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- PDB-4rma: Crystal structure of the FERM domain of human ezrin -

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Basic information

Entry
Database: PDB / ID: 4rma
TitleCrystal structure of the FERM domain of human ezrin
ComponentsEzrin
KeywordsPEPTIDE BINDING PROTEIN / ERM / ezrin / FERM domain / membrane cytoskeleton linkers
Function / homology
Function and homology information


terminal web assembly / intestinal D-glucose absorption / protein localization to cell cortex / regulation of microvillus length / establishment or maintenance of apical/basal cell polarity / 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 / regulation of microvillus length / establishment or maintenance of apical/basal cell polarity / regulation of organelle assembly / microvillus assembly / positive regulation of early endosome to late endosome transport / membrane to membrane docking / establishment of centrosome localization / Netrin-1 signaling / negative regulation of p38MAPK cascade / uropod / astral microtubule organization / postsynaptic actin cytoskeleton organization / positive regulation of protein localization to early endosome / cortical microtubule organization / filopodium assembly / protein-containing complex localization / positive regulation of multicellular organism growth / 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 / microvillus membrane / negative regulation of T cell receptor signaling pathway / leukocyte cell-cell adhesion / negative regulation of interleukin-2 production / cortical cytoskeleton / protein kinase A regulatory subunit binding / plasma membrane raft / protein kinase A catalytic subunit binding / Recycling pathway of L1 / brush border / microvillus / actin filament bundle assembly / immunological synapse / cellular response to cAMP / cell adhesion molecule binding / ruffle / protein kinase A signaling / ciliary basal body / filopodium / protein localization to plasma membrane / cell periphery / cell projection / actin filament / positive regulation of protein localization to plasma membrane / adherens junction / receptor internalization / negative regulation of ERK1 and ERK2 cascade / fibrillar center / ruffle membrane / positive regulation of protein catabolic process / disordered domain specific binding / actin filament binding / actin cytoskeleton / apical part of cell / regulation of cell shape / actin binding / ATPase binding / 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 / RNA binding / extracellular space / extracellular exosome / identical protein binding / membrane / 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 / Ezrin/radixin/moesin-like / FERM, C-terminal PH-like domain / FERM C-terminal PH-like domain ...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 / 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: 1.75 Å
AuthorsPhang, J.M. / Harrop, S.J. / 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ezrin
B: Ezrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,3496
Polymers69,9652
Non-polymers3844
Water8,107450
1
A: Ezrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1753
Polymers34,9821
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ezrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1753
Polymers34,9821
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.334, 110.579, 66.124
Angle α, β, γ (deg.)90.00, 101.57, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 34982.477 Da / Num. of mol.: 2 / Fragment: N-terminal FERM domain, UNP residues 1-296
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EZR, VIL2 / Plasmid: pQE16 / Production host: Escherichia coli (E. coli) / Strain (production host): M15(pREP4) / References: UniProt: P15311
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 450 / 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: 2.47 Å3/Da / Density % sol: 50.21 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2M Ammonium sulfate, 0.1M HEPES pH 7.5, 10% isopropanol, 18% PEG4000, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95369 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jul 29, 2010
RadiationMonochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95369 Å / Relative weight: 1
ReflectionResolution: 1.75→39.67 Å / Num. obs: 66327 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -4 / Redundancy: 3.8 % / Biso Wilson estimate: 21.3 Å2 / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Net I/σ(I): 10.9
Reflection shellResolution: 1.75→1.84 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.701 / Mean I/σ(I) obs: 1.9 / Num. unique all: 9415 / Rsym value: 0.701 / % possible all: 94.6

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Processing

Software
NameVersionClassification
Blu-IceICEdata collection
PHASERphasing
PHENIX(phenix.refine: dev_854)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NI2

1ni2


Resolution: 1.75→35.965 Å / SU ML: 0.52 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 29.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.246 3351 5.06 %RANDOM
Rwork0.2061 ---
all0.2082 66217 --
obs0.2082 66217 96.75 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.154 Å2 / ksol: 0.385 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.5116 Å20 Å2-1.8551 Å2
2--5.6133 Å20 Å2
3----3.1017 Å2
Refinement stepCycle: LAST / Resolution: 1.75→35.965 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4840 0 20 450 5310
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0125091
X-RAY DIFFRACTIONf_angle_d1.3456883
X-RAY DIFFRACTIONf_dihedral_angle_d15.7021953
X-RAY DIFFRACTIONf_chiral_restr0.1718
X-RAY DIFFRACTIONf_plane_restr0.006884
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.7750.3731160.36632538X-RAY DIFFRACTION94
1.775-1.80150.34461330.34992533X-RAY DIFFRACTION94
1.8015-1.82970.35521480.30932537X-RAY DIFFRACTION95
1.8297-1.85960.32711320.30412614X-RAY DIFFRACTION95
1.8596-1.89170.32251610.28032532X-RAY DIFFRACTION95
1.8917-1.92610.29141300.26762584X-RAY DIFFRACTION96
1.9261-1.96320.3171100.24262612X-RAY DIFFRACTION96
1.9632-2.00320.28531260.23232631X-RAY DIFFRACTION96
2.0032-2.04680.31111370.22972620X-RAY DIFFRACTION97
2.0468-2.09440.26981500.22652603X-RAY DIFFRACTION97
2.0944-2.14680.26251500.21872573X-RAY DIFFRACTION97
2.1468-2.20480.2581350.20732646X-RAY DIFFRACTION97
2.2048-2.26970.25341510.19122586X-RAY DIFFRACTION97
2.2697-2.34290.27211300.19522644X-RAY DIFFRACTION97
2.3429-2.42660.25231320.19522661X-RAY DIFFRACTION97
2.4266-2.52380.24361620.19362610X-RAY DIFFRACTION97
2.5238-2.63860.23531450.18852648X-RAY DIFFRACTION98
2.6386-2.77760.25091390.19232633X-RAY DIFFRACTION98
2.7776-2.95160.25471490.2062662X-RAY DIFFRACTION98
2.9516-3.17940.22441300.20372675X-RAY DIFFRACTION98
3.1794-3.49910.24921560.19382665X-RAY DIFFRACTION98
3.4991-4.00480.19591420.17562674X-RAY DIFFRACTION99
4.0048-5.04350.18961470.15872690X-RAY DIFFRACTION99
5.0435-35.97250.22651400.20472695X-RAY DIFFRACTION97
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)
10.56880.35880.06990.4747-0.05090.20540.0296-0.1515-0.10140.0974-0.0829-0.1533-0.02640.2126-0.3128-0.0348-0.0326-0.04060.276-0.06040.074427.21451.024936.4316
21.05920.43480.47021.3380.84830.8398-0.19620.08650.2817-0.3904-0.00850.2451-0.3027-0.00130.0260.22890.0141-0.10120.1218-0.10520.17577.379216.961724.269
30.933-0.0697-0.07222.00640.31591.16530.0568-0.2055-0.360.0693-0.0812-0.03470.3345-0.08780.10650.1564-0.0582-0.02730.1010.0280.30719.0303-17.272628.4987
43.721-1.4003-1.2034.11420.68725.43470.0101-0.5145-0.34250.53090.042-0.1720.36890.33680.18370.1599-0.0163-0.06730.16550.0330.246215.3995-12.15138.6767
50.8565-0.1177-0.12140.0426-0.00390.1044-0.00420.0634-0.1455-0.045-0.04810.0805-0.0101-0.19340.05620.07150.04390.01480.4149-0.10880.134512.437-0.4633-2.9307
60.30090.10310.32940.38950.17541.0972-0.01180.0894-0.01620.02040.0219-0.0123-0.0822-0.07990.07260.09420.0169-0.00040.2709-0.08040.068424.21273.1815-0.1126
71.62370.49921.11231.01130.06911.5029-0.09940.10470.14370.098-0.04520.0366-0.1864-0.0090.13160.1329-0.0165-0.03670.1715-0.08890.11236.510911.9699.9595
81.79310.29420.83212.6905-1.35862.8059-0.0857-0.28660.3190.5607-0.1393-0.1352-0.3267-0.27620.15830.3220.052-0.04660.2402-0.06420.224335.373614.992717.8784
92.81160.55772.24333.0530.02776.5942-0.2234-0.1560.51030.39580.0074-0.0259-0.21530.08220.3580.25150.0093-0.09010.2074-0.08870.276740.296420.733414.0141
103.33130.3221.00023.298-0.76162.9581-0.23870.54370.3362-0.35350.0156-0.0816-0.24040.27280.12630.1723-0.0799-0.01540.39640.01120.149837.454913.8228-0.4606
111.1983-0.0067-0.72570.9256-0.64381.905-0.06550.1475-0.349-0.07440.0123-0.05430.42120.2126-0.01210.14420.0991-0.01530.2705-0.11860.179636.0326-14.07377.6501
122.0935-0.678-0.48274.65970.13393.4545-0.19430.526-0.9175-0.4990.0646-0.450.93180.48920.53080.5970.1278-0.04070.3614-0.20320.572733.4081-24.69573.903
130.55440.47050.20042.3243-0.51473.2063-0.01910.278-0.1957-0.46520.0981-0.05630.43280.02650.5510.21190.0466-0.06220.3115-0.15790.196428.6314-12.3261-3.3422
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 2:111)
2X-RAY DIFFRACTION2chain 'A' and (resseq 112:197)
3X-RAY DIFFRACTION3chain 'A' and (resseq 198:273)
4X-RAY DIFFRACTION4chain 'A' and (resseq 274:296)
5X-RAY DIFFRACTION5chain 'B' and (resseq 2:67)
6X-RAY DIFFRACTION6chain 'B' and (resseq 68:111)
7X-RAY DIFFRACTION7chain 'B' and (resseq 112:134)
8X-RAY DIFFRACTION8chain 'B' and (resseq 135:164)
9X-RAY DIFFRACTION9chain 'B' and (resseq 165:179)
10X-RAY DIFFRACTION10chain 'B' and (resseq 180:197)
11X-RAY DIFFRACTION11chain 'B' and (resseq 198:251)
12X-RAY DIFFRACTION12chain 'B' and (resseq 252:273)
13X-RAY DIFFRACTION13chain 'B' and (resseq 274:296)

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