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- PDB-2uv5: Crystal Structure of a CBS domain pair from the regulatory gamma1... -

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Basic information

Entry
Database: PDB / ID: 2uv5
TitleCrystal Structure of a CBS domain pair from the regulatory gamma1 subunit of human AMPK in complex with AMP
Components5'-AMP-ACTIVATED PROTEIN KINASE SUBUNIT GAMMA-1
KeywordsTRANSFERASE / CBS DOMAIN / LIPID SYNTHESIS / FATTY ACID BIOSYNTHESIS / AMPK GAMMA1 SUBUNIT CBS 3 PLUS 4 AMP REGULATORY SUBUNIT.A
Function / homology
Function and homology information


Lipophagy / import into nucleus / cAMP-dependent protein kinase regulator activity / nucleotide-activated protein kinase complex / Energy dependent regulation of mTOR by LKB1-AMPK / protein kinase regulator activity / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / regulation of glycolytic process / cAMP-dependent protein kinase activity / Macroautophagy ...Lipophagy / import into nucleus / cAMP-dependent protein kinase regulator activity / nucleotide-activated protein kinase complex / Energy dependent regulation of mTOR by LKB1-AMPK / protein kinase regulator activity / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / regulation of glycolytic process / cAMP-dependent protein kinase activity / Macroautophagy / AMP binding / positive regulation of protein kinase activity / cellular response to nutrient levels / Activation of AMPK downstream of NMDARs / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / ADP binding / fatty acid biosynthetic process / spermatogenesis / Regulation of TP53 Activity through Phosphorylation / protein kinase activity / protein phosphorylation / positive regulation of gene expression / protein kinase binding / signal transduction / nucleoplasm / ATP binding / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
: / CBS-domain / CBS-domain / Domain in cystathionine beta-synthase and other proteins. / CBS domain superfamily / CBS domain / CBS domain / CBS domain profile. / Roll / Alpha Beta
Similarity search - Domain/homology
AMINOIMIDAZOLE 4-CARBOXAMIDE RIBONUCLEOTIDE / 5'-AMP-activated protein kinase subunit gamma-1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 1.69 Å
AuthorsDay, P. / Sharff, A. / Parra, L. / Cleasby, A. / Williams, M. / Horer, S. / Nar, H. / Redemann, N. / Tickle, I. / Yon, J.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2007
Title: Structure of a Cbs-Domain Pair from the Regulatory Gamma1 Subunit of Human Ampk in Complex with AMP and Zmp.
Authors: Day, P. / Sharff, A. / Parra, L. / Cleasby, A. / Williams, M. / Horer, S. / Nar, H. / Redemann, N. / Tickle, I. / Yon, J.
History
DepositionMar 9, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 8, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: 5'-AMP-ACTIVATED PROTEIN KINASE SUBUNIT GAMMA-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6172
Polymers17,2791
Non-polymers3381
Water4,648258
1
A: 5'-AMP-ACTIVATED PROTEIN KINASE SUBUNIT GAMMA-1
hetero molecules

A: 5'-AMP-ACTIVATED PROTEIN KINASE SUBUNIT GAMMA-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2344
Polymers34,5582
Non-polymers6762
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
MethodPQS
Unit cell
Length a, b, c (Å)66.056, 43.885, 55.798
Angle α, β, γ (deg.)90.00, 118.18, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2227-

HOH

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Components

#1: Protein 5'-AMP-ACTIVATED PROTEIN KINASE SUBUNIT GAMMA-1 / AMPK GAMMA-1 CHAIN / AMPKG / AMPK GAMMA1 CHAIN CBS DOMAINS 3 AND 4


Mass: 17278.875 Da / Num. of mol.: 1 / Fragment: CBS 3 AND 4 FRAGMENT, RESIDUES 182-325
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P54619
#2: Chemical ChemComp-AMZ / AMINOIMIDAZOLE 4-CARBOXAMIDE RIBONUCLEOTIDE / AICAR


Mass: 338.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H15N4O8P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 258 / 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: 1.79 Å3/Da / Density % sol: 30.91 %
Crystal growpH: 8 / Details: pH 8.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Aug 3, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.51→25 Å / Num. obs: 15986 / % possible obs: 97.9 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019Grefinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 1.69→25.34 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.944 / SU B: 2.844 / SU ML: 0.091 / Cross valid method: THROUGHOUT / ESU R: 0.114 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.227 789 5 %RANDOM
Rwork0.168 ---
obs0.171 14868 98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 15.55 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20 Å20.31 Å2
2---0.55 Å20 Å2
3---0.56 Å2
Refinement stepCycle: LAST / Resolution: 1.69→25.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1139 0 22 258 1419
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221181
X-RAY DIFFRACTIONr_bond_other_d0.0090.02753
X-RAY DIFFRACTIONr_angle_refined_deg1.3731.971608
X-RAY DIFFRACTIONr_angle_other_deg0.96931851
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4035141
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.52724.52853
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.63415.211213
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.848156
X-RAY DIFFRACTIONr_chiral_restr0.0870.2196
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021272
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02222
X-RAY DIFFRACTIONr_nbd_refined0.2450.2270
X-RAY DIFFRACTIONr_nbd_other0.1960.2843
X-RAY DIFFRACTIONr_nbtor_refined0.1720.2592
X-RAY DIFFRACTIONr_nbtor_other0.0850.2576
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1810.250
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1030.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1820.241
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1220.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.0995713
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.12761167
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.1166468
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.1527.5441
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.69→1.73 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.371 59
Rwork0.287 955

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