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- PDB-4y0g: beta2 carbohydrate binding module (CBM) of AMP-activated protein ... -

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Basic information

Entry
Database: PDB / ID: 4y0g
Titlebeta2 carbohydrate binding module (CBM) of AMP-activated protein kinase (AMPK)
Components5'-AMP-activated protein kinase subunit beta-2
KeywordsPROTEIN BINDING / carbohydrate binding module / AMPK
Function / homology
Function and homology information


AMPK inhibits chREBP transcriptional activation activity / Carnitine metabolism / Energy dependent regulation of mTOR by LKB1-AMPK / Regulation of TP53 Activity through Phosphorylation / Macroautophagy / TP53 Regulates Metabolic Genes / nucleotide-activated protein kinase complex / cAMP-dependent protein kinase complex / cellular response to nutrient levels / fatty acid biosynthetic process ...AMPK inhibits chREBP transcriptional activation activity / Carnitine metabolism / Energy dependent regulation of mTOR by LKB1-AMPK / Regulation of TP53 Activity through Phosphorylation / Macroautophagy / TP53 Regulates Metabolic Genes / nucleotide-activated protein kinase complex / cAMP-dependent protein kinase complex / cellular response to nutrient levels / fatty acid biosynthetic process / positive regulation of cold-induced thermogenesis / apical plasma membrane / protein kinase binding / enzyme binding / signal transduction / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Association with the SNF1 complex (ASC) domain / ASC domain superfamily / 5'-AMP-activated protein kinase beta subunit, interaction domain / 5'-AMP-activated protein kinase beta subunit, interation domain / AMP-activated protein kinase, glycogen-binding domain / Glycogen recognition site of AMP-activated protein kinase / Immunoglobulin E-set / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like ...Association with the SNF1 complex (ASC) domain / ASC domain superfamily / 5'-AMP-activated protein kinase beta subunit, interaction domain / 5'-AMP-activated protein kinase beta subunit, interation domain / AMP-activated protein kinase, glycogen-binding domain / Glycogen recognition site of AMP-activated protein kinase / Immunoglobulin E-set / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
5'-AMP-activated protein kinase subunit beta-2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.6 Å
AuthorsMobbs, J. / Gorman, M.A. / Parker, M.W. / Gooley, P.R. / Griffin, M.
CitationJournal: Biochem.J. / Year: 2015
Title: Determinants of oligosaccharide specificity of the carbohydrate-binding modules of AMP-activated protein kinase.
Authors: Mobbs, J.I. / Koay, A. / Di Paolo, A. / Bieri, M. / Petrie, E.J. / Gorman, M.A. / Doughty, L. / Parker, M.W. / Stapleton, D.I. / Griffin, M.D. / Gooley, P.R.
History
DepositionFeb 6, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 3, 2015Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / diffrn_source / entity_src_gen / pdbx_struct_assembly / pdbx_struct_oper_list / struct_keywords
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5'-AMP-activated protein kinase subunit beta-2
B: 5'-AMP-activated protein kinase subunit beta-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,87311
Polymers20,0442
Non-polymers8299
Water5,423301
1
A: 5'-AMP-activated protein kinase subunit beta-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,5757
Polymers10,0221
Non-polymers5536
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 5'-AMP-activated protein kinase subunit beta-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,2984
Polymers10,0221
Non-polymers2763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)112.973, 27.627, 78.882
Angle α, β, γ (deg.)90.00, 133.88, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-349-

HOH

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Components

#1: Protein 5'-AMP-activated protein kinase subunit beta-2 / AMPK subunit beta-2


Mass: 10022.198 Da / Num. of mol.: 2 / Fragment: UNP residues 74-155
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Prkab2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9QZH4
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 301 / Source method: isolated from a natural source / Formula: H2O

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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: 2.21 Å3/Da / Density % sol: 44.43 %
Crystal growTemperature: 281.15 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.17 M ammonium sulphate, 15% v/v glycerol and 25.5 % w/v PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.6→40.72 Å / Num. obs: 23221 / % possible obs: 97.6 % / Redundancy: 7.5 % / Biso Wilson estimate: 20.68 Å2 / Rsym value: 0.08 / Net I/σ(I): 17.8
Reflection shellResolution: 1.6→1.62 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.669 / Mean I/σ(I) obs: 2.8 / % possible all: 90.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
Cootmodel building
PHASERphasing
Aimlessdata scaling
XDSdata reduction
Blu-Icedata collection
RefinementResolution: 1.6→40.72 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.988 / SU ML: 0.054 / Cross valid method: THROUGHOUT / ESU R: 0.082 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18247 1184 5.1 %RANDOM
Rwork0.14985 ---
obs0.15154 22035 97.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.732 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å20 Å2-0.07 Å2
2--0.65 Å20 Å2
3----0.14 Å2
Refinement stepCycle: 1 / Resolution: 1.6→40.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1332 0 54 301 1687
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0191425
X-RAY DIFFRACTIONr_bond_other_d0.0010.021335
X-RAY DIFFRACTIONr_angle_refined_deg1.8891.9431929
X-RAY DIFFRACTIONr_angle_other_deg0.84633081
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.075168
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.04924.84866
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.94415220
X-RAY DIFFRACTIONr_dihedral_angle_4_deg27.633154
X-RAY DIFFRACTIONr_chiral_restr0.1070.2213
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211574
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02334
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2771.001666
X-RAY DIFFRACTIONr_mcbond_other1.2761.001665
X-RAY DIFFRACTIONr_mcangle_it2.0961.496830
X-RAY DIFFRACTIONr_mcangle_other2.0951.497831
X-RAY DIFFRACTIONr_scbond_it2.2741.393759
X-RAY DIFFRACTIONr_scbond_other2.2191.394759
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.471.9231098
X-RAY DIFFRACTIONr_long_range_B_refined7.76611.7081781
X-RAY DIFFRACTIONr_long_range_B_other7.3289.5611599
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.637 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 79 -
Rwork0.238 1545 -
obs--92.01 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.058-0.0276-0.3020.1913-0.15290.8439-0.084-0.0633-0.0423-0.0264-0.00460.028-0.00660.07720.08860.01610.0024-0.00830.02480.02050.028365.883-18.546766.9303
21.5729-0.4554-0.24840.143-0.05411.5609-0.0103-0.1328-0.03830.0090.04730.0112-0.0842-0.0576-0.0370.00980.00450.00730.0294-0.00410.020639.7111-11.627676.5826
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A75 - 156
2X-RAY DIFFRACTION2B73 - 156

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