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- PDB-6g2d: Citrate-induced acetyl-CoA carboxylase (ACC-Cit) filament at 5.4 ... -

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Basic information

Entry
Database: PDB / ID: 6g2d
TitleCitrate-induced acetyl-CoA carboxylase (ACC-Cit) filament at 5.4 A resolution
ComponentsAcetyl-CoA carboxylase 1
KeywordsLIGASE / Filament / Helical / Multienzyme / 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
Acetyl-CoA carboxylase, central domain / : / : / Acetyl-CoA carboxylase, central region / Acetyl-CoA carboxylase, BT domain / Acetyl-coenzyme A carboxyltransferase, C-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase C-terminal domain profile. / Acetyl-coenzyme A carboxyltransferase, N-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase N-terminal domain profile. / Acetyl-CoA carboxylase ...Acetyl-CoA carboxylase, central domain / : / : / Acetyl-CoA carboxylase, central region / Acetyl-CoA carboxylase, BT domain / Acetyl-coenzyme A carboxyltransferase, C-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase C-terminal domain profile. / Acetyl-coenzyme A carboxyltransferase, N-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase N-terminal domain profile. / Acetyl-CoA carboxylase / Carboxyl transferase domain / Biotin-binding site / Biotin-requiring enzymes attachment site. / Biotin carboxylase-like, N-terminal domain / Biotin carboxylase, C-terminal / Biotin carboxylation domain / Biotin carboxylase, N-terminal domain / Biotin carboxylase C-terminal domain / Biotin carboxylation domain profile. / Biotin carboxylase C-terminal domain / Carbamoyl-phosphate synthase subdomain signature 1. / Carbamoyl-phosphate synthetase large subunit-like, ATP-binding domain / Carbamoyl-phosphate synthase L chain, ATP binding domain / Biotin-requiring enzyme / Rudiment single hybrid motif / Biotinyl/lipoyl domain profile. / Biotin/lipoyl attachment / Single hybrid motif / ATP-grasp fold, subdomain 1 / Pre-ATP-grasp domain superfamily / ATP-grasp fold / ATP-grasp fold profile. / ClpP/crotonase-like domain superfamily / Carbamoyl-phosphate synthase subdomain signature 2.
Similarity search - Domain/homology
Acetyl-CoA carboxylase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.4 Å
AuthorsHunkeler, M. / Hagmann, A. / Stuttfeld, E. / Chami, M. / Stahlberg, H. / Maier, T.
Funding support Switzerland, 3items
OrganizationGrant numberCountry
Swiss National Science Foundation138262 Switzerland
Swiss National Science Foundation15696 Switzerland
Swiss National Science Foundation164074 Switzerland
CitationJournal: Nature / Year: 2018
Title: Structural basis for regulation of human acetyl-CoA carboxylase.
Authors: Moritz Hunkeler / Anna Hagmann / Edward Stuttfeld / Mohamed Chami / Yakir Guri / Henning Stahlberg / Timm Maier /
Abstract: Acetyl-CoA carboxylase catalyses the ATP-dependent carboxylation of acetyl-CoA, a rate-limiting step in fatty acid biosynthesis. Eukaryotic acetyl-CoA carboxylases are large, homodimeric multienzymes. ...Acetyl-CoA carboxylase catalyses the ATP-dependent carboxylation of acetyl-CoA, a rate-limiting step in fatty acid biosynthesis. Eukaryotic acetyl-CoA carboxylases are large, homodimeric multienzymes. Human acetyl-CoA carboxylase occurs in two isoforms: the metabolic, cytosolic ACC1, and ACC2, which is anchored to the outer mitochondrial membrane and controls fatty acid β-oxidation. ACC1 is regulated by a complex interplay of phosphorylation, binding of allosteric regulators and protein-protein interactions, which is further linked to filament formation. These filaments were discovered in vitro and in vivo 50 years ago, but the structural basis of ACC1 polymerization and regulation remains unknown. Here, we identify distinct activated and inhibited ACC1 filament forms. We obtained cryo-electron microscopy structures of an activated filament that is allosterically induced by citrate (ACC-citrate), and an inactivated filament form that results from binding of the BRCT domains of the breast cancer type 1 susceptibility protein (BRCA1). While non-polymeric ACC1 is highly dynamic, filament formation locks ACC1 into different catalytically competent or incompetent conformational states. This unique mechanism of enzyme regulation via large-scale conformational changes observed in ACC1 has potential uses in engineering of switchable biosynthetic systems. Dissecting the regulation of acetyl-CoA carboxylase opens new paths towards counteracting upregulation of fatty acid biosynthesis in disease.
History
DepositionMar 23, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 13, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 27, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 6, 2019Group: Data collection / Refinement description / Category: software / Item: _software.name
Revision 1.3Dec 11, 2019Group: Other / Category: atom_sites
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3]
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
B: Acetyl-CoA carboxylase 1
C: Acetyl-CoA carboxylase 1
D: Acetyl-CoA carboxylase 1
F: Acetyl-CoA carboxylase 1


Theoretical massNumber of molelcules
Total (without water)1,090,5314
Polymers1,090,5314
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27190 Å2
ΔGint-149 kcal/mol
Surface area274950 Å2
MethodPISA

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Components

#1: Protein
Acetyl-CoA carboxylase 1 / ACC1 / ACC-alpha


Mass: 272632.844 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACACA, ACAC, ACC1, ACCA / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q13085, acetyl-CoA carboxylase, biotin carboxylase

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Multienzyme / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
Details: Data was collected in movie mode with a total of 40 e-/A2 over a total of 40 frames. Frames 1-30 were used for final reconstruction.

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Processing

Software
NameVersionClassificationNB
PHENIX1.11.1_2575refinement
PHENIX1.11.1_2575refinement
EM softwareName: RELION / Version: 2.1b1 / Category: 3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 5.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 131062 / Symmetry type: POINT
RefinementStereochemistry target values: GeoStd + Monomer Library
Details: The clash score value (3.5) reported in the publication associated with this model was obtained directly from phenix.real_space_refine version 1.11.1-2575. We acknowledge that the current ...Details: The clash score value (3.5) reported in the publication associated with this model was obtained directly from phenix.real_space_refine version 1.11.1-2575. We acknowledge that the current validation toolchain of wwwPDB produces slightly higher values, possibly linked to the handling of cif files (required as this submission contains more than 100.000 atoms) and protons and have locally reproduced this difference by using earlier software versions.
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0063097058196889088
ELECTRON MICROSCOPYf_angle_d1.95064022357160928
ELECTRON MICROSCOPYf_chiral_restr0.1050821358526813
ELECTRON MICROSCOPYf_plane_restr0.007368841576413634
ELECTRON MICROSCOPYf_dihedral_angle_d10.754186093135821

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