[English] 日本語
Yorodumi
- PDB-4nm0: Crystal structure of peptide inhibitor-free GSK-3/Axin complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4nm0
TitleCrystal structure of peptide inhibitor-free GSK-3/Axin complex
Components
  • Axin-1
  • Glycogen synthase kinase-3 beta
KeywordsTRANSFERASE/PEPTIDE / Wnt / LRP6 / Auto-inhibited / GSK-3 / Axin / kinase / primed substrate / TRANSFERASE-PEPTIDE complex
Function / homology
Function and homology information


beta-catenin destruction complex assembly / armadillo repeat domain binding / head development / cell development / 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 / axial mesoderm formation ...beta-catenin destruction complex assembly / armadillo repeat domain binding / head development / cell development / 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 / axial mesoderm formation / dorsal/ventral axis specification / 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 cilium assembly / post-anal tail morphogenesis / CRMPs in Sema3A signaling / heart valve development / tau-protein kinase / 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 / regulation of protein export from nucleus / positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / 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 / cellular response to interleukin-3 / Maturation of nucleoprotein / I-SMAD binding / positive regulation of ubiquitin-dependent protein catabolic process / Wnt signalosome / regulation of long-term synaptic potentiation / negative regulation of TOR signaling / epigenetic programming in the zygotic pronuclei / regulation of microtubule-based process / negative regulation of protein localization to nucleus / AKT phosphorylates targets in the cytosol / Disassembly of the destruction complex and recruitment of AXIN to the membrane / negative regulation of calcineurin-NFAT signaling cascade / regulation of axon extension / negative regulation of protein metabolic process / nucleocytoplasmic transport / Maturation of nucleoprotein / tau-protein kinase activity / negative regulation of epithelial to mesenchymal transition / regulation of axonogenesis / positive regulation of cell-matrix adhesion / regulation of dendrite morphogenesis / RUNX1 regulates transcription of genes involved in WNT signaling / G protein-coupled dopamine receptor signaling pathway / RUNX1 regulates estrogen receptor mediated transcription / glycogen metabolic process / ER overload response / negative regulation of fat cell differentiation / SMAD binding / positive regulation of transforming growth factor beta receptor signaling pathway / regulation of neuron projection development / Constitutive Signaling by AKT1 E17K in Cancer / protein kinase A catalytic subunit binding / establishment of cell polarity / R-SMAD binding / dynactin binding / negative regulation of transcription elongation by RNA polymerase II / epithelial to mesenchymal transition / lateral plasma membrane / Regulation of HSF1-mediated heat shock response / canonical Wnt signaling pathway / NF-kappaB binding / negative regulation of osteoblast differentiation / positive regulation of protein binding / ubiquitin-like ligase-substrate adaptor activity / 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 / cellular response to retinoic acid / cytoplasmic microtubule organization / extrinsic apoptotic signaling pathway in absence of ligand / signaling adaptor activity / positive regulation of autophagy / presynaptic modulation of chemical synaptic transmission / Transcriptional and post-translational regulation of MITF-M expression and activity / protein serine/threonine kinase binding / regulation of microtubule cytoskeleton organization / negative regulation of cell migration / response to endoplasmic reticulum stress / positive regulation of protein export from nucleus / protein serine/threonine kinase activator activity / positive regulation of protein ubiquitination / cell periphery / TCF dependent signaling in response to WNT
Similarity search - Function
Axin beta-catenin binding / Axin-1/2, tankyrase-binding domain / Axin-like / Axin beta-catenin binding motif / Axin-1 tankyrase binding domain / DIX domain / RGS, subdomain 1/3 / DIX domain superfamily / DIX domain / DIX domain profile. ...Axin beta-catenin binding / Axin-1/2, tankyrase-binding domain / Axin-like / Axin beta-catenin binding motif / Axin-1 tankyrase binding domain / DIX domain / RGS, subdomain 1/3 / DIX domain superfamily / DIX domain / DIX domain profile. / Domain present in Dishevelled and axin / Glycogen synthase kinase 3, catalytic domain / : / Regulator of G protein signaling domain / RGS domain / RGS domain profile. / Regulator of G protein signalling domain / RGS, subdomain 2 / RGS domain superfamily / Ubiquitin-like domain superfamily / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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
ADENOSINE-5'-DIPHOSPHATE / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / Axin-1 / Glycogen synthase kinase-3 beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsChu, M.L.-H. / Stamos, J.L. / Enos, M.D. / Shah, N. / Weis, W.I.
CitationJournal: Elife / Year: 2014
Title: Structural basis of GSK-3 inhibition by N-terminal phosphorylation and by the Wnt receptor LRP6.
Authors: Stamos, J.L. / Chu, M.L. / Enos, M.D. / Shah, N. / Weis, W.I.
History
DepositionNov 14, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 26, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 23, 2014Group: Database references
Revision 1.2Sep 20, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glycogen synthase kinase-3 beta
B: Axin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,04512
Polymers46,9192
Non-polymers1,12610
Water2,954164
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4070 Å2
ΔGint-56 kcal/mol
Surface area17540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.303, 81.303, 280.829
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

-
Components

-
Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein Glycogen synthase kinase-3 beta / GSK-3 beta / Serine/threonine-protein kinase GSK3B


Mass: 44180.625 Da / Num. of mol.: 1 / Fragment: Residues 1-383
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GSK3B / Plasmid: pET29b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Codon-plus RIL
References: UniProt: P49841, tau-protein kinase, non-specific serine/threonine protein kinase
#2: Protein/peptide Axin-1 / Axis inhibition protein 1 / hAxin


Mass: 2738.144 Da / Num. of mol.: 1 / Fragment: Residues 383-402
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AXIN, AXIN1 / Plasmid: Modified pGEX-KG / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Codon-plus RIL / References: UniProt: O15169

-
Non-polymers , 6 types, 174 molecules

#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#6: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.83 Å3/Da / Density % sol: 56.5 % / Mosaicity: 0.18 °
Crystal growTemperature: 277 K / Method: microdialysis / pH: 7.5
Details: 10% PEG 35,000, 20mM Tris 7.5, 300mM NaCl, 5% glycerol, 20mM MgCl2, 400uM ATP, and 5mM DTT, MICRODIALYSIS, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1.033 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 9, 2013
RadiationMonochromator: Si(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.5→39.05 Å / Num. obs: 20069 / % possible obs: 100 % / Redundancy: 9.6 % / CC1/2: 0.999 / Rpim(I) all: 0.036 / Rrim(I) all: 0.112 / Rsym value: 0.106 / Net I/σ(I): 18.4 / Num. measured all: 192347
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allRsym value% possible all
2.5-2.69.91.22177022060.7260.5761.8391.74399.9
396910.0060.017

-
Processing

Software
NameVersionClassification
Blu-Icedata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NM7

4nm7


Resolution: 2.5→39.048 Å / SU ML: 0.34 / σ(F): 1.91 / Phase error: 25.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2395 979 4.91 %Transfer from related dataset
Rwork0.1908 ---
obs0.1931 19958 99.81 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→39.048 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2934 0 68 164 3166
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033079
X-RAY DIFFRACTIONf_angle_d0.6264198
X-RAY DIFFRACTIONf_dihedral_angle_d11.8611128
X-RAY DIFFRACTIONf_chiral_restr0.041479
X-RAY DIFFRACTIONf_plane_restr0.003536
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.63180.32491380.31632621X-RAY DIFFRACTION100
2.6318-2.79670.28711390.26172638X-RAY DIFFRACTION100
2.7967-3.01250.29651380.23372650X-RAY DIFFRACTION100
3.0125-3.31560.30461170.21142681X-RAY DIFFRACTION100
3.3156-3.7950.24711390.17872696X-RAY DIFFRACTION100
3.795-4.77990.20191530.15422752X-RAY DIFFRACTION100
4.7799-39.05270.22241550.18362941X-RAY DIFFRACTION100
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)
15.49370.748-0.24182.0887-1.70323.3373-0.118-0.48310.62140.583-0.02840.3761-0.784-0.0901-0.69550.5247-0.10220.16890.5912-0.06730.482-16.195545.74723.2834
22.19150.4531-0.56592.63961.47321.73520.17720.4220.16230.1901-0.30180.66540.3517-0.56240.03850.409-0.05220.0580.58230.03540.4175-19.443741.3012-4.8623
32.8757-0.2407-0.69522.3589-0.1692.25720.1949-0.18520.02050.2539-0.1097-0.12380.3694-0.2114-0.01340.4153-0.0349-0.05730.3319-0.0090.2876-5.73933.209-14.342
41.86710.34660.09061.1119-0.61373.78430.02380.0276-0.3168-0.12850.0498-0.03210.52610.0699-0.00050.41480.0044-0.07250.2774-0.07190.3561-3.895726.9964-24.9416
54.40111.07380.76093.3652-0.66733.7710.09480.53680.8424-0.53320.0070.2285-0.7624-0.2608-0.0320.672-0.1132-0.02260.44760.00170.3617-5.500843.8954-43.5287
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 26 through 90 )
2X-RAY DIFFRACTION2chain 'A' and (resid 91 through 136 )
3X-RAY DIFFRACTION3chain 'A' and (resid 137 through 218 )
4X-RAY DIFFRACTION4chain 'A' and (resid 219 through 383 )
5X-RAY DIFFRACTION5chain 'B' and (resid 381 through 401 )

+
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