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- PDB-5trc: Crystal structure of phosphorylated AC3-AC5 domains of yeast acet... -

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Basic information

Entry
Database: PDB / ID: 5trc
TitleCrystal structure of phosphorylated AC3-AC5 domains of yeast acetyl-CoA carboxylase
ComponentsAcetyl-CoA carboxylase
KeywordsLIGASE / Phosphorylation / Inhibition
Function / homology
Function and homology information


: / Biotin transport and metabolism / Fatty acyl-CoA biosynthesis / Carnitine metabolism / acetyl-CoA carboxylase / carboxyl- or carbamoyltransferase activity / acetyl-CoA binding / biotin carboxylase / acetyl-CoA carboxylase complex / biotin carboxylase activity ...: / Biotin transport and metabolism / Fatty acyl-CoA biosynthesis / Carnitine metabolism / acetyl-CoA carboxylase / carboxyl- or carbamoyltransferase activity / acetyl-CoA binding / biotin carboxylase / acetyl-CoA carboxylase complex / biotin carboxylase activity / malonyl-CoA biosynthetic process / acetyl-CoA carboxylase activity / acetyl-CoA biosynthetic process / long-chain fatty acid biosynthetic process / fatty acid biosynthetic process / protein import into nucleus / endoplasmic reticulum membrane / protein homodimerization activity / 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
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.9 Å
AuthorsWei, J. / Tong, L.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)R01DK067238 United States
National Institutes of Health/Office of the DirectorS10OD012018 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM041784 United States
CitationJournal: Cell Discov / Year: 2016
Title: A unified molecular mechanism for the regulation of acetyl-CoA carboxylase by phosphorylation.
Authors: Wei, J. / Zhang, Y. / Yu, T.Y. / Sadre-Bazzaz, K. / Rudolph, M.J. / Amodeo, G.A. / Symington, L.S. / Walz, T. / Tong, L.
History
DepositionOct 26, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 4, 2017Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acetyl-CoA carboxylase
B: Acetyl-CoA carboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,5344
Polymers107,4642
Non-polymers712
Water0
1
A: Acetyl-CoA carboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7672
Polymers53,7321
Non-polymers351
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Acetyl-CoA carboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7672
Polymers53,7321
Non-polymers351
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.433, 93.191, 110.944
Angle α, β, γ (deg.)90.000, 99.570, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Acetyl-CoA carboxylase / / ACC / Fatty acid synthetase 3 / mRNA transport-defective protein 7


Mass: 53731.754 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: ACC1, ABP2, FAS3, MTR7, YNR016C, N3175 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Rosetta
References: UniProt: Q00955, acetyl-CoA carboxylase, biotin carboxylase
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.68 Å3/Da / Density % sol: 54.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100 mM HEPES (pH 7.5), 3% (v/v) MPD, 2.5 mM sodium citrate, and 5% (v/v) glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 25115 / % possible obs: 98.3 % / Redundancy: 2.7 % / Biso Wilson estimate: 82.61 Å2 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.037 / Rrim(I) all: 0.063 / Χ2: 1.104 / Net I/av σ(I): 19.233 / Net I/σ(I): 13.7 / Num. measured all: 68733
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2.9-32.70.5040.798199.2
3-3.122.80.3430.892199.4
3.12-3.272.80.2280.948199.5
3.27-3.442.80.1480.969199.1
3.44-3.652.80.0950.985199.2
3.65-3.942.80.0650.993199.2
3.94-4.332.80.0430.995199.2
4.33-4.962.70.0370.996199
4.96-6.242.70.0420.994198
6.24-502.70.0290.997191.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PDB_EXTRACT3.2data extraction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CS4

5cs4


Resolution: 2.9→46.569 Å / SU ML: 0.51 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 33.44
RfactorNum. reflection% reflection
Rfree0.2866 1272 5.07 %
Rwork0.2228 --
obs0.2262 25106 97.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 168.85 Å2 / Biso mean: 86.989 Å2 / Biso min: 28.12 Å2
Refinement stepCycle: final / Resolution: 2.9→46.569 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6626 0 2 0 6628
Biso mean--73.93 --
Num. residues----824
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016752
X-RAY DIFFRACTIONf_angle_d1.3139149
X-RAY DIFFRACTIONf_chiral_restr0.0521050
X-RAY DIFFRACTIONf_plane_restr0.0051174
X-RAY DIFFRACTIONf_dihedral_angle_d17.6342514
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.883-2.99840.37521330.33382504263792
2.9984-3.13480.36961590.30412662282199
3.1348-3.30010.37441380.265327062844100
3.3001-3.50680.29521480.25582655280399
3.5068-3.77740.31571230.24652688281199
3.7774-4.15730.3241290.21792702283199
4.1573-4.75840.23641350.18642710284599
4.7584-5.99310.26571540.212655280998
5.9931-46.57480.2661530.20242552270592

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