[English] 日本語
Yorodumi
- PDB-1wsp: Crystal structure of axin dix domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1wsp
TitleCrystal structure of axin dix domain
ComponentsAxin 1 protein
KeywordsSIGNALING PROTEIN
Function / homology
Function and homology information


Beta-catenin phosphorylation cascade / Disassembly of the destruction complex and recruitment of AXIN to the membrane / TCF dependent signaling in response to WNT / Degradation of beta-catenin by the destruction complex / Degradation of AXIN / embryonic skeletal joint morphogenesis / armadillo repeat domain binding / response to quercetin / hemoglobin metabolic process / head development ...Beta-catenin phosphorylation cascade / Disassembly of the destruction complex and recruitment of AXIN to the membrane / TCF dependent signaling in response to WNT / Degradation of beta-catenin by the destruction complex / Degradation of AXIN / embryonic skeletal joint morphogenesis / armadillo repeat domain binding / response to quercetin / hemoglobin metabolic process / head development / cell development / Ub-specific processing proteases / dorsal/ventral axis specification / axial mesoderm formation / post-anal tail morphogenesis / axial mesoderm development / beta-catenin destruction complex / positive regulation of ubiquitin-dependent protein catabolic process / epigenetic programming in the zygotic pronuclei / nervous system process / I-SMAD binding / dorsal/ventral pattern formation / Wnt signalosome / regulation of canonical Wnt signaling pathway / negative regulation of protein metabolic process / adult walking behavior / erythrocyte homeostasis / nucleocytoplasmic transport / negative regulation of fat cell differentiation / positive regulation of transforming growth factor beta receptor signaling pathway / negative regulation of Wnt signaling pathway / negative regulation of transcription elongation by RNA polymerase II / SMAD binding / R-SMAD binding / lateral plasma membrane / ubiquitin-like ligase-substrate adaptor activity / canonical Wnt signaling pathway / cytoplasmic microtubule organization / positive regulation of peptidyl-threonine phosphorylation / positive regulation of protein ubiquitination / cell periphery / positive regulation of JNK cascade / sensory perception of sound / regulation of protein phosphorylation / negative regulation of canonical Wnt signaling pathway / protein catabolic process / Wnt signaling pathway / beta-catenin binding / protein polyubiquitination / positive regulation of protein catabolic process / microtubule cytoskeleton / p53 binding / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / positive regulation of peptidyl-serine phosphorylation / cell cortex / protein-containing complex assembly / cytoplasmic vesicle / in utero embryonic development / molecular adaptor activity / positive regulation of protein phosphorylation / protein domain specific binding / negative regulation of gene expression / signaling receptor binding / ubiquitin protein ligase binding / synapse / protein kinase binding / apoptotic process / perinuclear region of cytoplasm / enzyme binding / protein homodimerization activity / protein-containing complex / identical protein binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Ribosomal Protein L25; Chain P - #130 / Axin beta-catenin binding / Axin-1/2, tankyrase-binding domain / Axin-like / Axin beta-catenin binding motif / Axin-1 tankyrase binding domain / DIX domain / DIX domain superfamily / DIX domain / DIX domain profile. ...Ribosomal Protein L25; Chain P - #130 / Axin beta-catenin binding / Axin-1/2, tankyrase-binding domain / Axin-like / Axin beta-catenin binding motif / Axin-1 tankyrase binding domain / DIX domain / DIX domain superfamily / DIX domain / DIX domain profile. / Domain present in Dishevelled and axin / RGS, subdomain 1/3 / Ribosomal Protein L25; Chain P / 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 / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
BENZOIC ACID / : / : / Axin-1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9 Å
AuthorsShibata, N. / Hanamura, T. / Yamamoto, R. / Ueda, Y. / Yamamoto, H. / Kikuchi, A. / Higuchi, Y.
CitationJournal: to be published
Title: Crystal structure of axin dix domain
Authors: Shibata, N. / Hanamura, T. / Yamamoto, R. / Ueda, Y. / Yamamoto, H. / Kikuchi, A. / Higuchi, Y.
History
DepositionNov 8, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 14, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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_conn.ptnr2_label_seq_id / _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: Axin 1 protein
B: Axin 1 protein
C: Axin 1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,13013
Polymers29,2033
Non-polymers1,92710
Water3,675204
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.130, 92.130, 85.540
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
DetailsEach one of the chains (A, B, and C) is the minimum biological unit.

-
Components

#1: Protein Axin 1 protein / Axis inhibition protein 1 / rAxin


Mass: 9734.206 Da / Num. of mol.: 3 / Fragment: DIX DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: pMALc2 / Production host: Escherichia coli (E. coli) / References: GenBank: 2982198, UniProt: O70239*PLUS
#2: Chemical
ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Hg
#3: Chemical ChemComp-BEZ / BENZOIC ACID


Mass: 122.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / 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: 3.33 Å3/Da / Density % sol: 63 %
Crystal growTemperature: 283 K / Method: vapor diffusion / pH: 7.5 / Details: PEG8000, pH 7.5, VAPOR DIFFUSION, temperature 283K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 10, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.9→58.772 Å / Num. all: 9245 / Num. obs: 9237 / % possible obs: 100 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Biso Wilson estimate: 157 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 7.5
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.224 / Mean I/σ(I) obs: 3.3 / Num. unique all: 1335 / % possible all: 100

-
Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.9→29.17 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 1214210.2 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.311 963 10.5 %RANDOM
Rwork0.246 ---
obs0.246 9206 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 73.362 Å2 / ksol: 0.326264 e/Å3
Displacement parametersBiso mean: 49.4 Å2
Baniso -1Baniso -2Baniso -3
1-1.14 Å22.37 Å20 Å2
2--1.14 Å20 Å2
3----2.28 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.56 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.58 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.9→29.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2051 0 18 204 2273
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.71
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it5.931.5
X-RAY DIFFRACTIONc_mcangle_it8.822
X-RAY DIFFRACTIONc_scbond_it13.182
X-RAY DIFFRACTIONc_scangle_it14.882.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.9→3 Å / Rfactor Rfree error: 0.044 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.463 109 11.9 %
Rwork0.313 807 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4PCMB.PARAMPCMB.TOP

+
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