[English] 日本語
Yorodumi
- PDB-1isn: Crystal structure of merlin FERM domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1isn
TitleCrystal structure of merlin FERM domain
Componentsmerlin
KeywordsCELL ADHESION / FERM domain
Function / homology
Function and homology information


regulation of hippo signaling / RHO GTPases activate PAKs / regulation of organelle assembly / regulation of gliogenesis / positive regulation of early endosome to late endosome transport / Schwann cell proliferation / osteoblast proliferation / negative regulation of Schwann cell proliferation / negative regulation of osteoblast proliferation / negative regulation of tyrosine phosphorylation of STAT protein ...regulation of hippo signaling / RHO GTPases activate PAKs / regulation of organelle assembly / regulation of gliogenesis / positive regulation of early endosome to late endosome transport / Schwann cell proliferation / osteoblast proliferation / negative regulation of Schwann cell proliferation / negative regulation of osteoblast proliferation / negative regulation of tyrosine phosphorylation of STAT protein / Regulation of actin dynamics for phagocytic cup formation / ectoderm development / lens fiber cell differentiation / positive regulation of protein localization to early endosome / regulation of neural precursor cell proliferation / regulation of stem cell proliferation / negative regulation of receptor signaling pathway via JAK-STAT / cell-cell junction organization / regulation of protein localization to nucleus / cortical actin cytoskeleton / negative regulation of MAPK cascade / negative regulation of cell-cell adhesion / odontogenesis of dentin-containing tooth / cleavage furrow / mesoderm formation / regulation of neurogenesis / positive regulation of stress fiber assembly / ruffle / filopodium / hippocampus development / positive regulation of cell differentiation / adherens junction / brain development / regulation of protein stability / negative regulation of cell growth / beta-catenin binding / MAPK cascade / integrin binding / apical part of cell / lamellipodium / cell body / actin binding / regulation of cell population proliferation / regulation of cell shape / actin cytoskeleton organization / regulation of apoptotic process / cytoskeleton / early endosome / regulation of cell cycle / neuron projection / protein domain specific binding / negative regulation of cell population proliferation / nucleolus / perinuclear region of cytoplasm / protein-containing complex / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Ezrin/radixin/moesin, alpha-helical domain / Ezrin/radixin/moesin, alpha-helical domain / Moesin tail domain superfamily / Ezrin/radixin/moesin / Ezrin/radixin/moesin, C-terminal / ERM family, FERM domain C-lobe / Ezrin/radixin/moesin family C terminal / Acyl-CoA Binding Protein - #10 / Ezrin/radixin/moesin-like / Acyl-CoA Binding Protein ...Ezrin/radixin/moesin, alpha-helical domain / Ezrin/radixin/moesin, alpha-helical domain / Moesin tail domain superfamily / Ezrin/radixin/moesin / Ezrin/radixin/moesin, C-terminal / ERM family, FERM domain C-lobe / Ezrin/radixin/moesin family C terminal / Acyl-CoA Binding Protein - #10 / Ezrin/radixin/moesin-like / Acyl-CoA Binding Protein / FERM, C-terminal PH-like domain / FERM C-terminal PH-like domain / FERM C-terminal PH-like domain / FERM, N-terminal / FERM N-terminal domain / FERM domain signature 1. / FERM conserved site / FERM domain signature 2. / FERM central domain / FERM/acyl-CoA-binding protein superfamily / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / FERM central domain / PH-domain like / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / PH-like domain superfamily / Ubiquitin-like domain superfamily / Roll / Roll / Up-down Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsShimizu, T. / Seto, A. / Maita, N. / Hamada, K. / Tsukita, S. / Tsukita, S. / Hakoshima, T.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Structural basis for neurofibromatosis type 2. Crystal structure of the merlin FERM domain.
Authors: Shimizu, T. / Seto, A. / Maita, N. / Hamada, K. / Tsukita, S. / Tsukita, S. / Hakoshima, T.
History
DepositionDec 13, 2001Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 3, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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: merlin


Theoretical massNumber of molelcules
Total (without water)38,3671
Polymers38,3671
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.408, 67.408, 179.137
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein merlin /


Mass: 38367.320 Da / Num. of mol.: 1 / Fragment: FERM domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: neurofibromatosis type 2 / Plasmid: pGEX-4T-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: P46662

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.65 Å3/Da / Density % sol: 53.6 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG6000, LiCl, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 6.8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
113.6 mg/mlprotein1drop
210 mMMES1droppH6.8
37.5 %PEG60001drop
4150 mM1dropNaCl
5250 mM1dropLiCl
60.5 mMdithiothreitol1drop
750 mMHEPES1reservoirpH7.0
815 %PEG60001reservoir
9500 mM1reservoirLiCl

-
Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9198 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 10, 2000
RadiationMonochromator: double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9198 Å / Relative weight: 1
ReflectionResolution: 2.9→30 Å / Num. all: 8825 / Num. obs: 8807 / % possible obs: 90.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 50.8 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 8.4
Reflection shellResolution: 2.9→3.03 Å / Rmerge(I) obs: 0.316 / Mean I/σ(I) obs: 2.4 / % possible all: 75.8
Reflection
*PLUS
Lowest resolution: 30 Å / Num. measured all: 32050 / Rmerge(I) obs: 0.069
Reflection shell
*PLUS
% possible obs: 75.8 % / Rmerge(I) obs: 0.316

-
Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
DPSdata reduction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GC6

1gc6


Resolution: 2.9→20 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.284 907 11.6 %RANDOM
Rwork0.229 ---
all0.237 8728 --
obs0.235 7821 --
Refine analyze
FreeObs
Luzzati coordinate error0.51 Å0.4 Å
Luzzati d res low-5 Å
Luzzati sigma a0.63 Å0.53 Å
Refinement stepCycle: LAST / Resolution: 2.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2617 0 0 0 2617
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_improper_angle_d1.24
LS refinement shellResolution: 2.9→3.03 Å
RfactorNum. reflection
Rfree0.4065 83
Rwork0.3728 -
obs-796
Refinement
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 20 Å / σ(F): 2 / % reflection Rfree: 10 % / Rfactor all: 0.237 / Rfactor obs: 0.229 / Rfactor Rfree: 0.284 / Rfactor Rwork: 0.229
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.24
LS refinement shell
*PLUS
Highest resolution: 2.9 Å / Rfactor Rfree: 0.4065 / Rfactor Rwork: 0.3728 / Rfactor obs: 0.373

+
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