[English] 日本語
Yorodumi
- PDB-6ibe: The FERM domain of Human EPB41L3 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ibe
TitleThe FERM domain of Human EPB41L3
ComponentsBand 4.1-like protein 3
KeywordsCELL ADHESION / Ferm domain / Alzheimer's Disease
Function / homology
Function and homology information


protein localization to paranode region of axon / cytoskeletal protein-membrane anchor activity / paranodal junction assembly / protein localization to juxtaparanode region of axon / myelin maintenance / paranode region of axon / cortical cytoskeleton organization / actomyosin structure organization / juxtaparanode region of axon / Neurexins and neuroligins ...protein localization to paranode region of axon / cytoskeletal protein-membrane anchor activity / paranodal junction assembly / protein localization to juxtaparanode region of axon / myelin maintenance / paranode region of axon / cortical cytoskeleton organization / actomyosin structure organization / juxtaparanode region of axon / Neurexins and neuroligins / Sensory processing of sound by inner hair cells of the cochlea / Sensory processing of sound by outer hair cells of the cochlea / cortical actin cytoskeleton organization / neuron projection morphogenesis / protein localization to plasma membrane / structural constituent of cytoskeleton / cell-cell junction / cell junction / actin binding / regulation of cell shape / cytoskeleton / apoptotic process / plasma membrane / cytosol
Similarity search - Function
Band 4.1-like protein 3 / SAB domain / Band 4.1, C-terminal / SAB domain / 4.1 protein C-terminal domain (CTD) / FERM adjacent (FA) / FERM adjacent (FA) / FERM adjacent (FA) / Acyl-CoA Binding Protein - #10 / Ezrin/radixin/moesin-like ...Band 4.1-like protein 3 / SAB domain / Band 4.1, C-terminal / SAB domain / 4.1 protein C-terminal domain (CTD) / FERM adjacent (FA) / FERM adjacent (FA) / FERM adjacent (FA) / 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
Band 4.1-like protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsBradshaw, W.J. / Katis, V.L. / Newman, J.A. / Fernandez-Cid, A. / Burgess-Brown, N. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / Gileadi, O.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Aging (NIH/NIA) United States
CitationJournal: To Be Published
Title: The FERM domain of Human EPB41L3
Authors: Bradshaw, W.J. / Katis, V.L. / Newman, J.A. / Fernandez-Cid, A. / Burgess-Brown, N. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / Gileadi, O.
History
DepositionNov 29, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 19, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 30, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.2Jan 24, 2024Group: 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: Band 4.1-like protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9638
Polymers33,3951
Non-polymers5687
Water3,297183
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint19 kcal/mol
Surface area15870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.915, 78.687, 98.981
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Band 4.1-like protein 3 / 4.1B / Differentially expressed in adenocarcinoma of the lung protein 1 / DAL-1


Mass: 33395.305 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EPB41L3, DAL1, KIAA0987 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y2J2
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 2.27 Å3/Da / Density % sol: 45.79 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.15 M ammonium nitrate, 0.1 M MES, 5% (v/v) ethylene glycol, 5% (w/v) PEG 2000, 5% (w/v) PEG 3350, 5% (w/v) PEG 4000, 5% (w/v) PEG 5000 MME

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.45→78.69 Å / Num. obs: 54827 / % possible obs: 100 % / Redundancy: 6.1 % / CC1/2: 0.944 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.043 / Rrim(I) all: 0.079 / Χ2: 0.81 / Net I/σ(I): 13.5
Reflection shellResolution: 1.45→1.48 Å / Redundancy: 5.4 % / Rmerge(I) obs: 1.536 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2741 / CC1/2: 0.401 / Rpim(I) all: 1.098 / Rrim(I) all: 1.896 / Χ2: 0.5 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HE7
Resolution: 1.45→61.59 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.926 / SU ML: 0.049 / Cross valid method: THROUGHOUT / ESU R: 0.07 / ESU R Free: 0.067 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19994 1984 3.6 %RANDOM
Rwork0.15393 ---
obs0.15562 52770 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 25.261 Å2
Baniso -1Baniso -2Baniso -3
1-0.66 Å2-0 Å20 Å2
2---0.04 Å2-0 Å2
3----0.62 Å2
Refinement stepCycle: 1 / Resolution: 1.45→61.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2334 0 36 183 2553
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0132599
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172402
X-RAY DIFFRACTIONr_angle_refined_deg1.6951.6493507
X-RAY DIFFRACTIONr_angle_other_deg1.4591.5815596
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6695317
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.93521.8150
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.64515466
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9461519
X-RAY DIFFRACTIONr_chiral_restr0.0920.2315
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022893
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02584
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.4032.2671214
X-RAY DIFFRACTIONr_mcbond_other3.4042.2651213
X-RAY DIFFRACTIONr_mcangle_it3.9573.4181525
X-RAY DIFFRACTIONr_mcangle_other3.9563.421526
X-RAY DIFFRACTIONr_scbond_it4.5392.8011385
X-RAY DIFFRACTIONr_scbond_other4.5362.81383
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.6834.0071975
X-RAY DIFFRACTIONr_long_range_B_refined5.25626.4352826
X-RAY DIFFRACTIONr_long_range_B_other5.24226.1982796
X-RAY DIFFRACTIONr_rigid_bond_restr3.03235001
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 147 -
Rwork0.263 3864 -
obs--99.98 %

+
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