[English] 日本語
Yorodumi
- PDB-3cbz: The Dvl2 PDZ Domain in Complex with the N2 Inhibitory Peptide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3cbz
TitleThe Dvl2 PDZ Domain in Complex with the N2 Inhibitory Peptide
ComponentsDishevelled-2
KeywordsPROTEIN BINDING / PDZ DOMAIN / PHAGE DERIVED HIGH AFFINITY LIGAND / Cytoplasm / Developmental protein / Phosphoprotein / Wnt signaling pathway / SIGNALING PROTEIN
Function / homology
Function and homology information


Negative regulation of TCF-dependent signaling by DVL-interacting proteins / convergent extension involved in neural plate elongation / planar cell polarity pathway involved in neural tube closure / cochlea morphogenesis / segment specification / WNT5A-dependent internalization of FZD4 / positive regulation of neuron projection arborization / non-canonical Wnt signaling pathway / WNT5:FZD7-mediated leishmania damping / clathrin-coated endocytic vesicle ...Negative regulation of TCF-dependent signaling by DVL-interacting proteins / convergent extension involved in neural plate elongation / planar cell polarity pathway involved in neural tube closure / cochlea morphogenesis / segment specification / WNT5A-dependent internalization of FZD4 / positive regulation of neuron projection arborization / non-canonical Wnt signaling pathway / WNT5:FZD7-mediated leishmania damping / clathrin-coated endocytic vesicle / frizzled binding / PCP/CE pathway / WNT mediated activation of DVL / Signaling by Hippo / aggresome / Disassembly of the destruction complex and recruitment of AXIN to the membrane / Wnt signaling pathway, planar cell polarity pathway / heart looping / outflow tract morphogenesis / canonical Wnt signaling pathway / lateral plasma membrane / positive regulation of JUN kinase activity / Asymmetric localization of PCP proteins / TCF dependent signaling in response to WNT / neural tube closure / RHO GTPases Activate Formins / Degradation of DVL / regulation of actin cytoskeleton organization / positive regulation of JNK cascade / protein localization / small GTPase binding / : / positive regulation of DNA-binding transcription factor activity / protein-macromolecule adaptor activity / Cargo recognition for clathrin-mediated endocytosis / apical part of cell / Clathrin-mediated endocytosis / regulation of cell population proliferation / heart development / cytoplasmic vesicle / nuclear body / intracellular signal transduction / positive regulation of protein phosphorylation / protein domain specific binding / regulation of DNA-templated transcription / protein kinase binding / positive regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Dishevelled-2 / Dishevelled protein domain / Dishevelled family / Dishevelled C-terminal / Dishevelled specific domain / Segment polarity protein dishevelled (Dsh) C terminal / Dishevelled-related protein / DIX domain / DIX domain superfamily / DIX domain ...Dishevelled-2 / Dishevelled protein domain / Dishevelled family / Dishevelled C-terminal / Dishevelled specific domain / Segment polarity protein dishevelled (Dsh) C terminal / Dishevelled-related protein / DIX domain / DIX domain superfamily / DIX domain / DIX domain profile. / Domain present in Dishevelled and axin / Domain found in Dishevelled, Egl-10, and Pleckstrin (DEP) / DEP domain profile. / Domain found in Dishevelled, Egl-10, and Pleckstrin / DEP domain / PDZ domain / Pdz3 Domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Ubiquitin-like domain superfamily / Winged helix DNA-binding domain superfamily / Roll / Winged helix-like DNA-binding domain superfamily / Mainly Beta
Similarity search - Domain/homology
PHOSPHATE ION / Segment polarity protein dishevelled homolog DVL-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.38 Å
AuthorsAppleton, B.A. / Wiesmann, C.
CitationJournal: Nat.Chem.Biol. / Year: 2009
Title: Inhibition of Wnt signaling by Dishevelled PDZ peptides
Authors: Zhang, Y. / Appleton, B.A. / Wiesmann, C. / Lau, T. / Costa, M. / Hannoush, R.N. / Sidhu, S.S.
History
DepositionFeb 23, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Dishevelled-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,6444
Polymers11,4251
Non-polymers2193
Water1,56787
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.675, 43.554, 54.860
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsMULTIMER: PDZ-peptide pairs form an extended head-to-tail assembly coincident with a crystallographic axis

-
Components

#1: Protein Dishevelled-2 / / Segment polarity protein dishevelled homolog DVL-2 / DSH homolog 2


Mass: 11424.912 Da / Num. of mol.: 1 / Fragment: PDZ domain (UNP residues 264-354) / Mutation: C341S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DVL2 / Production host: Escherichia coli (E. coli) / References: UniProt: O14641
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 87 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE PEPTIDE LIGAND WAS FUSED TO THE C TERMINUS OF THE LINKER

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.87 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES, 0.8 M sodium phosphate, 0.8 M Potassium phosphate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 9, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.38→50 Å / Num. obs: 21576 / % possible obs: 99.3 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.046 / Χ2: 1.005 / Net I/σ(I): 32.1
Reflection shellResolution: 1.38→1.43 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.397 / Mean I/σ(I) obs: 2.8 / Num. unique all: 2018 / Χ2: 0.972 / % possible all: 94.6

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.004data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CBX

3cbx


Resolution: 1.38→20 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.972 / SU B: 1.569 / SU ML: 0.029 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.052 / ESU R Free: 0.049 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.166 1096 5.1 %RANDOM
Rwork0.137 ---
obs0.139 20391 99.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.494 Å2
Baniso -1Baniso -2Baniso -3
1--0.66 Å20 Å20 Å2
2---0.17 Å20 Å2
3---0.82 Å2
Refinement stepCycle: LAST / Resolution: 1.38→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms801 0 13 87 901
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.022825
X-RAY DIFFRACTIONr_bond_other_d0.0030.02557
X-RAY DIFFRACTIONr_angle_refined_deg1.61.9811115
X-RAY DIFFRACTIONr_angle_other_deg0.93631371
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0895112
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.52825.42935
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.61515149
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.42155
X-RAY DIFFRACTIONr_chiral_restr0.1030.2125
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02924
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02148
X-RAY DIFFRACTIONr_nbd_refined0.2080.2132
X-RAY DIFFRACTIONr_nbd_other0.1930.2551
X-RAY DIFFRACTIONr_nbtor_refined0.1740.2388
X-RAY DIFFRACTIONr_nbtor_other0.0870.2473
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1890.261
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1910.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1840.252
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1110.27
X-RAY DIFFRACTIONr_mcbond_it4.7042.5677
X-RAY DIFFRACTIONr_mcbond_other2.9422.5223
X-RAY DIFFRACTIONr_mcangle_it5.385845
X-RAY DIFFRACTIONr_scbond_it5.4342.5336
X-RAY DIFFRACTIONr_scangle_it7.2285265
X-RAY DIFFRACTIONr_rigid_bond_restr3.20531647
X-RAY DIFFRACTIONr_sphericity_free16.502387
X-RAY DIFFRACTIONr_sphericity_bonded8.47531371
LS refinement shellResolution: 1.38→1.408 Å / Total num. of bins used: 25
RfactorNum. reflection% reflection
Rfree0.328 53 -
Rwork0.194 1121 -
all-1174 -
obs--92.88 %

+
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