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- PDB-1ni2: Structure of the active FERM domain of Ezrin -

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Basic information

Entry
Database: PDB / ID: 1ni2
TitleStructure of the active FERM domain of Ezrin
ComponentsEzrin
KeywordsSTRUCTURAL PROTEIN / FERM / KEYSTONE / UBIQUITIN-LIKE DOMAIN / ACYL-COA-LIKE DOMAIN / PH/PTB-LIKE DOMAIN
Function / homology
Function and homology information


positive regulation of interleukin-2-mediated signaling pathway / terminal web assembly / intestinal D-glucose absorption / regulation of microvillus length / protein localization to cell cortex / regulation of organelle assembly / microvillus assembly / postsynaptic actin cytoskeleton organization / positive regulation of early endosome to late endosome transport / membrane to membrane docking ...positive regulation of interleukin-2-mediated signaling pathway / terminal web assembly / intestinal D-glucose absorption / regulation of microvillus length / protein localization to cell cortex / regulation of organelle assembly / microvillus assembly / postsynaptic actin cytoskeleton organization / positive regulation of early endosome to late endosome transport / membrane to membrane docking / establishment of centrosome localization / Netrin-1 signaling / uropod / positive regulation of multicellular organism growth / filopodium assembly / negative regulation of p38MAPK cascade / positive regulation of protein localization to early endosome / cortical microtubule organization / astral microtubule organization / protein-containing complex localization / S100 protein binding / sphingosine-1-phosphate receptor signaling pathway / establishment of endothelial barrier / Sensory processing of sound by outer hair cells of the cochlea / Sensory processing of sound by inner hair cells of the cochlea / leukocyte cell-cell adhesion / microvillus membrane / protein kinase A regulatory subunit binding / protein kinase A catalytic subunit binding / protein kinase A binding / Recycling pathway of L1 / microvillus / cortical cytoskeleton / brush border / immunological synapse / actin filament bundle assembly / plasma membrane raft / negative regulation of T cell receptor signaling pathway / cAMP/PKA signal transduction / cell projection / ruffle / cell adhesion molecule binding / protein localization to plasma membrane / cell periphery / positive regulation of protein localization to plasma membrane / adherens junction / filopodium / actin filament / negative regulation of ERK1 and ERK2 cascade / ruffle membrane / regulation of cell shape / apical part of cell / disordered domain specific binding / positive regulation of protein catabolic process / actin filament binding / actin cytoskeleton organization / actin cytoskeleton / ATPase binding / actin binding / ciliary basal body / microtubule binding / vesicle / basolateral plasma membrane / endosome / apical plasma membrane / cadherin binding / protein domain specific binding / focal adhesion / positive regulation of gene expression / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / protein-containing complex / : / RNA binding / extracellular exosome / membrane / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Moesin tail domain superfamily / Ezrin/radixin/moesin / Ezrin/radixin/moesin, C-terminal / ERM family, FERM domain C-lobe / Ezrin/radixin/moesin, alpha-helical domain / Ezrin/radixin/moesin family C terminal / Ezrin/radixin/moesin, alpha-helical domain / Acyl-CoA Binding Protein - #10 / Acyl-CoA Binding Protein / Ezrin/radixin/moesin-like ...Moesin tail domain superfamily / Ezrin/radixin/moesin / Ezrin/radixin/moesin, C-terminal / ERM family, FERM domain C-lobe / Ezrin/radixin/moesin, alpha-helical domain / Ezrin/radixin/moesin family C terminal / Ezrin/radixin/moesin, alpha-helical domain / Acyl-CoA Binding Protein - #10 / Acyl-CoA Binding Protein / Ezrin/radixin/moesin-like / 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 / Roll / Ubiquitin-like domain superfamily / Roll / Up-down Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSmith, W.J. / Nassar, N. / Bretscher, A.P. / Cerione, R.A. / Karplus, P.A.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Structure of the Active N-terminal Domain of Ezrin. CONFORMATIONAL AND MOBILITY CHANGES IDENTIFY KEYSTONE INTERACTIONS.
Authors: Smith, W.J. / Nassar, N. / Bretscher, A.P. / Cerione, R.A. / Karplus, P.A.
History
DepositionDec 20, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 25, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Aug 16, 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
Remark 600Heterogen compared to the published model this has 11 less waters. The author requested the removal ...Heterogen compared to the published model this has 11 less waters. The author requested the removal of these waters because they were in unreasonable positions.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ezrin
B: Ezrin


Theoretical massNumber of molelcules
Total (without water)69,8972
Polymers69,8972
Non-polymers00
Water5,549308
1
A: Ezrin


Theoretical massNumber of molelcules
Total (without water)34,9481
Polymers34,9481
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ezrin


Theoretical massNumber of molelcules
Total (without water)34,9481
Polymers34,9481
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.489, 112.802, 66.301
Angle α, β, γ (deg.)90.00, 102.32, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Ezrin / p81 / Cytovillin / Villin 2


Mass: 34948.395 Da / Num. of mol.: 2 / Fragment: residue 1-296
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VIL2 / Plasmid: PQE16 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P15311
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 308 / 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: 2.42 Å3/Da / Density % sol: 48.79 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 10% PEG 2K, 10% GLYCEROL, 5% ISOPROPANOL, TRIS-HCL, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 18K
Crystal grow
*PLUS
pH: 8.1
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails (eV)
110-15 %(w/v)PEG2000 MME1reservoir
215 %glycerol1reservoir
310 %(w/v)2-propanol1reservoir
40.1 Msodium HEPES1reservoirpH8.1

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Data collection

DiffractionMean temperature: 123 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.901 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 8, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.901 Å / Relative weight: 1
ReflectionResolution: 2.3→36.27 Å / Num. obs: 27658 / % possible obs: 89.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.1 % / Biso Wilson estimate: 43 Å2 / Limit h max: 20 / Limit h min: -21 / Limit k max: 46 / Limit k min: -21 / Limit l max: 28 / Limit l min: 0 / Observed criterion F max: 1312241.54 / Observed criterion F min: 4.7 / Net I/σ(I): 7.1
Reflection shellResolution: 2.3→2.4 Å / % possible all: 89.3
Reflection
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 26 Å / Num. obs: 27498 / Num. measured all: 183710 / Rmerge(I) obs: 0.072
Reflection shell
*PLUS
% possible obs: 77.2 % / Rmerge(I) obs: 0.256

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Processing

Software
NameVersionClassificationNB
CNS1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb is 1EF1

1ef1


Resolution: 2.3→25.86 Å / Rfactor Rfree error: 0.005 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.283 2740 10 %Random
Rwork0.2299 ---
all0.231 30930 --
obs0.23 27490 88.9 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 51.9763 Å2 / ksol: 0.318812 e/Å3
Displacement parametersBiso max: 126.11 Å2 / Biso mean: 57.79 Å2 / Biso min: 17.24 Å2
Baniso -1Baniso -2Baniso -3
1--14.89 Å20 Å2-8.14 Å2
2--21.42 Å20 Å2
3----6.53 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.43 Å0.34 Å
Luzzati d res high-2.3
Refinement stepCycle: LAST / Resolution: 2.3→25.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4908 0 0 308 5216
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_torsion_deg22.9
X-RAY DIFFRACTIONx_torsion_impr_deg0.95
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
2.3-2.40.3443238.40.34826350.0193855295876.7
2.4-2.530.28927270.29227880.0183860306079.3
2.53-2.690.273368.70.27326890.0153864302578.3
2.69-2.90.242967.70.23927130.0143829300978.6
2.9-3.190.2783739.60.27834970.0143890387099.5
3.19-3.650.2493579.30.24334730.0133843383099.7
3.65-4.590.2093729.60.20334920.0113881386499.5
4.59-25.860.18541110.50.1934630.0093933387498.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater_rep.top
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 26 Å / Rfactor Rfree: 0.282 / Rfactor Rwork: 0.229
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg2.2
LS refinement shell
*PLUS
Rfactor Rfree: 0.364 / Rfactor Rwork: 0.399

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