[English] 日本語
![](img/lk-miru.gif)
- EMDB-23713: 6-Deoxyerythronolide B synthase (DEBS) module 1 in complex with a... -
+
Open data
-
Basic information
Entry | Database: EMDB / ID: EMD-23713 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | 6-Deoxyerythronolide B synthase (DEBS) module 1 in complex with antibody fragment 1B2: State 1' | |||||||||
![]() | intermediate | |||||||||
![]() |
| |||||||||
Function / homology | ![]() 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 | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.1 Å | |||||||||
![]() | Cogan DP / Zhang K / Chiu W / Khosla C | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() 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 |
|
-
Structure visualization
Movie |
![]() |
---|---|
Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
-
Downloads & links
-EMDB archive
Map data | ![]() | 72.2 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 16 KB 16 KB | Display Display | ![]() |
Images | ![]() | 114.7 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7m7hMC ![]() 7m7eC ![]() 7m7fC ![]() 7m7gC ![]() 7m7iC ![]() 7m7jC C: citing same article ( M: atomic model generated by this map |
---|---|
Similar structure data |
-
Links
EMDB pages | ![]() ![]() |
---|---|
Related items in Molecule of the Month |
-
Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | intermediate | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-
Sample components
-Entire : Complex between DEBS (3)M1TE and antibody fragment 1B2
Entire | Name: Complex between DEBS (3)M1TE and antibody fragment 1B2 |
---|---|
Components |
|
-Supramolecule #1: Complex between DEBS (3)M1TE and antibody fragment 1B2
Supramolecule | Name: Complex between DEBS (3)M1TE and antibody fragment 1B2 type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
---|---|
Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 480 KDa |
-Macromolecule #1: EryAI,6-deoxyerythronolide-B synthase EryA3, modules 5 and 6 chimera
Macromolecule | Name: 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: ![]() |
Molecular weight | Theoretical: 188.550891 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: 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 |
-Macromolecule #2: 1B2 (heavy chain)
Macromolecule | Name: 1B2 (heavy chain) / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 26.447611 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: 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 |
-Macromolecule #3: 1B2 (light chain)
Macromolecule | Name: 1B2 (light chain) / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 25.715832 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: 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 |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
![]() | single particle reconstruction |
Aggregation state | particle |
-
Sample preparation
Concentration | 10 mg/mL | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Buffer | pH: 7.2 Component:
| ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV |
-
Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average exposure time: 8.5 sec. / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
-
Image processing
Particle selection | Number selected: 1406538 |
---|---|
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 58206 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |