
Map releaseNov 17, 2021-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.53
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.53
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7m7f
  • Surface level: 0.53
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23711.png

Downloads & links

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Map

FileDownload / File: emd_23711.map.gz / Format: CCP4 / Size: 144.7 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 Å/pix.
x 336 pix.
= 336. Å		1 Å/pix.
x 336 pix.
= 336. Å		1 Å/pix.
x 336 pix.
= 336. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.53 / Movie #1: 0.53
Minimum - Maximum-4.601682 - 7.734035
Average (Standard dev.)0.0048982617 (±0.13816544)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions336336336
Spacing336336336
CellA=B=C: 336.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z111
M x/y/z336336336
origin x/y/z0.0000.0000.000
length x/y/z336.000336.000336.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ376376376
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS336336336
D min/max/mean-4.6027.7340.005

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Supplemental data

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Sample components

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Entire : Complex between DEBS (3)M1TE and antibody fragment 1B2

EntireName: Complex between DEBS (3)M1TE and antibody fragment 1B2
Components
  • Complex: Complex between DEBS (3)M1TE and antibody fragment 1B2
    • Protein or peptide: EryAI,6-deoxyerythronolide-B synthase EryA3, modules 5 and 6 chimera
    • Protein or peptide: 1B2 (heavy chain)
    • Protein or peptide: 1B2 (light chain)
  • Ligand: N~3~-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-N-(2-sulfanylethyl)-beta-alaninamide

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Supramolecule #1: Complex between DEBS (3)M1TE and antibody fragment 1B2

SupramoleculeName: Complex between DEBS (3)M1TE and antibody fragment 1B2
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Saccharopolyspora erythraea (bacteria)
Molecular weightTheoretical: 480 KDa

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Macromolecule #1: EryAI,6-deoxyerythronolide-B synthase EryA3, modules 5 and 6 chimera

MacromoleculeName: EryAI,6-deoxyerythronolide-B synthase EryA3, modules 5 and 6 chimera
type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: 6-deoxyerythronolide-B synthase
Source (natural)Organism: Saccharopolyspora erythraea (bacteria)
Molecular weightTheoretical: 188.550891 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MASTDSEKVA EYLRRATLDL RAARQRIREL EGEPVAVVAM ACRLPGGVST PEEFWELLSE GRDAVAGLPT DRGWDLDSLF HPDPTRSGT AHQRGGGFLT EATAFDPAFF GMSPREALAV DPQQRLMLEL SWEVLERAGI PPTSLQASPT GVFVGLIPQE Y GPRLAEGG ...String:
MASTDSEKVA EYLRRATLDL RAARQRIREL EGEPVAVVAM ACRLPGGVST PEEFWELLSE GRDAVAGLPT DRGWDLDSLF HPDPTRSGT AHQRGGGFLT EATAFDPAFF GMSPREALAV DPQQRLMLEL SWEVLERAGI PPTSLQASPT GVFVGLIPQE Y GPRLAEGG EGVEGYLMTG TTTSVASGRI AYTLGLEGPA ISVDTACSSS LVAVHLACQS LRRGESSLAM AGGVTVMPTP GM LVDFSRM NSLAPDGRCK AFSAGANGFG MAEGAGMLLL ERLSDARRNG HPVLAVLRGT AVNSDGASNG LSAPNGRAQV RVI QQALAE SGLGPADIDA VEAHGTGTRL GDPIEARALF EAYGRDREQP LHLGSVKSNL GHTQAAAGVA GVIKMVLAMR AGTL PRTLH ASERSKEIDW SSGAISLLDE PEPWPAGARP RRAGVSSFGI SGTNAHAIIE EAPQVVEGER VEAGDVVAPW VLSAS SAEG LRAQAARLAA HLREHPGQDP RDIAYSLATG RAALPHRAAF APVDESAALR VLDGLATGNA DGAAVGTSRA QQRAVF VFP GQGWQWAGMA VDLLDTSPVF AAALRECADA LEPHLDFEVI PFLRAEAARR EQDAALSTER VDVVQPVMFA VMVSLAS MW RAHGVEPAAV IGHSQGEIAA ACVAGALSLD DAARVVALRS RVIATMPGNK GMASIAAPAG EVRARIGDRV EIAAVNGP R SVVVAGDSDE LDRLVASCTT ECIRAKRLAV DYASHSSHVE TIRDALHAEL GEDFHPLPGF VPFFSTVTGR WTQPDELDA GYWYRNLRRT VRFADAVRAL AEQGYRTFLE VSAHPILTAA IEEIGDGSGA DLSAIHSLRR GDGSLADFGE ALSRAFAAGV AVDWESVHL GTGARRVPLP TYPFQRERVW LEPKPVARRS TEVDEVSALR YRIEWRPTGA GEPARLDGTW LVAKYAGTAD E TSTAAREA LESAGARVRE LVVDARCGRD ELAERLRSVG EVAGVLSLLA VDEAEPEEAP LALASLADTL SLVQAMVSAE LG CPLWTVT ESAVATGPFE RVRNAAHGAL WGVGRVIALE NPAVWGGLVD VPAGSVAELA RHLAAVVSGG AGEDQLALRA DGV YGRRWV RAAAPATDDE WKPTGTVLVT GGTGGVGGQI ARWLARRGAP HLLLVSRSGP DADGAGELVA ELEALGARTT VAAC DVTDR ESVRELLGGI GDDVPLSAVF HAAATLDDGT VDTLTGERIE RASRAKVLGA RNLHELTREL DLTAFVLFSS FASAF GAPG LGGYAPGNAY LDGLAQQRRS DGLPATAVAW GTWAGSGMAE GPVADRFRRH GVIEMPPETA CRALQNALDR AEVCPI VID VRWDRFLLAY TAQRPTRLFD EIDDARRAAP QAAAEPRVGA LASLPAPERE KALFELVRSH AAAVLGHASA ERVPADQ AF AELGVDSLSA LELRNRLGAA TGVRLPTTTV FDHPDVRTLA AHLTSELGSG TPAREASSAL RDGYRQAGVS GRVRSYLD L LAGLSDFREH FDGSDGFSLD LVDMADGPGE VTVICCAGTA AISGPHEFTR LAGALRGIAP VRAVPQPGYE EGEPLPSSM AAVAAVQADA VIRTQGDKPF VVAGHSAGAL MAYALATELL DRGHPPRGVV LIDVYPPGHQ DAMNAWLEEL TATLFDRETV RMDDTRLTA LGAYDRLTGQ WRPRETGLPT LLVSAGEPMG PWPDDSWKPT WPFEHDTVAV PGDHFTMVQE HADAIARHID A WLGGGNSS SVDKLAAALE HHHHHH

UniProtKB: EryAI, 6-deoxyerythronolide-B synthase EryA3, modules 5 and 6

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Macromolecule #2: 1B2 (heavy chain)

MacromoleculeName: 1B2 (heavy chain) / type: protein_or_peptide / ID: 2 / Number of copies: 2 / 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: 1B2 (light chain)

MacromoleculeName: 1B2 (light chain) / type: protein_or_peptide / ID: 3 / Number of copies: 2 / 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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Macromolecule #4: N~3~-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-N-(2-...

MacromoleculeName: N~3~-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-N-(2-sulfanylethyl)-beta-alaninamide
type: ligand / ID: 4 / Number of copies: 1 / Formula: PN7
Molecular weightTheoretical: 358.348 Da
Chemical component information

ChemComp-PN7:
N~3~-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-N-(2-sulfanylethyl)-beta-alaninamide

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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

Concentration10 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: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 40 sec.
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: FEI FALCON IV (4k x 4k) / Number real images: 10234 / Average exposure time: 8.5 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD
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: 1406538
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v2) / Number images used: 172352
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. V2)

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