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- PDB-2qrd: Crystal Structure of the Adenylate Sensor from AMP-activated Prot... -

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Basic information

Entry
Database: PDB / ID: 2qrd
TitleCrystal Structure of the Adenylate Sensor from AMP-activated Protein Kinase in complex with ADP and ATP
Components
  • Protein C1556.08c
  • SNF1-like protein kinase ssp2
  • SPCC1919.03c protein
KeywordsTRANSFERASE / AMPK / ADP / ATP-binding / Kinase / Nucleotide-binding / Serine/threonine-protein kinase / CBS domain
Function / homology
Function and homology information


positive regulation of flocculation / positive regulation of cell cycle switching, mitotic to meiotic cell cycle / AMPK inhibits chREBP transcriptional activation activity / Carnitine shuttle / induction of conjugation with cellular fusion / Energy dependent regulation of mTOR by LKB1-AMPK / TP53 Regulates Metabolic Genes / Macroautophagy / mitotic spindle pole body / SREBP signaling pathway ...positive regulation of flocculation / positive regulation of cell cycle switching, mitotic to meiotic cell cycle / AMPK inhibits chREBP transcriptional activation activity / Carnitine shuttle / induction of conjugation with cellular fusion / Energy dependent regulation of mTOR by LKB1-AMPK / TP53 Regulates Metabolic Genes / Macroautophagy / mitotic spindle pole body / SREBP signaling pathway / regulation of carbon utilization / CAMKK-AMPK signaling cascade / nucleotide-activated protein kinase complex / protein kinase regulator activity / regulation of glycolytic process / AMP binding / protein kinase activator activity / cellular response to glucose starvation / negative regulation of cytoplasmic translation / negative regulation of TORC1 signaling / positive regulation of gluconeogenesis / ADP binding / non-specific serine/threonine protein kinase / protein serine kinase activity / protein serine/threonine kinase activity / regulation of transcription by RNA polymerase II / protein kinase binding / signal transduction / positive regulation of transcription by RNA polymerase II / ATP binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
N-terminal domain of TfIIb - #290 / Carbon catabolite-derepressing protein kinase, ubiquitin-associated domain / Ubiquitin associated domain (UBA) / Kinase associated domain 1, KA1 / : / 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 ...N-terminal domain of TfIIb - #290 / Carbon catabolite-derepressing protein kinase, ubiquitin-associated domain / Ubiquitin associated domain (UBA) / Kinase associated domain 1, KA1 / : / 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 / AMPK, C-terminal adenylate sensor domain / Adenylate sensor of SNF1-like protein kinase / AMP-activated protein kinase, glycogen-binding domain / Glycogen recognition site of AMP-activated protein kinase / CBS-domain / CBS-domain / KA1 domain/Ssp2, C-terminal / TATA-Binding Protein / N-terminal domain of TfIIb / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / Domain in cystathionine beta-synthase and other proteins. / CBS domain superfamily / CBS domain / CBS domain / CBS domain profile. / Single Sheet / Immunoglobulin E-set / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Roll / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / SNF1-like protein kinase ssp2 / 5'-AMP-activated protein kinase subunit beta / 5'-AMP-activated protein kinase subunit gamma
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.41 Å
AuthorsJin, X. / Townley, R. / Shapiro, L.
CitationJournal: Structure / Year: 2007
Title: Structural Insight into AMPK Regulation: ADP Comes into Play.
Authors: Jin, X. / Townley, R. / Shapiro, L.
History
DepositionJul 28, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SNF1-like protein kinase ssp2
B: SPCC1919.03c protein
G: Protein C1556.08c
C: SNF1-like protein kinase ssp2
D: SPCC1919.03c protein
E: Protein C1556.08c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,29312
Polymers128,4106
Non-polymers2,8836
Water7,422412
1
A: SNF1-like protein kinase ssp2
B: SPCC1919.03c protein
G: Protein C1556.08c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,6466
Polymers64,2053
Non-polymers1,4423
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10700 Å2
MethodPISA
2
C: SNF1-like protein kinase ssp2
D: SPCC1919.03c protein
E: Protein C1556.08c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,6466
Polymers64,2053
Non-polymers1,4423
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10970 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.263, 78.365, 109.014
Angle α, β, γ (deg.)90.00, 124.18, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe biological unit is a heterotrimer (There are two such trimers: A+B+G and C+D+E in the asymmetric unit). The dimer of these heterotrimers is also physiologically relevant.

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Components

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Protein , 3 types, 6 molecules ACBDGE

#1: Protein SNF1-like protein kinase ssp2


Mass: 15903.413 Da / Num. of mol.: 2 / Fragment: C-terminal residues:440-576
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Gene: ssp2 / Plasmid: PSMT3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: O74536, non-specific serine/threonine protein kinase
#2: Protein SPCC1919.03c protein


Mass: 10865.345 Da / Num. of mol.: 2 / Fragment: C-terminal residues:203-298
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Plasmid: PET-DUET-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P78789
#3: Protein Protein C1556.08c


Mass: 37436.070 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Plasmid: PET-DUET-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q10343

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Non-polymers , 3 types, 418 molecules

#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 412 / 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: 2.32 Å3/Da / Density % sol: 46.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 6-10% PEG 3350, 0.1M Sodium Citrate, pH 5.5, 5mM ADP, 5mM ATP, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97926 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 15, 2007
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 47233 / Num. obs: 45186 / % possible obs: 99.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 19.7
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.517 / Mean I/σ(I) obs: 3.5 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 2ooy

2ooy


Resolution: 2.41→35.94 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.924 / SU B: 17.487 / SU ML: 0.215 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.52 / ESU R Free: 0.294 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26155 2279 5 %RANDOM
Rwork0.18793 ---
all0.199 ---
obs0.19171 42900 98.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 52.553 Å2
Baniso -1Baniso -2Baniso -3
1--2.15 Å20 Å2-1.86 Å2
2--0.56 Å20 Å2
3----0.5 Å2
Refinement stepCycle: LAST / Resolution: 2.41→35.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8350 0 178 412 8940
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0228716
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7481.99811860
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9451053
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.65923.934361
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.365151494
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8931549
X-RAY DIFFRACTIONr_chiral_restr0.1170.21365
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026387
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.230.23855
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.25813
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3280.2429
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2370.250
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3540.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7511.55471
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.23628591
X-RAY DIFFRACTIONr_scbond_it1.9333741
X-RAY DIFFRACTIONr_scangle_it2.9624.53267
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.41→2.47 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 139 -
Rwork0.253 2877 -
obs--89.58 %
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)
13.59440.34070.85084.42080.43623.8482-0.02260.48710.3859-0.1849-0.06260.0755-0.32870.09960.0852-0.2424-0.0119-0.0453-0.04350.1238-0.1735-11.31222.4939.303
23.706-0.86360.82796.1596-1.51432.83610.02170.11370.62170.42680.01830.0793-0.5269-0.0677-0.04-0.09290.0438-0.0434-0.0044-0.0266-0.0787-12.74828.99115.85
34.45732.91330.18748.5607-1.02572.2817-0.12820.1498-0.12090.35480.06140.0242-0.4009-0.23080.0668-0.266-0.0324-0.0284-0.14310.0205-0.2785-11.9269.07422.02
43.4205-0.54660.86816.07861.26574.07690.02580.6208-0.1999-0.62630.2681-0.34190.17720.597-0.2939-0.2061-0.04330.04840.0511-0.1506-0.158537.372-5.64412.42
53.3935-1.60480.20138.47482.17046.41540.19130.5385-0.62320.1485-0.01310.07240.94210.1943-0.1782-0.21340.07350.00970.0736-0.11340.042238.032-11.75918.762
64.68442.00711.3939.34721.24731.4886-0.14840.1207-0.15760.22820.13550.02230.08980.3240.0129-0.2638-0.1060.0225-0.10860.0206-0.272136.7468.35924.332
73.0144-0.19770.44381.0911-0.41680.7346-0.03760.3623-0.1735-0.13550.0089-0.10470.1494-0.08790.0288-0.2202-0.0731-0.0051-0.1343-0.0367-0.1585-5.43-8.73919.548
83.75431.00970.29881.5576-0.43222.02430.08530.153-0.02320.10350.00080.00880.1009-0.1688-0.0861-0.1489-0.010.0044-0.2455-0.0023-0.1066-0.424-19.78133.647
92.7121-0.61690.11061.62320.37040.8087-0.0830.40330.1885-0.27230.0680.0466-0.26060.18760.0149-0.1284-0.1616-0.0452-0.09710.1111-0.158830.89626.22521.406
103.43460.7244-0.43131.4648-0.06141.9234-0.07820.15010.1007-0.02610.1057-0.0229-0.17890.1979-0.0275-0.0719-0.0613-0.0923-0.20080.0332-0.05124.56137.35834.905
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA450 - 57611 - 137
2X-RAY DIFFRACTION2BB206 - 2475 - 46
3X-RAY DIFFRACTION3BB248 - 29747 - 96
4X-RAY DIFFRACTION4CD450 - 57611 - 137
5X-RAY DIFFRACTION5DE206 - 2475 - 46
6X-RAY DIFFRACTION6DE248 - 29747 - 96
7X-RAY DIFFRACTION7GC2 - 1752 - 175
8X-RAY DIFFRACTION8GC176 - 334176 - 334
9X-RAY DIFFRACTION9EF2 - 1752 - 175
10X-RAY DIFFRACTION10EF176 - 334176 - 334

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