[English] 日本語
Yorodumi
- PDB-6jjy: Crystal Structure of KIBRA and beta-Dystroglycan -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6jjy
TitleCrystal Structure of KIBRA and beta-Dystroglycan
Components
  • Peptide from Dystroglycan
  • Protein KIBRA
KeywordsSIGNALING PROTEIN / WW tandem / PY tandem / KIBRA / PTPN14
Function / homology
Function and homology information


Defective POMT2 causes MDDGA2, MDDGB2 and MDDGC2 / Defective POMT1 causes MDDGA1, MDDGB1 and MDDGC1 / DAG1 core M3 glycosylations / dystroglycan complex / nerve maturation / Defective POMGNT1 causes MDDGA3, MDDGB3 and MDDGC3 / DAG1 core M2 glycosylations / DAG1 core M1 glycosylations / muscle attachment / retrograde trans-synaptic signaling by trans-synaptic protein complex ...Defective POMT2 causes MDDGA2, MDDGB2 and MDDGC2 / Defective POMT1 causes MDDGA1, MDDGB1 and MDDGC1 / DAG1 core M3 glycosylations / dystroglycan complex / nerve maturation / Defective POMGNT1 causes MDDGA3, MDDGB3 and MDDGC3 / DAG1 core M2 glycosylations / DAG1 core M1 glycosylations / muscle attachment / retrograde trans-synaptic signaling by trans-synaptic protein complex / Signaling by Hippo / Matriglycan biosynthesis on DAG1 / contractile ring / calcium-dependent cell-matrix adhesion / microtubule anchoring / positive regulation of skeletal muscle acetylcholine-gated channel clustering / dystrophin-associated glycoprotein complex / laminin-1 binding / extracellular matrix assembly / negative regulation of organ growth / response to denervation involved in regulation of muscle adaptation / regulation of hippo signaling / basement membrane organization / nerve development / positive regulation of hippo signaling / photoreceptor ribbon synapse / synaptic assembly at neuromuscular junction / dystroglycan binding / vinculin binding / myelination in peripheral nervous system / positive regulation of myelination / cellular response to cholesterol / inhibitory synapse / hippo signaling / morphogenesis of an epithelium / EGR2 and SOX10-mediated initiation of Schwann cell myelination / skeletal muscle tissue regeneration / protein localization to synapse / costamere / Formation of the dystrophin-glycoprotein complex (DGC) / angiogenesis involved in wound healing / positive regulation of cell-matrix adhesion / heparan sulfate proteoglycan binding / axon regeneration / node of Ranvier / inhibitory synapse assembly / structural constituent of muscle / positive regulation of Rac protein signal transduction / positive regulation of oligodendrocyte differentiation / regulation of synapse organization / laminin receptor activity / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / membrane protein ectodomain proteolysis / basement membrane / alpha-actinin binding / Non-integrin membrane-ECM interactions / plasma membrane raft / ECM proteoglycans / negative regulation of hippo signaling / postsynaptic cytosol / extracellular matrix organization / postsynaptic density, intracellular component / negative regulation of MAPK cascade / laminin binding / signaling adaptor activity / nuclear periphery / axon guidance / SH2 domain binding / negative regulation of cell migration / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / filopodium / adherens junction / cellular response to mechanical stimulus / tubulin binding / sarcolemma / Golgi lumen / response to peptide hormone / GABA-ergic synapse / kinase binding / ruffle membrane / Regulation of expression of SLITs and ROBOs / cell migration / lamellipodium / virus receptor activity / actin binding / extracellular matrix / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / molecular adaptor activity / basolateral plasma membrane / cytoskeleton / positive regulation of MAPK cascade / protein-macromolecule adaptor activity / transcription coactivator activity / postsynaptic membrane / negative regulation of cell population proliferation / endoplasmic reticulum lumen / serine-type endopeptidase activity / external side of plasma membrane / Golgi membrane / focal adhesion
Similarity search - Function
WWC, C2 domain / : / : / WWC1-like, helical hairpin / Dystroglycan-type cadherin-like / Dystroglycan, C-terminal / Alpha-dystroglycan domain 2 / DG-type SEA domain / Alpha-dystroglycan N-terminal domain 2 / Dystroglycan domain 4 ...WWC, C2 domain / : / : / WWC1-like, helical hairpin / Dystroglycan-type cadherin-like / Dystroglycan, C-terminal / Alpha-dystroglycan domain 2 / DG-type SEA domain / Alpha-dystroglycan N-terminal domain 2 / Dystroglycan domain 4 / Alpha-Dystroglycan N-terminal domain 2 / DG-type SEA domain profile. / Dystroglycan-type cadherin-like domains. / Putative Ig domain / Cadherin-like superfamily / C2 domain / WW domain / WW/rsp5/WWP domain signature. / C2 domain / C2 domain profile. / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / C2 domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Dystroglycan 1 / Protein KIBRA
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.298 Å
AuthorsLin, Z. / Yang, Z. / Ji, Z. / Zhang, M.
CitationJournal: Elife / Year: 2019
Title: Decoding WW domain tandem-mediated target recognitions in tissue growth and cell polarity.
Authors: Lin, Z. / Yang, Z. / Xie, R. / Ji, Z. / Guan, K. / Zhang, M.
History
DepositionFeb 27, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 25, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein KIBRA
U: Peptide from Dystroglycan
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5274
Polymers18,3352
Non-polymers1922
Water1,35175
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1450 Å2
ΔGint-9 kcal/mol
Surface area11170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.483, 73.483, 105.322
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-201-

SO4

21A-201-

SO4

31U-901-

SO4

41U-901-

SO4

-
Components

#1: Protein Protein KIBRA / Kidney and brain protein / KIBRA / WW domain-containing protein 1


Mass: 16036.611 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Wwc1, Kiaa0869 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SXA9
#2: Protein/peptide Peptide from Dystroglycan / Dystrophin-associated glycoprotein 1


Mass: 2298.641 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DAG1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q14118
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 4.48 Å3/Da / Density % sol: 72.53 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 3.0-4.0M NaCl, 100mM Bis-Tris (pH 6.5)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 15114 / % possible obs: 99.7 % / Redundancy: 10.5 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 40
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 10.7 % / Rmerge(I) obs: 0.886 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 724 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6J68

6j68


Resolution: 2.298→40.571 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 25.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2529 1439 10 %
Rwork0.2056 --
obs0.2103 14386 94.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.298→40.571 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1193 0 10 75 1278
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091249
X-RAY DIFFRACTIONf_angle_d1.1011711
X-RAY DIFFRACTIONf_dihedral_angle_d15.926467
X-RAY DIFFRACTIONf_chiral_restr0.04174
X-RAY DIFFRACTIONf_plane_restr0.006229
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2976-2.37970.34891310.27721142X-RAY DIFFRACTION86
2.3797-2.4750.29931350.25281164X-RAY DIFFRACTION88
2.475-2.58760.25471360.24481215X-RAY DIFFRACTION91
2.5876-2.7240.29021330.24821268X-RAY DIFFRACTION93
2.724-2.89460.31171400.26651284X-RAY DIFFRACTION96
2.8946-3.1180.29041500.24871344X-RAY DIFFRACTION98
3.118-3.43160.32391490.22011342X-RAY DIFFRACTION99
3.4316-3.92780.21711530.18141357X-RAY DIFFRACTION99
3.9278-4.94730.19741530.1591387X-RAY DIFFRACTION99
4.9473-40.57760.21531590.16831444X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: -94.2259 Å / Origin y: 65.4788 Å / Origin z: 127.1158 Å
111213212223313233
T0.3127 Å20.0122 Å20.0522 Å2-0.2697 Å20.0342 Å2--0.3133 Å2
L0.7193 °20.5142 °2-1.4105 °2--0.0379 °2-0.6824 °2--2.6504 °2
S-0.1048 Å °-0.0338 Å °0.0505 Å °0.1623 Å °0.0939 Å °0.0559 Å °0.1397 Å °-0.1175 Å °0.0396 Å °
Refinement TLS groupSelection details: ALL

+
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