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- PDB-2lu3: Solution NMR structure of the apo-form of the beta2 carbohydrate ... -

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Basic information

Entry
Database: PDB / ID: 2lu3
TitleSolution NMR structure of the apo-form of the beta2 carbohydrate module of AMP-activated protein kinase
Components5'-AMP-activated protein kinase subunit beta-2
KeywordsSUGAR BINDING PROTEIN / carbohydrate binding module / glycogen binding
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)
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model1
AuthorsGooley, P. / Koay, A. / Stapleton, D.
CitationJournal: To be Published
Title: Structure and carbohydrate binding of the beta2-subunit of AMP-activated protein kinase
Authors: Koay, A. / Petrie, E. / Gorman, M. / di Paolo, A. / Mobbs, J. / Parker, M. / Stapleton, D. / Gooley, P.
History
DepositionJun 8, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 12, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)11,8261
Polymers11,8261
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1lowest energy

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Components

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


Mass: 11826.209 Da / Num. of mol.: 1 / Fragment: UNP residues 67-163
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

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1123D CBCA(CO)NH
1223D HN(CA)CB
1323D HNCO
1423D HBHA(CO)NH
1523D H(CCO)NH
1623D C(CO)NH
1743D (H)CCH-TOCSY
1832D 1H-1H TOCSY
1932D 1H-1H NOESY
11013D 1H-15N NOESY
11143D 1H-13C NOESY aliphatic
11213D HNHA
11313D HNHB
11443D HACAHB-COSY
11512D 1H-15N HSQC
11652D 1H-13C HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.7 mM [U-98% 15N] protein, 50 mM sodium phosphate, 0.02 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
20.7 mM [U-98% 13C; U-98% 15N] protein, 50 mM sodium phosphate, 0.02 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
30.7 mM protein, 50 mM sodium phosphate, 0.02 % sodium azide, 100% D2O100% D2O
40.7 mM [U-98% 13C; U-98% 15N] protein, 50 mM sodium phosphate, 0.02 % sodium azide, 100% D2O100% D2O
50.7 mM [U-10% 13C] protein, 50 mM sodium phosphate, 0.02 % sodium azide, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.7 mMentity-1[U-98% 15N]1
50 mMsodium phosphate-21
.02 %sodium azide-31
0.7 mMentity-4[U-98% 13C; U-98% 15N]2
50 mMsodium phosphate-52
.02 %sodium azide-62
0.7 mMentity-73
50 mMsodium phosphate-83
.02 %sodium azide-93
0.7 mMentity-10[U-98% 13C; U-98% 15N]4
50 mMsodium phosphate-114
0.02 %sodium azide-124
0.7 mMentity-13[U-10% 13C]5
50 mMsodium phosphate-145
0.02 %sodium azide-155
Sample conditionsIonic strength: 0.05 / pH: 6.9 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE6002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TALOSCornilescu, Delaglio and Baxdata analysis
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 2110 / NOE intraresidue total count: 447 / NOE long range total count: 877 / NOE medium range total count: 267 / NOE sequential total count: 519 / Protein phi angle constraints total count: 65 / Protein psi angle constraints total count: 65
NMR representativeSelection criteria: lowest energy
NMR ensembleAverage torsion angle constraint violation: 1.51 ° / Conformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 / Maximum torsion angle constraint violation: 2.1 ° / Maximum upper distance constraint violation: 0.3 Å
NMR ensemble rmsDistance rms dev: 0.0046 Å / Distance rms dev error: 0.0008 Å

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