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- PDB-6ibe: The FERM domain of Human EPB41L3 -

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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 / Sensory processing of sound by outer hair cells of the cochlea ...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 / Sensory processing of sound by outer hair cells of the cochlea / Neurexins and neuroligins / Sensory processing of sound by inner 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 / regulation of cell shape / actin binding / 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) / PH-domain like / FERM central domain / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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


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


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


Mass: 18.015 Da / Num. of mol.: 183 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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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

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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

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HE7

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 %

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