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Yorodumi- PDB-8tjo: Crosslinked 6-deoxyerythronolide B synthase (DEBS) Module 1 in co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8tjo | |||||||||||||||
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Title | Crosslinked 6-deoxyerythronolide B synthase (DEBS) Module 1 in complex with antibody fragment 1B2: Crosslinked Intra-State 1 | |||||||||||||||
Components |
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Keywords | BIOSYNTHETIC PROTEIN/IMMUNE SYSTEM / polyketide synthase / antibody / BIOSYNTHETIC PROTEIN-IMMUNE SYSTEM complex | |||||||||||||||
Biological species | Saccharopolyspora erythraea (bacteria) Homo sapiens (human) | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.61 Å | |||||||||||||||
Authors | Cogan, D.P. / Soohoo, A.M. / Chen, M. / Brodsky, K.L. / Liu, Y. / Khosla, C. | |||||||||||||||
Funding support | United States, 4items
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Citation | Journal: To Be Published Title: Structural Basis for Intermodular Communication in Assembly-Line Polyketide Biosynthesis Authors: Cogan, D.P. / Soohoo, A.M. / Chen, M. / Liu, Y. / Brodsky, K.L. / Khosla, C. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8tjo.cif.gz | 520.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8tjo.ent.gz | 411.6 KB | Display | PDB format |
PDBx/mmJSON format | 8tjo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tj/8tjo ftp://data.pdbj.org/pub/pdb/validation_reports/tj/8tjo | HTTPS FTP |
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-Related structure data
Related structure data | 41306MC 8tjnC 8tjpC 8tkoC 8tpwC 8tpxC M: map data used to model this data C: citing same article (ref.) |
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-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 188891.219 Da / Num. of mol.: 2 Fragment: DEBS Module 1, Subunit A (UNP residues 557-2015) + EryA3 (UNP residues 2896-3172),DEBS Module 1, Subunit A (UNP residues 557-2015) + EryA3 (UNP residues 2896-3172),DEBS Module 1, Subunit A ...Fragment: DEBS Module 1, Subunit A (UNP residues 557-2015) + EryA3 (UNP residues 2896-3172),DEBS Module 1, Subunit A (UNP residues 557-2015) + EryA3 (UNP residues 2896-3172),DEBS Module 1, Subunit A (UNP residues 557-2015) + EryA3 (UNP residues 2896-3172),DEBS Module 1, Subunit A (UNP residues 557-2015) + EryA3 (UNP residues 2896-3172),DEBS Module 1, Subunit A (UNP residues 557-2015) + EryA3 (UNP residues 2896-3172),DEBS Module 1, Subunit A (UNP residues 557-2015) + EryA3 (UNP residues 2896-3172),DEBS Module 1, Subunit A (UNP residues 557-2015) + EryA3 (UNP residues 2896-3172),DEBS Module 1, Subunit A (UNP residues 557-2015) + EryA3 (UNP residues 2896-3172) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharopolyspora erythraea (bacteria) / Gene: eryAI, eryA / Plasmid: pDC1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BAP1 / References: 6-deoxyerythronolide-B synthase #2: Antibody | Mass: 26447.611 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria) #3: Antibody | Mass: 25715.832 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria) Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Crosslinked DEBS Module 1 in complex with Antibody Fragment 1B2 Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES | ||||||||||||||||||||
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Molecular weight | Value: 0.48 MDa / Experimental value: YES | ||||||||||||||||||||
Source (natural) | Organism: Saccharopolyspora erythraea (bacteria) | ||||||||||||||||||||
Source (recombinant) | Organism: Escherichia coli BL21(DE3) (bacteria) / Strain: BAP1 / Plasmid: pDC1 | ||||||||||||||||||||
Buffer solution | pH: 7.2 | ||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1 | ||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 150 µm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 3.76 sec. / Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 9523 |
-Processing
EM software | Name: PHENIX / Version: 1.21.1_5286 / Category: model refinement |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
Particle selection | Num. of particles selected: 434136 |
Symmetry | Point symmetry: C1 (asymmetric) |
3D reconstruction | Resolution: 3.61 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 92037 / Symmetry type: POINT |
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL |
Atomic model building | PDB-ID: 7M7F Accession code: 7M7F / Source name: PDB / Type: experimental model |