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- PDB-4rm9: Crystal structure of human ezrin in space group C2221 -

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Basic information

Entry
Database: PDB / ID: 4rm9
TitleCrystal structure of human ezrin in space group C2221
ComponentsEzrin
KeywordsPEPTIDE BINDING PROTEIN / FERM domain / C-ERMAD domain / membrane cytoskeleton linkers / actin binding
Function / homology
Function and homology information


terminal web assembly / intestinal D-glucose absorption / protein localization to cell cortex / establishment or maintenance of apical/basal cell polarity / regulation of microvillus length / regulation of organelle assembly / microvillus assembly / positive regulation of early endosome to late endosome transport / membrane to membrane docking / establishment of centrosome localization ...terminal web assembly / intestinal D-glucose absorption / protein localization to cell cortex / establishment or maintenance of apical/basal cell polarity / regulation of microvillus length / regulation of organelle assembly / microvillus assembly / positive regulation of early endosome to late endosome transport / membrane to membrane docking / establishment of centrosome localization / cortical microtubule organization / negative regulation of p38MAPK cascade / Netrin-1 signaling / uropod / astral microtubule organization / postsynaptic actin cytoskeleton organization / positive regulation of protein localization to early endosome / filopodium assembly / positive regulation of multicellular organism growth / protein-containing complex localization / sphingosine-1-phosphate receptor signaling pathway / establishment of endothelial barrier / S100 protein binding / Sensory processing of sound by outer hair cells of the cochlea / Sensory processing of sound by inner hair cells of the cochlea / protein kinase A binding / negative regulation of interleukin-2 production / microvillus membrane / negative regulation of T cell receptor signaling pathway / leukocyte cell-cell adhesion / cortical cytoskeleton / Recycling pathway of L1 / protein kinase A regulatory subunit binding / protein kinase A catalytic subunit binding / plasma membrane raft / actin filament bundle assembly / microvillus / brush border / immunological synapse / protein kinase A signaling / cellular response to cAMP / ruffle / cell adhesion molecule binding / ciliary basal body / filopodium / cell projection / actin filament / cell periphery / protein localization to plasma membrane / positive regulation of protein localization to plasma membrane / adherens junction / negative regulation of ERK1 and ERK2 cascade / receptor internalization / fibrillar center / ruffle membrane / positive regulation of protein catabolic process / disordered domain specific binding / actin filament binding / actin cytoskeleton / apical part of cell / actin binding / ATPase binding / regulation of cell shape / actin cytoskeleton organization / microtubule binding / basolateral plasma membrane / vesicle / endosome / cadherin binding / apical plasma membrane / 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 / extracellular space / RNA binding / extracellular exosome / membrane / identical protein binding / 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 / Ezrin/radixin/moesin-like / FERM, C-terminal PH-like domain / FERM C-terminal PH-like domain ...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 / 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 / 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 / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPhang, J.M. / Harrop, S.J. / Davies, R. / Duff, A.P. / Wilk, K.E. / Curmi, P.M.G.
CitationJournal: Biochem. J. / Year: 2016
Title: Structural characterization suggests models for monomeric and dimeric forms of full-length ezrin.
Authors: Phang, J.M. / Harrop, S.J. / Duff, A.P. / Sokolova, A.V. / Crossett, B. / Walsh, J.C. / Beckham, S.A. / Nguyen, C.D. / Davies, R.B. / Glockner, C. / Bromley, E.H. / Wilk, K.E. / Curmi, P.M.
History
DepositionOct 21, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Database references / Refinement description / Category: citation / citation_author / software
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _software.name
Revision 1.2Sep 20, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ezrin


Theoretical massNumber of molelcules
Total (without water)69,5841
Polymers69,5841
Non-polymers00
Water2,648147
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.433, 113.517, 111.773
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-739-

HOH

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Components

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


Mass: 69583.969 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EZR, VIL2 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P15311
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 1.54 Å3/Da / Density % sol: 19.97 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1M Bis-Tris pH 5.5, 18% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.954 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 14, 2010
RadiationMonochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2→57.97 Å / Num. obs: 28759 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -4 / Redundancy: 14 % / Biso Wilson estimate: 24.9 Å2 / Rmerge(I) obs: 0.118 / Rsym value: 0.118 / Net I/σ(I): 14.1
Reflection shellResolution: 2→2.11 Å / Redundancy: 14.4 % / Rmerge(I) obs: 0.809 / Mean I/σ(I) obs: 3.7 / Num. unique all: 4123 / Rsym value: 0.809 / % possible all: 97.7

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Processing

Software
NameVersionClassification
Blu-IceICEdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.3_473)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2I1J

2i1j


Resolution: 2→40.236 Å / SU ML: 0.3 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 26.53 / Stereochemistry target values: ML
Details: AUTHORS DO NOT OBSERVE RESIDUES 298-515 (THE ALPHA-HELICAL DOMAIN) IN THE CRYSTAL STRUCTURE. THEY SUSPECT LIMITED PROTEOLYSIS DURING CRYSTALLISATION
RfactorNum. reflection% reflectionSelection details
Rfree0.2592 1467 5.1 %RANDOM
Rwork0.2093 ---
all0.2117 28746 --
obs0.2117 28746 97.94 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.333 Å2 / ksol: 0.324 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-10.2854 Å2-0 Å2-0 Å2
2---1.3589 Å20 Å2
3----8.9265 Å2
Refinement stepCycle: LAST / Resolution: 2→40.236 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3075 0 0 147 3222
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033151
X-RAY DIFFRACTIONf_angle_d0.7354239
X-RAY DIFFRACTIONf_dihedral_angle_d12.6371235
X-RAY DIFFRACTIONf_chiral_restr0.057447
X-RAY DIFFRACTIONf_plane_restr0.003550
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.07150.30571400.26362675X-RAY DIFFRACTION97
2.0715-2.15450.32711730.2662630X-RAY DIFFRACTION97
2.1545-2.25250.32851460.25342700X-RAY DIFFRACTION98
2.2525-2.37120.33741460.24962706X-RAY DIFFRACTION98
2.3712-2.51980.30451400.24192705X-RAY DIFFRACTION98
2.5198-2.71430.30281280.23742732X-RAY DIFFRACTION98
2.7143-2.98740.27311550.2282727X-RAY DIFFRACTION98
2.9874-3.41950.25221540.20372737X-RAY DIFFRACTION98
3.4195-4.30740.20351340.17652790X-RAY DIFFRACTION98
4.3074-40.2440.22311510.17942877X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.6924-0.12050.0750.63950.46914.06370.1461-0.37490.03930.0759-0.09950.06420.0430.3337-0.11380.0611-0.09470.03450.1483-0.02070.0046-18.46243.918325.8414
21.53010.1573-0.50581.8062-0.95742.05550.05830.15410.0961-0.51470.0558-0.32470.54490.5334-0.08920.37460.06640.01810.3852-0.02490.0996-17.9806-8.82195.465
30.63860.16410.80392.63682.4863.2526-0.17780.1270.0612-0.7911-0.11570.2197-0.6023-0.25270.24270.24640.0287-0.06170.2226-0.03770.2085-26.60134.55055.6994
41.49310.6007-0.45610.3533-0.45290.7734-0.0228-0.01380.7809-0.33460.0730.3302-1.38010.0982-0.04431.5806-0.1299-0.00880.1607-0.04360.3726-19.932826.24587.6066
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and (resseq 1:297)
2X-RAY DIFFRACTION2chain A and (resseq 516:540)
3X-RAY DIFFRACTION3chain A and (resseq 541:574)
4X-RAY DIFFRACTION4chain A and (resseq 575:586)

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