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- PDB-2qrc: Crystal structure of the adenylate sensor from AMP-activated prot... -

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Basic information

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


positive regulation of flocculation / positive regulation of ascus development / positive regulation of cell cycle switching, mitotic to meiotic cell cycle / AMPK inhibits chREBP transcriptional activation activity / Carnitine metabolism / induction of conjugation with cellular fusion / Energy dependent regulation of mTOR by LKB1-AMPK / TP53 Regulates Metabolic Genes / Macroautophagy / mitotic spindle pole body ...positive regulation of flocculation / positive regulation of ascus development / positive regulation of cell cycle switching, mitotic to meiotic cell cycle / AMPK inhibits chREBP transcriptional activation activity / Carnitine metabolism / 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 / CAMKK-AMPK signaling cascade / nucleotide-activated protein kinase complex / protein kinase regulator activity / protein kinase activator activity / AMP binding / negative regulation of cytoplasmic translation / negative regulation of TORC1 signaling / ADP binding / carbohydrate metabolic process / non-specific serine/threonine protein kinase / phosphorylation / 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 / cytosol / cytoplasm
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 / AMPK, C-terminal adenylate sensor domain / Adenylate sensor of SNF1-like protein kinase ...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 / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / CBS domain superfamily / Domain in cystathionine beta-synthase and other proteins. / N-terminal domain of TfIIb / 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 MONOPHOSPHATE / 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: 2.7 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)130,03810
Polymers128,4106
Non-polymers1,6294
Water1,42379
1
A: SNF1-like protein kinase ssp2
B: SPCC1919.03c protein
G: Protein C1556.08c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,9795
Polymers64,2053
Non-polymers7742
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9900 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)65,0595
Polymers64,2053
Non-polymers8542
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9870 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.293, 78.087, 108.553
Angle α, β, γ (deg.)90.00, 124.13, 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, 83 molecules

#4: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#5: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 46.5 %
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 AMP, 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: 2.7→50 Å / Num. all: 31934 / Num. obs: 30918 / % possible obs: 96.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.4 % / Rmerge(I) obs: 0.107 / Net I/σ(I): 7.4
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.472 / Mean I/σ(I) obs: 1.5 / % possible all: 81.6

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Processing

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

2ooy


Resolution: 2.7→48.28 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.893 / SU B: 33.343 / SU ML: 0.335 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.435 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28945 1558 5 %RANDOM
Rwork0.20641 ---
obs0.2106 29358 96.31 %-
all-30918 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 52.865 Å2
Baniso -1Baniso -2Baniso -3
1--1.7 Å20 Å2-1.58 Å2
2---0.57 Å20 Å2
3---0.5 Å2
Refinement stepCycle: LAST / Resolution: 2.7→48.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8349 0 104 79 8532
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0228638
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6091.98811732
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.03951050
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.55223.867362
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.538151504
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1711551
X-RAY DIFFRACTIONr_chiral_restr0.1120.21357
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026359
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2390.23978
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3210.25939
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1840.2319
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2030.248
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1150.21
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5261.55403
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.92828579
X-RAY DIFFRACTIONr_scbond_it1.32233639
X-RAY DIFFRACTIONr_scangle_it2.1394.53152
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.774 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.488 83 -
Rwork0.396 1637 -
obs--73.57 %
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)
15.03150.44661.75133.75350.19225.5771-0.1050.43030.4661-0.09120.08860.0475-0.3192-0.00040.0164-0.2081-0.0115-0.0686-0.06030.1242-0.1954-11.54522.4329.422
26.07851.16010.77036.5177-1.65556.92950.0499-0.17341.28850.199-0.14380.8139-0.79870.59610.0939-0.14220.1931-0.0666-0.0017-0.07950.1426-12.82429.79315.661
35.91631.07670.69388.0127-0.28972.09510.1454-0.12710.02750.5377-0.03030.1432-0.2999-0.3401-0.1152-0.19540.0022-0.0202-0.08470.0092-0.3593-11.9378.83222.04
44.74150.3066-0.32636.34291.06724.0433-0.08530.5622-0.372-0.59630.3838-0.32370.24060.5711-0.2985-0.19920.04960.01770.1337-0.1557-0.204637.419-5.81212.422
52.5301-0.54970.82748.86013.671310.87380.19530.3652-0.50950.77970.05680.18741.49220.1874-0.2521-0.26910.0991-0.02940.1302-0.10780.197138.411-11.71118.981
610.10712.66821.08019.19260.59681.87170.14950.2876-0.43580.29520.0834-0.28850.2570.5142-0.2329-0.1855-0.04580.0179-0.0628-0.0131-0.37837.0318.11223.9
73.69650.35370.26351.7789-0.55640.6161-0.04670.3378-0.3993-0.1905-0.0064-0.0470.266-0.05930.0531-0.16-0.0468-0.0132-0.0688-0.0436-0.1705-5.068-8.7219.203
85.77051.35340.87310.97650.22043.01250.1455-0.04410.04140.1663-0.05610.06710.1168-0.3333-0.0894-0.0868-0.0078-0.0159-0.2012-0.003-0.114-0.695-19.25335.44
93.4368-0.21560.97931.57420.60390.6279-0.06430.41880.2833-0.26610.05480.0607-0.3380.27770.0095-0.0376-0.1259-0.0444-0.01930.062-0.155530.6125.94320.952
105.09480.7933-0.34191.1856-0.1562.3184-0.13630.05270.12610.01850.1385-0.1261-0.21020.2366-0.00220.0185-0.0455-0.1313-0.18930.0031-0.09262536.73136.745
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA451 - 57612 - 137
2X-RAY DIFFRACTION2BB207 - 2476 - 46
3X-RAY DIFFRACTION3BB248 - 29747 - 96
4X-RAY DIFFRACTION4CD450 - 57611 - 137
5X-RAY DIFFRACTION5DE207 - 2476 - 46
6X-RAY DIFFRACTION6DE248 - 29747 - 96
7X-RAY DIFFRACTION7GC2 - 1722 - 172
8X-RAY DIFFRACTION8GC173 - 317173 - 317
9X-RAY DIFFRACTION9EF3 - 1723 - 172
10X-RAY DIFFRACTION10EF173 - 317173 - 317

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