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Yorodumi- EMDB-41355: KS-AT core of 6-deoxyerythronolide B synthase (DEBS) Module 3 cro... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-41355 | |||||||||||||||
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Title | KS-AT core of 6-deoxyerythronolide B synthase (DEBS) Module 3 crosslinked with its translocation ACP partner of Module 2 | |||||||||||||||
Map data | ||||||||||||||||
Sample |
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Keywords | polyketide synthase / antibody / BIOSYNTHETIC PROTEIN | |||||||||||||||
Function / homology | Function and homology information 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 / oxidoreductase activity / plasma membrane / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | Saccharopolyspora erythraea (bacteria) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.05 Å | |||||||||||||||
Authors | Cogan DP / Soohoo AM / Chen M / Brodsky KL / Liu Y / Khosla C | |||||||||||||||
Funding support | United States, 4 items
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Citation | Journal: To Be Published Title: Structural Basis for Intermodular Communication in Assembly-Line Polyketide Biosynthesis Authors: Cogan DP / Soohoo AM / Chen M / Liu Y / Brodsky KL / Khosla C | |||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_41355.map.gz | 171.9 MB | EMDB map data format | |
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Header (meta data) | emd-41355-v30.xml emd-41355.xml | 19.2 KB 19.2 KB | Display Display | EMDB header |
Images | emd_41355.png | 35.7 KB | ||
Filedesc metadata | emd-41355.cif.gz | 6.9 KB | ||
Others | emd_41355_half_map_1.map.gz emd_41355_half_map_2.map.gz | 318.1 MB 318.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-41355 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-41355 | HTTPS FTP |
-Related structure data
Related structure data | 8tkoMC 8tjnC 8tjoC 8tjpC 8tpwC 8tpxC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_41355.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.946 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_41355_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_41355_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : KS-AT core of DEBS Module 3 crosslinked with its translocation AC...
Entire | Name: KS-AT core of DEBS Module 3 crosslinked with its translocation ACP partner of Module 2 |
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Components |
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-Supramolecule #1: KS-AT core of DEBS Module 3 crosslinked with its translocation AC...
Supramolecule | Name: KS-AT core of DEBS Module 3 crosslinked with its translocation ACP partner of Module 2 type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Saccharopolyspora erythraea (bacteria) |
Molecular weight | Theoretical: 220 KDa |
-Macromolecule #1: EryAII
Macromolecule | Name: EryAII / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Saccharopolyspora erythraea (bacteria) |
Molecular weight | Theoretical: 99.76575 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MVTDSEKVAE YLRRATLDLR AARQRIRELE SDPIAIVSMA CRLPGGVNTP QRLWELLREG GETLSGFPTD RGWDLARLHH PDPDNPGTS YVDKGGFLDD AAGFDAEFFG VSPREAAAMD PQQRLLLETS WELVENAGID PHSLRGTATG VFLGVAKFGY G EDTAAAED ...String: MVTDSEKVAE YLRRATLDLR AARQRIRELE SDPIAIVSMA CRLPGGVNTP QRLWELLREG GETLSGFPTD RGWDLARLHH PDPDNPGTS YVDKGGFLDD AAGFDAEFFG VSPREAAAMD PQQRLLLETS WELVENAGID PHSLRGTATG VFLGVAKFGY G EDTAAAED VEGYSVTGVA PAVASGRISY TMGLEGPSIS VDTACSSSLV ALHLAVESLR KGESSMAVVG GAAVMATPGV FV DFSRQRA LAADGRSKAF GAGADGFGFS EGVTLVLLER LSEARRNGHE VLAVVRGSAL NQDGASNGLS APSGPAQRRV IRQ ALESCG LEPGDVDAVE AHGTGTALGD PIEANALLDT YGRDRDADRP LWLGSVKSNI GHTQAAAGVT GLLKVVLALR NGEL PATLH VEEPTPHVDW SSGGVALLAG NQPWRRGERT RRAAVSAFGI SGTNAHVIVE EAPEREHRET TAHDGRPVPL VVSAR STAA LRAQAAQIAE LLERPDADLA GVGLGLATTR ARHEHRAAVV ASTREEAVRG LREIAAGAAT ADAVVEGVTE VDGRNV VFL FPGQGSQWAG MGAELLSSSP VFAGKIRACD ESMAPMQDWK VSDVLRQAPG APGLDRVDVV QPVLFAVMVS LAELWRS YG VEPAAVVGHS QGEIAAAHVA GALTLEDAAK LVVGRSRLMR SLSGEGGMAA VALGEAAVRE RLRPWQDRLS VAAVNGPR S VVVSGEPGAL RAFSEDCAAE GIRVRDIDVD YASHSPQIER VREELLETTG DIAPRPARVT FHSTVESRSM DGTELDARY WYRNLRETVR FADAVTRLAE SGYDAFIEVS PHPVVVQAVE EAVEEADGAE DAVVVGSLHR DGGDLSAFLR SMATAHVSGV DIRWDVALP GAAPFALPTY PFQRKRYWLQ PAAPAAASDE LAYRSSSVDK LAAALEHHHH HH UniProtKB: EryAII |
-Macromolecule #2: EryAI
Macromolecule | Name: EryAI / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Saccharopolyspora erythraea (bacteria) |
Molecular weight | Theoretical: 20.857295 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MGSSHHHHHH SSGLVPRGSH MLRDRLAGLP RAERTAELVR LVRTSTATVL GHDDPKAVRA TTPFKELGFD (4HH)LAAVR LRN LLNAATGLRL PSTLVFDHPN ASAVAGFLDA ELGTEVRGEA PSALAGLDAL EAALPEVPAT EREELVQRLE RMLAALR PV AQAADASGTG ...String: MGSSHHHHHH SSGLVPRGSH MLRDRLAGLP RAERTAELVR LVRTSTATVL GHDDPKAVRA TTPFKELGFD (4HH)LAAVR LRN LLNAATGLRL PSTLVFDHPN ASAVAGFLDA ELGTEVRGEA PSALAGLDAL EAALPEVPAT EREELVQRLE RMLAALR PV AQAADASGTG ANPSGDDLGE AGVDELLEAL GRELDGD UniProtKB: EryAI |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 8 mg/mL | ||||||||||||
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Buffer | pH: 7.2 Component:
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Grid | Model: 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. / Pretreatment - Atmosphere: AIR | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 7500 / Average exposure time: 6.45 sec. / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 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 stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |