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- PDB-1z0m: the glycogen-binding domain of the AMP-activated protein kinase b... -

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Basic information

Entry
Database: PDB / ID: 1z0m
Titlethe glycogen-binding domain of the AMP-activated protein kinase beta1 subunit
Components5'-AMP-activated protein kinase, beta-1 subunit
KeywordsSUGAR BINDING PROTEIN / beta sandwich
Function / homology
Function and homology information


Energy dependent regulation of mTOR by LKB1-AMPK / Regulation of TP53 Activity through Phosphorylation / Macroautophagy / TP53 Regulates Metabolic Genes / nail development / nucleotide-activated protein kinase complex / cellular response to nutrient levels / fatty acid biosynthetic process / positive regulation of cold-induced thermogenesis / protein kinase binding ...Energy dependent regulation of mTOR by LKB1-AMPK / Regulation of TP53 Activity through Phosphorylation / Macroautophagy / TP53 Regulates Metabolic Genes / nail development / nucleotide-activated protein kinase complex / cellular response to nutrient levels / fatty acid biosynthetic process / positive regulation of cold-induced thermogenesis / protein kinase binding / signal transduction / protein-containing complex / nucleus / cytoplasm / cytosol
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 / Immunoglobulin-like fold / Immunoglobulins ...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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
beta-cyclodextrin / 5'-AMP-activated protein kinase subunit beta-1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIR, NCS averaging / MIR / Resolution: 1.91 Å
AuthorsPolekhina, G. / Gupta, A. / van Denderen, B.J. / Feil, S.C. / Kemp, B.E. / Stapleton, D. / Parker, M.W.
Citation
Journal: Structure / Year: 2005
Title: Structural Basis for Glycogen Recognition by AMP-Activated Protein Kinase.
Authors: Polekhina, G. / Gupta, A. / van Denderen, B.J. / Feil, S.C. / Kemp, B.E. / Stapleton, D. / Parker, M.W.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2005
Title: Crystallization of the glycogen-binding domain of the AMP-activated protein kinase beta subunit and preliminary X-ray analysis
Authors: Polekhina, G. / Feil, S.C. / Gupta, A. / O'Donnell, P. / Stapleton, D. / Parker, M.W.
History
DepositionMar 2, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 25, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_validate_symm_contact / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _pdbx_validate_symm_contact.auth_asym_id_1 / _pdbx_validate_symm_contact.auth_atom_id_1 / _pdbx_validate_symm_contact.auth_comp_id_1 / _pdbx_validate_symm_contact.auth_seq_id_1
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Mar 13, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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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, beta-1 subunit
B: 5'-AMP-activated protein kinase, beta-1 subunit
C: 5'-AMP-activated protein kinase, beta-1 subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1836
Polymers32,7243
Non-polymers3,4593
Water3,603200
1
A: 5'-AMP-activated protein kinase, beta-1 subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,0612
Polymers10,9081
Non-polymers1,1531
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 5'-AMP-activated protein kinase, beta-1 subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,0612
Polymers10,9081
Non-polymers1,1531
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: 5'-AMP-activated protein kinase, beta-1 subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,0612
Polymers10,9081
Non-polymers1,1531
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.735, 44.891, 50.335
Angle α, β, γ (deg.)70.72, 68.77, 65.79
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41A
51B
61C
71A
81B
91C
101A
111B
121C
12A
22B
32C
42A
52B
62C
72A
82B
92C

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111PROPROGLYGLY2AA79 - 9512 - 28
211PROPROGLYGLY2BB79 - 9512 - 28
311PROPROGLYGLY2CC79 - 9512 - 28
421LYSLYSPROPRO2AA102 - 10435 - 37
521LYSLYSPROPRO2BB102 - 10435 - 37
621LYSLYSPROPRO2CC102 - 10435 - 37
731PHEPHETHRTHR2AA112 - 14345 - 76
831PHEPHETHRTHR2BB112 - 14345 - 76
931PHEPHETHRTHR2CC112 - 14345 - 76
1041VALVALILEILE2AA149 - 15282 - 85
1141VALVALILEILE2BB149 - 15282 - 85
1241VALVALILEILE2CC149 - 15282 - 85
112SERSERSERSER5AA96 - 10129 - 34
212SERSERSERSER5BB96 - 10129 - 34
312SERSERSERSER5CC96 - 10129 - 34
422LEULEUASNASN5AA105 - 11138 - 44
522LEULEUASNASN5BB105 - 11138 - 44
622LEULEUASNASN5CC105 - 11138 - 44
732SERSERTHRTHR5AA144 - 14877 - 81
832SERSERTHRTHR5BB144 - 14877 - 81
932SERSERTHRTHR5CC144 - 14877 - 81

NCS ensembles :
ID
1
2

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Components

#1: Protein 5'-AMP-activated protein kinase, beta-1 subunit / AMPK beta-1 chain / AMPKb / 40 kDa subunit


Mass: 10908.112 Da / Num. of mol.: 3 / Fragment: 68-163 of beta1 subunit
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: pProEX HT / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P80386
#2: Polysaccharide Cycloheptakis-(1-4)-(alpha-D-glucopyranose) / beta-cyclodextrin


Type: oligosaccharide, Oligosaccharide / Class: Drug delivery / Mass: 1153.001 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: cyclic oligosaccharide / References: beta-cyclodextrin
DescriptorTypeProgram
WURCS=2.0/1,7,7/[a2122h-1a_1-5]/1-1-1-1-1-1-1/a1-g4_a4-b1_b4-c1_c4-d1_d4-e1_e4-f1_f4-g1WURCSPDB2Glycan 1.1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / 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: 2.3 Å3/Da / Density % sol: 50.93 %
Crystal growTemperature: 299 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG, monomethyl ether 5000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 299K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 4, 2001
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. all: 23738 / Num. obs: 23738 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.039 / Χ2: 1.585
Reflection shellResolution: 1.9→1.97 Å / % possible obs: 81.6 % / Rmerge(I) obs: 0.181 / Num. measured obs: 2004 / Χ2: 1.872 / % possible all: 81.6

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Phasing

PhasingMethod: MIR

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
CNSrefinement
REFMAC5.2.0005refinement
PDB_EXTRACT1.6data extraction
DMphasing
RefinementMethod to determine structure: SIR, NCS averaging / Resolution: 1.91→30 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.937 / SU B: 4.108 / SU ML: 0.119 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.161 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24268 1213 5.1 %RANDOM
Rwork0.19059 ---
all0.195 23738 --
obs0.227 23738 95.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.75 Å2
Baniso -1Baniso -2Baniso -3
1--1.14 Å20.94 Å2-1.29 Å2
2---0.29 Å2-2.13 Å2
3---3.01 Å2
Refinement stepCycle: LAST / Resolution: 1.91→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2001 0 231 200 2432
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222313
X-RAY DIFFRACTIONr_angle_refined_deg1.7392.0483186
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8185245
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.90224.615104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.49915322
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.741159
X-RAY DIFFRACTIONr_chiral_restr0.2010.2403
X-RAY DIFFRACTIONr_gen_planes_refined0.0360.021740
X-RAY DIFFRACTIONr_nbd_refined0.2110.2901
X-RAY DIFFRACTIONr_nbtor_refined0.320.21580
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2156
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2340.292
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2410.251
X-RAY DIFFRACTIONr_mcbond_it2.88821255
X-RAY DIFFRACTIONr_mcangle_it4.13232008
X-RAY DIFFRACTIONr_scbond_it3.08921180
X-RAY DIFFRACTIONr_scangle_it4.1953.51178
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A212tight positional0.260.25
12B212tight positional0.220.25
13C212tight positional0.310.25
11A213medium positional0.670.6
12B213medium positional0.590.6
13C213medium positional0.680.6
11A212tight thermal3.143
12B212tight thermal3.773
13C212tight thermal5.253
11A213medium thermal4.75
12B213medium thermal4.125
13C213medium thermal5.765
21A72medium positional0.360.8
22B72medium positional0.570.8
23C72medium positional0.410.8
21A72loose positional0.95
22B72loose positional1.15
23C72loose positional0.975
21A72medium thermal5.612
22B72medium thermal2.822
23C72medium thermal5.532
21A72loose thermal6.1610
22B72loose thermal3.9410
23C72loose thermal6.9410
LS refinement shellResolution: 1.905→1.955 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 73 -
Rwork0.237 1280 -
obs--74.26 %

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