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Yorodumi- EMDB-41496: Crosslinked 6-deoxyerythronolide B synthase (DEBS) Module 3 in co... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-41496 | |||||||||||||||
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Title | Crosslinked 6-deoxyerythronolide B synthase (DEBS) Module 3 in complex with antibody fragment 1B2: trans-oriented 1B2 and ACP | |||||||||||||||
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 / fatty acid biosynthetic process / oxidoreductase activity / plasma membrane / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | Saccharopolyspora erythraea (bacteria) / Homo sapiens (human) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 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_41496.map.gz | 257.1 MB | EMDB map data format | |
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Header (meta data) | emd-41496-v30.xml emd-41496.xml | 21.5 KB 21.5 KB | Display Display | EMDB header |
Images | emd_41496.png | 29.5 KB | ||
Filedesc metadata | emd-41496.cif.gz | 7.7 KB | ||
Others | emd_41496_half_map_1.map.gz emd_41496_half_map_2.map.gz | 474.6 MB 474.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-41496 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-41496 | HTTPS FTP |
-Validation report
Summary document | emd_41496_validation.pdf.gz | 823.8 KB | Display | EMDB validaton report |
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Full document | emd_41496_full_validation.pdf.gz | 823.4 KB | Display | |
Data in XML | emd_41496_validation.xml.gz | 19.1 KB | Display | |
Data in CIF | emd_41496_validation.cif.gz | 22.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41496 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41496 | HTTPS FTP |
-Related structure data
Related structure data | 8tpxMC 8tjnC 8tjoC 8tjpC 8tkoC 8tpwC C: citing same article (ref.) M: atomic model generated by this map |
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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_41496.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.1 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_41496_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_41496_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Crosslinked DEBS Module 3 in complex with Antibody Fragment 1B2
Entire | Name: Crosslinked DEBS Module 3 in complex with Antibody Fragment 1B2 |
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Components |
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-Supramolecule #1: Crosslinked DEBS Module 3 in complex with Antibody Fragment 1B2
Supramolecule | Name: Crosslinked DEBS Module 3 in complex with Antibody Fragment 1B2 type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Saccharopolyspora erythraea (bacteria) |
Molecular weight | Theoretical: 420 KDa |
-Macromolecule #1: EryAII,EryAII,EryAII,6-deoxyerythronolide-B synthase EryA3, modul...
Macromolecule | Name: 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 |
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Source (natural) | Organism: Saccharopolyspora erythraea (bacteria) |
Molecular weight | Theoretical: 186.489578 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: 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: EryAII |
-Macromolecule #2: Antibody Fragment 1B2, Heavy Chain
Macromolecule | Name: Antibody Fragment 1B2, Heavy Chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 26.447611 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
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: Antibody Fragment 1B2, Light Chain
Macromolecule | Name: Antibody Fragment 1B2, Light Chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 25.715832 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
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 |
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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 | ||||||||||||
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: 10480 / Average exposure time: 2.79 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 |