[English] 日本語
Yorodumi
- PDB-1eg3: STRUCTURE OF A DYSTROPHIN WW DOMAIN FRAGMENT IN COMPLEX WITH A BE... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1eg3
TitleSTRUCTURE OF A DYSTROPHIN WW DOMAIN FRAGMENT IN COMPLEX WITH A BETA-DYSTROGLYCAN PEPTIDE
ComponentsDYSTROPHIN
KeywordsSTRUCTURAL PROTEIN / EF-hand like domain / WW domain
Function / homology
Function and homology information


regulation of muscle system process / regulation of cellular response to growth factor stimulus / regulation of skeletal muscle contraction / syntrophin complex / negative regulation of peptidyl-cysteine S-nitrosylation / regulation of voltage-gated calcium channel activity / synaptic signaling / cardiac muscle cell action potential / dystrophin-associated glycoprotein complex / positive regulation of sodium ion transmembrane transporter activity ...regulation of muscle system process / regulation of cellular response to growth factor stimulus / regulation of skeletal muscle contraction / syntrophin complex / negative regulation of peptidyl-cysteine S-nitrosylation / regulation of voltage-gated calcium channel activity / synaptic signaling / cardiac muscle cell action potential / dystrophin-associated glycoprotein complex / positive regulation of sodium ion transmembrane transporter activity / cell-substrate junction / motile cilium assembly / peptide biosynthetic process / dystroglycan binding / regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion / Formation of the dystrophin-glycoprotein complex (DGC) / vinculin binding / costamere / muscle cell development / neuron projection terminus / Striated Muscle Contraction / filopodium membrane / structural constituent of muscle / muscle cell cellular homeostasis / nitric-oxide synthase binding / muscle organ development / myosin binding / maintenance of blood-brain barrier / Non-integrin membrane-ECM interactions / regulation of ryanodine-sensitive calcium-release channel activity / neuron development / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / skeletal muscle tissue development / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / cardiac muscle contraction / response to muscle stretch / positive regulation of neuron differentiation / regulation of heart rate / filopodium / sarcolemma / positive regulation of neuron projection development / structural constituent of cytoskeleton / Z disc / intracellular protein localization / actin binding / protein-containing complex assembly / postsynaptic membrane / cytoskeleton / membrane raft / synapse / cell surface / protein-containing complex / zinc ion binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Helix Hairpins - #70 / Dystrophin/utrophin / EF-hand domain, type 1 / EF-hand domain, type 2 / EF hand / EF-hand / : / Ubiquitin Ligase Nedd4; Chain: W; - #10 / Ubiquitin Ligase Nedd4; Chain: W; / Spectrin repeat ...Helix Hairpins - #70 / Dystrophin/utrophin / EF-hand domain, type 1 / EF-hand domain, type 2 / EF hand / EF-hand / : / Ubiquitin Ligase Nedd4; Chain: W; - #10 / Ubiquitin Ligase Nedd4; Chain: W; / Spectrin repeat / Spectrin repeat / Spectrin/alpha-actinin / Spectrin repeats / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. / Actinin-type actin-binding domain, conserved site / Calponin homology domain / Zinc finger ZZ-type signature. / Calponin homology (CH) domain / Zinc-binding domain, present in Dystrophin, CREB-binding protein. / Zinc finger, ZZ type / Zinc finger, ZZ-type / Zinc finger, ZZ-type superfamily / Zinc finger ZZ-type profile. / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / Helix Hairpins / WW domain / WW/rsp5/WWP domain signature. / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / EF-hand / Single Sheet / Recoverin; domain 1 / Helix non-globular / Special / EF-hand domain pair / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsHuang, X. / Poy, F. / Zhang, R. / Joachimiak, A. / Sudol, M. / Eck, M.J.
CitationJournal: Nat.Struct.Biol. / Year: 2000
Title: Structure of a WW domain containing fragment of dystrophin in complex with beta-dystroglycan.
Authors: Huang, X. / Poy, F. / Zhang, R. / Joachimiak, A. / Sudol, M. / Eck, M.J.
History
DepositionFeb 11, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 23, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DYSTROPHIN


Theoretical massNumber of molelcules
Total (without water)29,8451
Polymers29,8451
Non-polymers00
Water4,792266
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.710, 67.470, 85.490
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein DYSTROPHIN


Mass: 29845.232 Da / Num. of mol.: 1 / Fragment: WW DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PGEX-2TK / Production host: Escherichia coli (E. coli) / References: UniProt: P11532
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 266 / 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: 2.4 Å3/Da / Density % sol: 48.77 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: ammonium sulfate, glycerol, DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
Temperature: 22 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
220 mMMOPS1drop
3100 mM1dropNaCl
45 mMdithiothreitol1drop
5100 mMMOPS1reservoir
61.0 Mammonium sulfate1reservoir
710 %(v/v)glycerol1reservoir
85 mMdithiothreitol1reservoir

-
Data collection

DiffractionMean temperature: 213 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.922
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 5, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.922 Å / Relative weight: 1
ReflectionResolution: 2→25 Å / Num. all: 144120 / Num. obs: 19962 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Biso Wilson estimate: 26 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 7.8
Reflection shellResolution: 2→2.07 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.347 / Num. unique all: 1929 / % possible all: 97.5
Reflection
*PLUS
Num. measured all: 144120

-
Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementResolution: 2→20 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.257 998 -RANDOM
Rwork0.194 ---
all-20123 --
obs-19962 99.2 %-
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2089 0 0 266 2355
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_angle_deg1.563
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 20 Å / σ(F): 2 / Rfactor obs: 0.194
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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