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- EMDB-71446: Antibody (1B2) Bound Rifamycin Synthetase Module 1 in the Elongat... -

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Basic information

Entry
Database: EMDB / ID: EMD-71446
TitleAntibody (1B2) Bound Rifamycin Synthetase Module 1 in the Elongation Mode
Map dataAntibody (1B2) Bound Rifamycin Synthetase Module 1 in the Elongation Mode
Sample
  • Complex: Two antibody fragments (Fabs) in complex with homodimeric polyketide synthase module 1 of the rifamycin synthetase
    • Protein or peptide: Antibody Fragment 1B2 Heavy Chain
    • Protein or peptide: Antibody Fragment 1B2 Light Chain
    • Protein or peptide: 6-deoxyerythronolide-B synthase
    • Protein or peptide: 6-deoxyerythronolide-B synthase
KeywordsPolyketide Synthase Module / Antibody (Fab) / Transferase-Immune System complex
Function / homology
Function and homology information


6-deoxyerythronolide-B synthase / fatty acid synthase activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / antibiotic biosynthetic process / fatty acid biosynthetic process
Similarity search - Function
Polyketide synthase dimerisation element domain / Polyketide synthase dimerisation element domain / Polyketide synthase, dehydratase domain / PKS_DH / : / Polyketide synthase dehydratase domain / PKS_PP_betabranch / Polyketide synthase, dehydratase domain superfamily / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension ...Polyketide synthase dimerisation element domain / Polyketide synthase dimerisation element domain / Polyketide synthase, dehydratase domain / PKS_DH / : / Polyketide synthase dehydratase domain / PKS_PP_betabranch / 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 / ANL, N-terminal domain / : / AMP-binding enzyme C-terminal domain / AMP-binding enzyme, C-terminal domain / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase domain superfamily / AMP-binding, conserved site / Putative AMP-binding domain signature. / Acyl transferase/acyl hydrolase/lysophospholipase / AMP-dependent synthetase/ligase / AMP-binding enzyme / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / PKS_KR / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Beta-ketoacyl synthase / 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 / AMP-binding enzyme, C-terminal domain 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 speciesAmycolatopsis mediterranei (bacteria) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.22 Å
AuthorsCogan DP / Liu C / West RC / Chen M
Funding support United States, 1 items
OrganizationGrant numberCountry
Other private United States
CitationJournal: bioRxiv / Year: 2025
Title: Molecular Basis for Asynchronous Chain Elongation During Rifamycin Antibiotic Biosynthesis.
Authors: Chengli Liu / Ryan C West / Muyuan Chen / Whitaker Cohn / George Wang / Aryan M Mandot / Selena Kim / Dillon P Cogan /
Abstract: The rifamycin synthetase (RIFS) from the bacterium is a large (3.5 MDa) multienzyme system that catalyzes over 40 chemical reactions to generate a complex precursor to the antibiotic rifamycin B. It ...The rifamycin synthetase (RIFS) from the bacterium is a large (3.5 MDa) multienzyme system that catalyzes over 40 chemical reactions to generate a complex precursor to the antibiotic rifamycin B. It is considered a hybrid enzymatic assembly line and consists of an N-terminal nonribosomal peptide synthetase loading module followed by a decamodular polyketide synthase (PKS). While the biosynthetic functions are known for each enzymatic domain of RIFS, structural and biochemical analyses of this system from purified components are relatively scarce. Here, we examine the biosynthetic mechanism of RIFS through complementary crosslinking, kinetic, and structural analyses of its first PKS module (M1). Thiol-selective crosslinking of M1 provided a plausible molecular basis for previously observed conformational asymmetry with respect to ketosynthase (KS)-substrate carrier protein (CP) interactions during polyketide chain elongation. Our data suggest that C-terminal dimeric interfaces-which are ubiquitous in bacterial PKSs-force their adjacent CP domains to co-migrate between two equivalent KS active site chambers. Cryogenic electron microscopy analysis of M1 further supported this observation while uncovering its unique architecture. Single-turnover kinetic analysis of M1 indicated that although removal of C-terminal dimeric interfaces supported 2-fold greater KS-CP interactions, it did not increase the partial product occupancy of the homodimeric protein. Our findings cast light on molecular details of natural antibiotic biosynthesis that will aid in the design of artificial megasynth(et)ases with untold product structures and bioactivities.
History
DepositionJun 25, 2025-
Header (metadata) releaseJul 23, 2025-
Map releaseJul 23, 2025-
UpdateJul 23, 2025-
Current statusJul 23, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_71446.png

Downloads & links

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Map

FileDownload / File: emd_71446.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAntibody (1B2) Bound Rifamycin Synthetase Module 1 in the Elongation Mode
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 448 pix.
= 492.8 Å		1.1 Å/pix.
x 448 pix.
= 492.8 Å		1.1 Å/pix.
x 448 pix.
= 492.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.13
Minimum - Maximum-0.26049533 - 0.7687979
Average (Standard dev.)-0.00013523303 (±0.016598733)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 492.80002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map B

Fileemd_71446_half_map_1.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map A

Fileemd_71446_half_map_2.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Two antibody fragments (Fabs) in complex with homodimeric polyket...

EntireName: Two antibody fragments (Fabs) in complex with homodimeric polyketide synthase module 1 of the rifamycin synthetase
Components
  • Complex: Two antibody fragments (Fabs) in complex with homodimeric polyketide synthase module 1 of the rifamycin synthetase
    • Protein or peptide: Antibody Fragment 1B2 Heavy Chain
    • Protein or peptide: Antibody Fragment 1B2 Light Chain
    • Protein or peptide: 6-deoxyerythronolide-B synthase
    • Protein or peptide: 6-deoxyerythronolide-B synthase

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Supramolecule #1: Two antibody fragments (Fabs) in complex with homodimeric polyket...

SupramoleculeName: Two antibody fragments (Fabs) in complex with homodimeric polyketide synthase module 1 of the rifamycin synthetase
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Amycolatopsis mediterranei (bacteria) / Strain: NRRL B-3240
Molecular weightTheoretical: 454.49469 KDa

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Macromolecule #1: Antibody Fragment 1B2 Heavy Chain

MacromoleculeName: Antibody Fragment 1B2 Heavy Chain / type: protein_or_peptide / ID: 1 / 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 #2: Antibody Fragment 1B2 Light Chain

MacromoleculeName: Antibody Fragment 1B2 Light Chain / type: protein_or_peptide / ID: 2 / 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 #3: 6-deoxyerythronolide-B synthase

MacromoleculeName: 6-deoxyerythronolide-B synthase / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO / EC number: 6-deoxyerythronolide-B synthase
Source (natural)Organism: Amycolatopsis mediterranei (bacteria) / Strain: NRRL B-3240
Molecular weightTheoretical: 175.359844 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MASTDSEKVA EYLRRATLDL RAARQRIREL EGEPIAIVGM ACRLPGGVAS PEDLWRLVAE RVDAVSEFPG DRGWDLDSLI DPDRERAGT SYVGQGGFLH DAGEFDAGFF GISPREAVAM DPQQRLLLET SWEALENAGV DPIALKGTDT GVFSGLMGQG Y GSGAVAPE ...String:
MASTDSEKVA EYLRRATLDL RAARQRIREL EGEPIAIVGM ACRLPGGVAS PEDLWRLVAE RVDAVSEFPG DRGWDLDSLI DPDRERAGT SYVGQGGFLH DAGEFDAGFF GISPREAVAM DPQQRLLLET SWEALENAGV DPIALKGTDT GVFSGLMGQG Y GSGAVAPE LEGFVTTGVA SSVASGRVSY VLGLEGPAVT VDTACSSSLV AMHLAAQALR QGECSMALAG GVTVMATPGS FV EFSRQRA LAPDGRCKAF AAAADGTGWS EGVGVVVLER LSVARERGHR ILAVLRGSAV NQDGASNGLT APNGLSQQRV IRR ALAAAG LAPSDVDVVE AHGTGTTLGD PIEAQALLAT YGQERKQPLW LGSLKSNIGH AQAAAGVAGV IKMVQALRHE TLPP TLHVD KPTLEVDWSA GAIELLTEAR AWPRNGRPRR AGVSSFGVSG TNAHLILEEA PAEEPVAAPE LPVVPLVVSA RSTES LSGQ AERLASLLEG DVSLTEVAGA LVSRRAVLDE RAVVVAGSRE EAVTGLRALN TAGSGTPGKV VWVFPGQGTQ WAGMGR ELL AESPVFAERI AECAAALAPW IDWSLVDVLR GEGDLGRVDV LQPACFAVMV GLAAVWESVG VRPDAVVGHS QGEIAAA CV SGALSLEDAA KVVALRSQAI AAELSGRGGM ASVALGEDDV VSRLVDGVEV AAVNGPSSVV IAGDAHALDA TLEILSGE G IRVRRVAVDY ASHTRHVEDI RDTLAETLAG ISAQAPAVPF YSTVTSEWVR DAGVLDGGYW YRNLRNQVRF GAAATALLE QGHTVFVEVS AHPVTVQPLS ELTGDAIGTL RREDGGLRRL LASMGELFVR GIDVDWTAMV PAAGWVDLPT YAFEHRHYWL EPAEPASAG DPLLGTVVST PGSDRLTAVA QWSRRAQPWA VDGLVPNAAL VEAAIRLGDL AGTPVVGELV VDAPVVLPRR G SREVQLIV GEPGEQRRRP IEVFSREADE PWTRHAHGTL APAAAAVPEP AAAGDATDVT VAGLRDADRY GIHPALLDAA VR TVVGDDL LPSVWTGVSL LASGATAVTV TPTATGLRLT DPAGQPVLTV ESVRGTPFVA EQGTTDALFR VDWPEIPLPT AET ADFLPY EATSAEATLS ALQAWLADPA ETRLAVVTGD CTEPGAAAIW GLVRSAQSEH PGRIVLADLD DPAVLPAVVA SGEP QVRVR NGVASVPRLT RVTPRQDARP LDPEGTVLIT GGTGTLGALT ARHLVTAHGV RHLVLVSRRG EAPELQEELT ALGAS VAIA ACDVADRAQL EAVLRAIPAE HPLTAVIHTA GVLDDGVVTE LTPDRLATVR RPKVDAARLL DELTREADLA AFVLFS SAA GVLGNPGQAG YAAANAELDA LARQRNSLDL PAVSIAWGYW ATVSGMTEHL GDADLRRNQR IGMSGLPADE GMALLDA AI ATGGTLVAAK FDVAALRATA KAGGPVPPLL RGLAPLPRRA AAKTASLTER LAGLAETEQA AALLDLVRRH AAEVLGHS G AESVHSGRTF KDAGFDSLTA VELRNRLAAA TGLTLSPAMI FDYPKPPALA DHLRAKLFGT EVRGEAPSAL AGLDALEAA LPEVPATERE ELVQRLERML AALRPVAQAA DASGTGANPS GDDLGEAGVD ELLEALGREL DGDGNSSSVD KLAAALEHHH HHH

UniProtKB: 6-deoxyerythronolide-B synthase

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Macromolecule #4: 6-deoxyerythronolide-B synthase

MacromoleculeName: 6-deoxyerythronolide-B synthase / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: 6-deoxyerythronolide-B synthase
Source (natural)Organism: Amycolatopsis mediterranei (bacteria)
Molecular weightTheoretical: 175.700172 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MASTDSEKVA EYLRRATLDL RAARQRIREL EGEPIAIVGM ACRLPGGVAS PEDLWRLVAE RVDAVSEFPG DRGWDLDSLI DPDRERAGT SYVGQGGFLH DAGEFDAGFF GISPREAVAM DPQQRLLLET SWEALENAGV DPIALKGTDT GVFSGLMGQG Y GSGAVAPE ...String:
MASTDSEKVA EYLRRATLDL RAARQRIREL EGEPIAIVGM ACRLPGGVAS PEDLWRLVAE RVDAVSEFPG DRGWDLDSLI DPDRERAGT SYVGQGGFLH DAGEFDAGFF GISPREAVAM DPQQRLLLET SWEALENAGV DPIALKGTDT GVFSGLMGQG Y GSGAVAPE LEGFVTTGVA SSVASGRVSY VLGLEGPAVT VDTACSSSLV AMHLAAQALR QGECSMALAG GVTVMATPGS FV EFSRQRA LAPDGRCKAF AAAADGTGWS EGVGVVVLER LSVARERGHR ILAVLRGSAV NQDGASNGLT APNGLSQQRV IRR ALAAAG LAPSDVDVVE AHGTGTTLGD PIEAQALLAT YGQERKQPLW LGSLKSNIGH AQAAAGVAGV IKMVQALRHE TLPP TLHVD KPTLEVDWSA GAIELLTEAR AWPRNGRPRR AGVSSFGVSG TNAHLILEEA PAEEPVAAPE LPVVPLVVSA RSTES LSGQ AERLASLLEG DVSLTEVAGA LVSRRAVLDE RAVVVAGSRE EAVTGLRALN TAGSGTPGKV VWVFPGQGTQ WAGMGR ELL AESPVFAERI AECAAALAPW IDWSLVDVLR GEGDLGRVDV LQPACFAVMV GLAAVWESVG VRPDAVVGHS QGEIAAA CV SGALSLEDAA KVVALRSQAI AAELSGRGGM ASVALGEDDV VSRLVDGVEV AAVNGPSSVV IAGDAHALDA TLEILSGE G IRVRRVAVDY ASHTRHVEDI RDTLAETLAG ISAQAPAVPF YSTVTSEWVR DAGVLDGGYW YRNLRNQVRF GAAATALLE QGHTVFVEVS AHPVTVQPLS ELTGDAIGTL RREDGGLRRL LASMGELFVR GIDVDWTAMV PAAGWVDLPT YAFEHRHYWL EPAEPASAG DPLLGTVVST PGSDRLTAVA QWSRRAQPWA VDGLVPNAAL VEAAIRLGDL AGTPVVGELV VDAPVVLPRR G SREVQLIV GEPGEQRRRP IEVFSREADE PWTRHAHGTL APAAAAVPEP AAAGDATDVT VAGLRDADRY GIHPALLDAA VR TVVGDDL LPSVWTGVSL LASGATAVTV TPTATGLRLT DPAGQPVLTV ESVRGTPFVA EQGTTDALFR VDWPEIPLPT AET ADFLPY EATSAEATLS ALQAWLADPA ETRLAVVTGD CTEPGAAAIW GLVRSAQSEH PGRIVLADLD DPAVLPAVVA SGEP QVRVR NGVASVPRLT RVTPRQDARP LDPEGTVLIT GGTGTLGALT ARHLVTAHGV RHLVLVSRRG EAPELQEELT ALGAS VAIA ACDVADRAQL EAVLRAIPAE HPLTAVIHTA GVLDDGVVTE LTPDRLATVR RPKVDAARLL DELTREADLA AFVLFS SAA GVLGNPGQAG YAAANAELDA LARQRNSLDL PAVSIAWGYW ATVSGMTEHL GDADLRRNQR IGMSGLPADE GMALLDA AI ATGGTLVAAK FDVAALRATA KAGGPVPPLL RGLAPLPRRA AAKTASLTER LAGLAETEQA AALLDLVRRH AAEVLGHS G AESVHSGRTF KDAGFD(4HH)LTA VELRNRLAAA TGLTLSPAMI FDYPKPPALA DHLRAKLFGT EVRGEAPSAL AGLDA LEAA LPEVPATERE ELVQRLERML AALRPVAQAA DASGTGANPS GDDLGEAGVD ELLEALGREL DGDGNSSSVD KLAAAL EHH HHHH

UniProtKB: 6-deoxyerythronolide-B synthase

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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
10.0 mMC8H18N2O4Shepes

Details: 100 mM citric acid, 10 mM HEPES, pH 7.2 (NaOH)
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.036000000000000004 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 10005 / Average exposure time: 5.72 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.988 µm / Nominal defocus min: 1.188 µm
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: 443204
CTF correctionSoftware - Name: cryoSPARC (ver. 4.7.0) / Type: NONE
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.22 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7.0) / Number images used: 177509
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.7.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.7.0)
Final 3D classificationNumber classes: 8 / Software - Name: RELION (ver. 5.0)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9pav:
Antibody (1B2) Bound Rifamycin Synthetase Module 1 in the Elongation Mode

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