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- PDB-2jld: Extremely Tight Binding of Ruthenium Complex to Glycogen Synthase... -

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Basic information

Entry
Database: PDB / ID: 2jld
TitleExtremely Tight Binding of Ruthenium Complex to Glycogen Synthase Kinase 3
Components
  • GLYCOGEN SYNTHASE KINASE-3 BETA
  • PEPTIDE (ALA-GLY-GLY-ALA-ALA-ALA-ALA-ALA)
KeywordsTRANSFERASE / WNT SIGNALING PATHWAY / SERINE/THREONINE-PROTEIN KINASE / RUTHENIUM GLYCOGEN SYNTHASE KINASE PICOMOLAR / NUCLEOTIDE-BINDING / ALTERNATIVE SPLICING / KINASE / ATP-BINDING / PHOSPHOPROTEIN
Function / homology
Function and homology information


negative regulation of glycogen (starch) synthase activity / neuron projection organization / regulation of microtubule anchoring at centrosome / negative regulation of mesenchymal stem cell differentiation / beta-catenin destruction complex disassembly / negative regulation of type B pancreatic cell development / superior temporal gyrus development / positive regulation of protein localization to cilium / negative regulation of glycogen biosynthetic process / negative regulation of dopaminergic neuron differentiation ...negative regulation of glycogen (starch) synthase activity / neuron projection organization / regulation of microtubule anchoring at centrosome / negative regulation of mesenchymal stem cell differentiation / beta-catenin destruction complex disassembly / negative regulation of type B pancreatic cell development / superior temporal gyrus development / positive regulation of protein localization to cilium / negative regulation of glycogen biosynthetic process / negative regulation of dopaminergic neuron differentiation / maintenance of cell polarity / positive regulation of protein localization to centrosome / : / positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / positive regulation of cilium assembly / negative regulation of protein acetylation / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the destruction complex / beta-catenin destruction complex / tau-protein kinase / regulation of microtubule-based process / CRMPs in Sema3A signaling / regulation of protein export from nucleus / heart valve development / Beta-catenin phosphorylation cascade / Signaling by GSK3beta mutants / CTNNB1 S33 mutants aren't phosphorylated / CTNNB1 S37 mutants aren't phosphorylated / CTNNB1 S45 mutants aren't phosphorylated / CTNNB1 T41 mutants aren't phosphorylated / Maturation of nucleoprotein / cellular response to interleukin-3 / Wnt signalosome / regulation of axon extension / regulation of long-term synaptic potentiation / negative regulation of protein localization to nucleus / Disassembly of the destruction complex and recruitment of AXIN to the membrane / Maturation of nucleoprotein / AKT phosphorylates targets in the cytosol / positive regulation of cell-matrix adhesion / negative regulation of calcineurin-NFAT signaling cascade / dopamine receptor signaling pathway / regulation of dendrite morphogenesis / negative regulation of phosphoprotein phosphatase activity / regulation of axonogenesis / establishment of cell polarity / tau-protein kinase activity / glycogen metabolic process / ER overload response / regulation of neuron projection development / Constitutive Signaling by AKT1 E17K in Cancer / dynactin binding / protein kinase A catalytic subunit binding / NF-kappaB binding / canonical Wnt signaling pathway / Regulation of HSF1-mediated heat shock response / epithelial to mesenchymal transition / negative regulation of osteoblast differentiation / negative regulation of protein-containing complex assembly / positive regulation of autophagy / regulation of microtubule cytoskeleton organization / regulation of cellular response to heat / cellular response to retinoic acid / extrinsic apoptotic signaling pathway / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / extrinsic apoptotic signaling pathway in absence of ligand / excitatory postsynaptic potential / presynaptic modulation of chemical synaptic transmission / positive regulation of protein export from nucleus / positive regulation of protein ubiquitination / Ubiquitin-dependent degradation of Cyclin D / hippocampus development / positive regulation of protein-containing complex assembly / positive regulation of cell differentiation / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / peptidyl-threonine phosphorylation / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / negative regulation of canonical Wnt signaling pathway / tau protein binding / Degradation of beta-catenin by the destruction complex / B-WICH complex positively regulates rRNA expression / regulation of circadian rhythm / beta-catenin binding / positive regulation of GTPase activity / circadian rhythm / positive regulation of protein catabolic process / cellular response to amyloid-beta / neuron projection development / Regulation of RUNX2 expression and activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / p53 binding / presynapse / insulin receptor signaling pathway / positive regulation of protein binding / kinase activity / postsynapse / proteasome-mediated ubiquitin-dependent protein catabolic process / peptidyl-serine phosphorylation
Similarity search - Function
Glycogen synthase kinase 3, catalytic domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site ...Glycogen synthase kinase 3, catalytic domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
RUTHENIUM PYRIDOCARBAZOLE / Glycogen synthase kinase-3 beta
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsAtilla-Gokcumen, G.E. / Pagano, N. / Streu, C. / Maksimoska, J. / Filippakopoulos, P. / Knapp, S. / Meggers, E.
CitationJournal: Chembiochem / Year: 2008
Title: Extremely Tight Binding of a Ruthenium Complex to Glycogen Synthase Kinase 3.
Authors: Atilla-Gokcumen, G.E. / Pagano, N. / Streu, C. / Maksimoska, J. / Filippakopoulos, P. / Knapp, S. / Meggers, E.
History
DepositionSep 8, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 9, 2008Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 9, 2019Group: Data collection / Other / Source and taxonomy / Category: pdbx_database_status / pdbx_entity_src_syn / Item: _pdbx_database_status.status_code_sf
Revision 1.4Dec 13, 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_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GLYCOGEN SYNTHASE KINASE-3 BETA
B: GLYCOGEN SYNTHASE KINASE-3 BETA
E: PEPTIDE (ALA-GLY-GLY-ALA-ALA-ALA-ALA-ALA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,4205
Polymers94,1613
Non-polymers1,2592
Water3,279182
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3480 Å2
ΔGint-20.8 kcal/mol
Surface area37230 Å2
MethodPISA
2
B: GLYCOGEN SYNTHASE KINASE-3 BETA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4312
Polymers46,8011
Non-polymers6301
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: GLYCOGEN SYNTHASE KINASE-3 BETA
E: PEPTIDE (ALA-GLY-GLY-ALA-ALA-ALA-ALA-ALA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9893
Polymers47,3602
Non-polymers6301
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.041, 86.114, 177.398
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: 4 / Auth seq-ID: 35 - 384 / Label seq-ID: 35 - 384

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein GLYCOGEN SYNTHASE KINASE-3 BETA / / GSK-3 BETA


Mass: 46801.215 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA2(DE3) / References: UniProt: P49841, tau-protein kinase
#2: Protein/peptide PEPTIDE (ALA-GLY-GLY-ALA-ALA-ALA-ALA-ALA)


Mass: 558.586 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-AG1 / RUTHENIUM PYRIDOCARBAZOLE


Mass: 629.515 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H17FN4O7Ru
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 182 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsDISORDERED POLYPEPTIDE REGION THAT WAS NOT ASSIGNABLE TO SEQUENCE OF GSK-3BETA

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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: 4 Å3/Da / Density % sol: 68 % / Description: NONE
Crystal growpH: 7.2
Details: 100MM TRIS PH 7.4, 500MM NACL, 12.5% PEG 8000, 1MM MGCL2, 1MM DTT

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.978
DetectorType: ADSC CCD / Detector: CCD / Date: May 2, 2007 / Details: MIRRORS
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.35→88.74 Å / Num. obs: 52103 / % possible obs: 97 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 14.4
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 2.1 / % possible all: 97.4

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Processing

Software
NameVersionClassification
REFMAC5.4.0066refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1J1B

1j1b


Resolution: 2.35→88.74 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.938 / SU B: 9.346 / SU ML: 0.112 / Cross valid method: THROUGHOUT / ESU R: 0.214 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.227 2638 5.1 %RANDOM
Rwork0.19 ---
obs0.192 49335 96.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.79 Å2
Baniso -1Baniso -2Baniso -3
1-1.21 Å20 Å20 Å2
2--1.05 Å20 Å2
3----2.26 Å2
Refinement stepCycle: LAST / Resolution: 2.35→88.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5416 0 80 182 5678
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0225686
X-RAY DIFFRACTIONr_bond_other_d0.0010.023710
X-RAY DIFFRACTIONr_angle_refined_deg1.5112.0017854
X-RAY DIFFRACTIONr_angle_other_deg0.93339069
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7595706
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.09423.465228
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.61515848
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2411532
X-RAY DIFFRACTIONr_chiral_restr0.0860.2891
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216308
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021122
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.58433567
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.19355777
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it7.85482119
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it9.153112037
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
Refine LS restraints NCS

Ens-ID: 1 / Number: 4451 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional0.460.5
2Bmedium positional0.460.5
1Amedium thermal1.092
2Bmedium thermal1.092
LS refinement shellResolution: 2.35→2.41 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.353 182
Rwork0.315 3394
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)
10.75350.60080.28721.07010.28570.36960.01360.0646-0.0742-0.0978-0.00330.18510.0739-0.1332-0.01030.2040.00920.00740.21260.00610.188141.649370.958536.2564
21.07280.2111-0.34521.1175-0.0531.68170.01520.08430.0506-0.0893-0.0067-0.0553-0.04180.0157-0.00860.1187-0.0061-0.02320.1460.00040.138559.716983.427735.1215
31.3923-0.1516-0.43321.4134-0.01371.28980.02120.08790.0872-0.0658-0.0065-0.0998-0.10950.0475-0.01480.1693-0.0108-0.0510.1895-0.01830.190865.490886.626146.6297
41.11410.39110.06261.52060.44080.7708-0.0129-0.1610.15840.14740.0145-0.0994-0.15090.0718-0.00170.1790.00380.00420.18680.00750.172171.6182108.77647.2282
51.06780.1570.16361.1645-0.49071.4804-0.0223-0.1203-0.0390.10680.02880.0681-0.0059-0.0657-0.00650.153-0.00850.00080.1291-0.02410.132658.424488.85866.8146
61.4133-0.18850.01911.3745-0.32931.1028-0.0101-0.1251-0.14910.10970.03530.06070.0902-0.076-0.02530.1781-0.0121-0.00740.1727-0.05220.169155.718582.663-3.9544
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A35 - 146
2X-RAY DIFFRACTION2A147 - 271
3X-RAY DIFFRACTION3A272 - 385
4X-RAY DIFFRACTION4B35 - 136
5X-RAY DIFFRACTION5B137 - 271
6X-RAY DIFFRACTION6B272 - 384

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