[English] 日本語
Yorodumi- PDB-6wc7: Acyl carrier protein (ACP) domain bound to dehydratase (DH) domai... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6wc7 | ||||||
---|---|---|---|---|---|---|---|
Title | Acyl carrier protein (ACP) domain bound to dehydratase (DH) domain in fungal fatty acid synthase (FAS) | ||||||
Components |
| ||||||
Keywords | TRANSFERASE / Fatty acid synthase / acyl carrier protein / dehydratase / BIOSYNTHETIC PROTEIN | ||||||
Function / homology | Function and homology information : / fatty-acyl-CoA synthase system / fatty-acyl-CoA synthase activity / fatty acid synthase complex / [acyl-carrier-protein] S-acetyltransferase / palmitoyltransferase activity / (3R)-hydroxyacyl-[acyl-carrier-protein] dehydratase activity / [acyl-carrier-protein] S-acetyltransferase activity / fatty acyl-[ACP] hydrolase activity / oleoyl-[acyl-carrier-protein] hydrolase ...: / fatty-acyl-CoA synthase system / fatty-acyl-CoA synthase activity / fatty acid synthase complex / [acyl-carrier-protein] S-acetyltransferase / palmitoyltransferase activity / (3R)-hydroxyacyl-[acyl-carrier-protein] dehydratase activity / [acyl-carrier-protein] S-acetyltransferase activity / fatty acyl-[ACP] hydrolase activity / oleoyl-[acyl-carrier-protein] hydrolase / : / holo-[acyl-carrier-protein] synthase activity / [acyl-carrier-protein] S-malonyltransferase / [acyl-carrier-protein] S-malonyltransferase activity / 3-hydroxyacyl-[acyl-carrier-protein] dehydratase / beta-ketoacyl-[acyl-carrier-protein] synthase I / 3-oxoacyl-[acyl-carrier-protein] reductase / 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / enoyl-[acyl-carrier-protein] reductase (NADH) / long-chain fatty acid biosynthetic process / fatty acid synthase activity / enoyl-[acyl-carrier-protein] reductase (NADH) activity / 3-oxoacyl-[acyl-carrier-protein] synthase activity / lipid droplet / magnesium ion binding / mitochondrion / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.8 Å | ||||||
Authors | Lou, J.W. / Mazhab-Jafari, M.T. | ||||||
Funding support | Canada, 1items
| ||||||
Citation | Journal: Commun Biol / Year: 2020 Title: Steric occlusion regulates proximal interactions of acyl carrier protein domain in fungal fatty acid synthase. Authors: Jennifer W Lou / Mohammad T Mazhab-Jafari / Abstract: The acyl carrier protein (ACP) domain shuttles substrates and reaction intermediates in type I fungal fatty acid synthases via transient protein-protein interactions. Here, using electron cryo- ...The acyl carrier protein (ACP) domain shuttles substrates and reaction intermediates in type I fungal fatty acid synthases via transient protein-protein interactions. Here, using electron cryo-microscopy (cryoEM), we report the structure of a fungal FAS stalled at the dehydration reaction, which precedes the final enoyl reduction in the fatty acid biosynthesis cycle. This conformation revealed multiple contact sites between ACP and the dehydratase (DH) and enoyl reductase (ER) domains that occluded the ACP binding to the adjacent ER domain. Our data suggests a minimal path from the DH to the ER reaction site that requires minute changes in the coordinates of the structured N- and C- termini of the ACP domain. | ||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6wc7.cif.gz | 163.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6wc7.ent.gz | 77.7 KB | Display | PDB format |
PDBx/mmJSON format | 6wc7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6wc7_validation.pdf.gz | 885.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6wc7_full_validation.pdf.gz | 884.9 KB | Display | |
Data in XML | 6wc7_validation.xml.gz | 18.8 KB | Display | |
Data in CIF | 6wc7_validation.cif.gz | 27.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wc/6wc7 ftp://data.pdbj.org/pub/pdb/validation_reports/wc/6wc7 | HTTPS FTP |
-Related structure data
Related structure data | 21602MC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
#1: Protein | Mass: 229769.219 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: FAS1, YKL182W / Production host: Escherichia coli (E. coli) References: UniProt: P07149, fatty-acyl-CoA synthase system, 3-hydroxyacyl-[acyl-carrier-protein] dehydratase, enoyl-[acyl-carrier-protein] reductase (NADH), [acyl-carrier-protein] S- ...References: UniProt: P07149, fatty-acyl-CoA synthase system, 3-hydroxyacyl-[acyl-carrier-protein] dehydratase, enoyl-[acyl-carrier-protein] reductase (NADH), [acyl-carrier-protein] S-acetyltransferase, [acyl-carrier-protein] S-malonyltransferase, oleoyl-[acyl-carrier-protein] hydrolase |
---|---|
#2: Protein | Mass: 207184.422 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: FAS2, YPL231W, P1409 / Production host: Escherichia coli (E. coli) References: UniProt: P19097, fatty-acyl-CoA synthase system, 3-oxoacyl-[acyl-carrier-protein] reductase, beta-ketoacyl-[acyl-carrier-protein] synthase I |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Fatty acid synthase / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
---|---|
Molecular weight | Value: 2.6 MDa / Experimental value: NO |
Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7.6 |
Specimen | Conc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER/RHODIUM / Grid mesh size: 400 divisions/in. / Grid type: Homemade |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.3 K |
-Electron microscopy imaging
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TECNAI F20 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Cs: 2 mm |
Specimen holder | Cryogen: NITROGEN Specimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER |
Image recording | Average exposure time: 15 sec. / Electron dose: 36 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 3 |
Image scans | Movie frames/image: 30 / Used frames/image: 1-30 |
-Processing
Software | Name: PHENIX / Version: 1.17.1_3660: / Classification: refinement | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
EM software |
| ||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 5.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 15767 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL | ||||||||||||||||||||||||
Atomic model building | PDB-ID: 2UV8 Accession code: 2UV8 / Source name: PDB / Type: experimental model | ||||||||||||||||||||||||
Refine LS restraints |
|