[English] 日本語
Yorodumi
- PDB-2jld: Extremely Tight Binding of Ruthenium Complex to Glycogen Synthase... -

+
Open data


ID or keywords:

Loading...

-
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


neuron projection organization / regulation of microtubule anchoring at centrosome / negative regulation of type B pancreatic cell development / negative regulation of glycogen (starch) synthase activity / negative regulation of mesenchymal stem cell differentiation / beta-catenin destruction complex disassembly / superior temporal gyrus development / positive regulation of protein localization to cilium / negative regulation of glycogen biosynthetic process / negative regulation of TORC2 signaling ...neuron projection organization / regulation of microtubule anchoring at centrosome / negative regulation of type B pancreatic cell development / negative regulation of glycogen (starch) synthase activity / negative regulation of mesenchymal stem cell differentiation / beta-catenin destruction complex disassembly / superior temporal gyrus development / positive regulation of protein localization to cilium / negative regulation of glycogen biosynthetic process / negative regulation of TORC2 signaling / 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 / negative regulation of protein acetylation / positive regulation of cilium assembly / beta-catenin destruction complex / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the destruction complex / CRMPs in Sema3A signaling / heart valve development / tau-protein kinase / regulation of microtubule-based process / regulation of protein export from nucleus / 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 / negative regulation of TOR signaling / negative regulation of protein localization to nucleus / regulation of long-term synaptic potentiation / Disassembly of the destruction complex and recruitment of AXIN to the membrane / AKT phosphorylates targets in the cytosol / negative regulation of calcineurin-NFAT signaling cascade / Maturation of nucleoprotein / regulation of axon extension / negative regulation of epithelial to mesenchymal transition / G protein-coupled dopamine receptor signaling pathway / positive regulation of cell-matrix adhesion / tau-protein kinase activity / regulation of axonogenesis / regulation of dendrite morphogenesis / ER overload response / glycogen metabolic process / establishment of cell polarity / regulation of neuron projection development / Constitutive Signaling by AKT1 E17K in Cancer / protein kinase A catalytic subunit binding / dynactin binding / negative regulation of osteoblast differentiation / Regulation of HSF1-mediated heat shock response / epithelial to mesenchymal transition / NF-kappaB binding / canonical Wnt signaling pathway / negative regulation of protein-containing complex assembly / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / regulation of cellular response to heat / extrinsic apoptotic signaling pathway in absence of ligand / cellular response to retinoic acid / extrinsic apoptotic signaling pathway / positive regulation of autophagy / Transcriptional and post-translational regulation of MITF-M expression and activity / presynaptic modulation of chemical synaptic transmission / regulation of microtubule cytoskeleton organization / positive regulation of GTPase activity / negative regulation of cell migration / hippocampus development / positive regulation of protein export from nucleus / positive regulation of protein ubiquitination / excitatory postsynaptic potential / Ubiquitin-dependent degradation of Cyclin D / mitochondrion organization / positive regulation of cell differentiation / peptidyl-threonine phosphorylation / positive regulation of protein-containing complex assembly / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / negative regulation of canonical Wnt signaling pathway / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / regulation of circadian rhythm / Degradation of beta-catenin by the destruction complex / beta-catenin binding / tau protein binding / B-WICH complex positively regulates rRNA expression / circadian rhythm / cellular response to amyloid-beta / neuron projection development / positive regulation of protein catabolic process / Regulation of RUNX2 expression and activity / kinase activity / p53 binding / positive regulation of neuron apoptotic process / positive regulation of protein binding / insulin receptor signaling pathway
Similarity search - Function
Glycogen synthase kinase 3, catalytic domain / : / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain ...Glycogen synthase kinase 3, catalytic domain / : / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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


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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more