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Yorodumi- PDB-8xl0: Citrate-induced filament of human acetyl-coenzyme A carboxylase 1... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8xl0 | ||||||
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Title | Citrate-induced filament of human acetyl-coenzyme A carboxylase 1 (ACC1-citrate) | ||||||
Components | Acetyl-CoA carboxylase 1 | ||||||
Keywords | LIGASE / Biotin-dependent carboxylase | ||||||
Function / homology | Function and homology information fatty-acyl-CoA biosynthetic process / acetyl-CoA carboxylase / Defective HLCS causes multiple carboxylase deficiency / Biotin transport and metabolism / Fatty acyl-CoA biosynthesis / acetyl-CoA metabolic process / malonyl-CoA biosynthetic process / protein metabolic process / ChREBP activates metabolic gene expression / acetyl-CoA carboxylase activity ...fatty-acyl-CoA biosynthetic process / acetyl-CoA carboxylase / Defective HLCS causes multiple carboxylase deficiency / Biotin transport and metabolism / Fatty acyl-CoA biosynthesis / acetyl-CoA metabolic process / malonyl-CoA biosynthetic process / protein metabolic process / ChREBP activates metabolic gene expression / acetyl-CoA carboxylase activity / tissue homeostasis / Carnitine shuttle / lipid homeostasis / Activation of gene expression by SREBF (SREBP) / fibrillar center / fatty acid biosynthetic process / cellular response to prostaglandin E stimulus / actin cytoskeleton / protein homotetramerization / mitochondrion / ATP binding / identical protein binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.14 Å | ||||||
Authors | Zhou, F.Y. / Zhang, Y.Y. / Zhou, Q. / Hu, Q. | ||||||
Funding support | 1items
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Citation | Journal: Sci Adv / Year: 2024 Title: Filament structures unveil the dynamic organization of human acetyl-CoA carboxylase. Authors: Fayang Zhou / Yuanyuan Zhang / Yuyao Zhu / Qiang Zhou / Yigong Shi / Qi Hu / Abstract: Human acetyl-coenzyme A (CoA) carboxylases (ACCs) catalyze the carboxylation of acetyl-CoA, which is the rate-limiting step in fatty acid synthesis. The molecular mechanism underlying the dynamic ...Human acetyl-coenzyme A (CoA) carboxylases (ACCs) catalyze the carboxylation of acetyl-CoA, which is the rate-limiting step in fatty acid synthesis. The molecular mechanism underlying the dynamic organization of ACCs is largely unknown. Here, we determined the cryo-electron microscopy (EM) structure of human ACC1 in its inactive state, which forms a unique filament structure and is in complex with acetyl-CoA. We also determined the cryo-EM structure of human ACC1 activated by dephosphorylation and citrate treatment, at a resolution of 2.55 Å. Notably, the covalently linked biotin binds to a site that is distant from the acetyl-CoA binding site when acetyl-CoA is absent, suggesting a potential coordination between biotin binding and acetyl-CoA binding. These findings provide insights into the structural dynamics and regulatory mechanisms of human ACCs. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8xl0.cif.gz | 2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8xl0.ent.gz | 1.6 MB | Display | PDB format |
PDBx/mmJSON format | 8xl0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8xl0_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 8xl0_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 8xl0_validation.xml.gz | 270.5 KB | Display | |
Data in CIF | 8xl0_validation.cif.gz | 424.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xl/8xl0 ftp://data.pdbj.org/pub/pdb/validation_reports/xl/8xl0 | HTTPS FTP |
-Related structure data
Related structure data | 38433MC 8xkzC 8xl1C 8xl2C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 265869.375 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q13085, acetyl-CoA carboxylase #2: Chemical | ChemComp-BTN / Has ligand of interest | Y | Has protein modification | 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: Citrate-induced filament of human acetyl-coenzyme A carboxylase 1 (ACC1-citrate) Type: COMPLEX / Entity ID: #1 / Source: NATURAL |
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Source (natural) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-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 defocus max: 2200 nm / Nominal defocus min: 1200 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 4.14 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 36041 / Symmetry type: POINT |