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- PDB-4rm8: Crystal structure of human ezrin in space group P21 -

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Basic information

Entry
Database: PDB / ID: 4rm8
TitleCrystal structure of human ezrin in space group P21
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: 1.9 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 20, 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
B: Ezrin


Theoretical massNumber of molelcules
Total (without water)139,1682
Polymers139,1682
Non-polymers00
Water10,160564
1
A: Ezrin


Theoretical massNumber of molelcules
Total (without water)69,5841
Polymers69,5841
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ezrin


Theoretical massNumber of molelcules
Total (without water)69,5841
Polymers69,5841
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.007, 111.808, 68.384
Angle α, β, γ (deg.)90.00, 113.01, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 69583.969 Da / Num. of mol.: 2
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.: 564 / 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: 1.64 Å3/Da / Density % sol: 25.17 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.9
Details: 0.1M Bis-Tris pH 5.9, 15% 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 30, 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: 1.9→40.85 Å / Num. obs: 67737 / % possible obs: 95.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -4 / Redundancy: 3.6 % / Biso Wilson estimate: 24.4 Å2 / Rmerge(I) obs: 0.112 / Rsym value: 0.112 / Net I/σ(I): 7.1
Reflection shellResolution: 1.9→2 Å / Redundancy: 2 % / Rmerge(I) obs: 0.342 / Mean I/σ(I) obs: 2 / Num. unique all: 9410 / Rsym value: 0.342 / % possible all: 92

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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: 1.9→39.403 Å / SU ML: 0.28 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 21.41 / Stereochemistry target values: ML
Details: AUTHORS DO NOT OBSERVE RESIDUES 295-514 (THE ALPHA-HELICAL DOMAIN) IN THE CRYSTAL STRUCTURE. THEY SUSPECT LIMITED PROTEOLYSIS DURING CRYSTALLISATION
RfactorNum. reflection% reflectionSelection details
Rfree0.218 3430 5.07 %RANDOM
Rwork0.1807 ---
all0.1826 67702 --
obs0.1826 67702 95.75 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.725 Å2 / ksol: 0.319 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.2102 Å2-0 Å20.7326 Å2
2---5.395 Å2-0 Å2
3---2.1848 Å2
Refinement stepCycle: LAST / Resolution: 1.9→39.403 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6144 0 0 564 6708
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056330
X-RAY DIFFRACTIONf_angle_d0.8948521
X-RAY DIFFRACTIONf_dihedral_angle_d13.6752481
X-RAY DIFFRACTIONf_chiral_restr0.066897
X-RAY DIFFRACTIONf_plane_restr0.0031110
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.96790.33273240.27686122X-RAY DIFFRACTION92
1.9679-2.04670.27033290.20996122X-RAY DIFFRACTION91
2.0467-2.13990.24243420.19516046X-RAY DIFFRACTION91
2.1399-2.25270.22753190.1816041X-RAY DIFFRACTION90
2.2527-2.39380.24523260.19216446X-RAY DIFFRACTION96
2.3938-2.57860.24363510.19136704X-RAY DIFFRACTION100
2.5786-2.8380.23583680.18366712X-RAY DIFFRACTION100
2.838-3.24850.23573590.18816692X-RAY DIFFRACTION100
3.2485-4.09210.19063540.17026707X-RAY DIFFRACTION99
4.0921-39.4110.17953580.15796680X-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)
11.4802-0.09330.03771.90631.95812.2330.20050.06320.3232-0.2205-0.18050.0463-0.4488-0.1276-0.04020.34820.03730.02220.1016-0.00050.12321.514342.576911.9242
21.185-0.838-0.27562.3585-0.71141.2037-0.0631-0.09830.15840.2554-0.0283-0.4127-0.31950.08220.10630.2604-0.02-0.09820.1269-0.03340.203133.76618.229522.9778
31.2024-0.29560.40791.84780.20421.992-0.05810.1316-0.0158-0.289-0.03930.4081-0.3073-0.39250.10450.24780.0692-0.14940.2167-0.04210.2586.470921.1088.0997
40.4831-0.5033-0.26640.68910.68921.1683-0.08060.044-0.19040.0309-0.0928-0.20030.31650.05250.05520.25020.0156-0.0580.1513-0.03630.264231.1294.877420.0642
51.1196-1.6696-0.23124.1312-1.16161.4374-0.3085-0.3649-0.39380.87830.21470.39510.2881-0.26890.09210.29960.07010.05570.22170.02830.258316.4995.887628.9678
61.6343-1.25470.73041.34730.12092.5967-0.00140.5181-0.6061-0.51060.08080.60830.138-0.0043-0.11580.3328-0.0103-0.0290.2033-0.07350.305514.42436.546610.1315
73.62360.93362.54380.31170.46012.7785-0.18010.3346-0.7023-0.57470.03460.3220.3266-0.49350.0970.315-0.0856-0.20010.3361-0.05530.5542-1.08289.41847.5843
82.3561-0.738-1.06571.20981.29523.8662-0.16310.1389-0.51970.3181-0.07310.25030.7484-0.30180.24350.2464-0.03010.06550.1063-0.0210.27725.36214.866145.662
91.862-0.31950.8391.3930.19822.6569-0.00450.1517-0.07780.19850.0014-0.19760.05170.49110.0050.11690.021-0.03340.22530.00090.144625.072935.083348.6969
101.1212-0.35270.31772.2161-0.171.9534-0.08290.1259-0.1513-0.10370.00170.41280.062-0.1670.07010.0708-0.0172-0.02750.1728-0.03390.2648-4.398937.064638.2239
113.4259-0.17950.20091.03060.00370.788-0.1239-0.26190.89170.42150.1186-0.0149-0.37350.25950.07640.254-0.0743-0.04650.20810.02840.258321.5549.059849.5302
121.00230.1525-0.49510.95510.34921.7620.06060.37670.0216-0.4819-0.0632-0.2707-0.47610.3750.02560.1823-0.0710.02280.24120.04880.120719.16549.225832.9716
133.1945-0.88751.9040.7752-0.40912.1044-0.1362-0.19060.28280.0169-0.04260.0176-0.0039-0.18490.18080.16840.00430.01370.14460.00040.20564.101250.185643.7728
143.72951.8971-2.53860.9655-1.325.10510.0753-0.14980.7308-0.28760.12520.819-0.7447-0.3180.16160.18510.0605-0.15880.19590.05690.4093-8.222149.667633.7954
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:85 )A1 - 85
2X-RAY DIFFRACTION2( CHAIN A AND RESID 86:200 )A86 - 200
3X-RAY DIFFRACTION3( CHAIN A AND RESID 201:297 )A201 - 297
4X-RAY DIFFRACTION4( CHAIN A AND RESID 516:542 )A516 - 542
5X-RAY DIFFRACTION5( CHAIN A AND RESID 543:562 )A543 - 562
6X-RAY DIFFRACTION6( CHAIN A AND RESID 563:573 )A563 - 573
7X-RAY DIFFRACTION7( CHAIN A AND RESID 574:586 )A574 - 586
8X-RAY DIFFRACTION8( CHAIN B AND RESID 3:85 )B3 - 85
9X-RAY DIFFRACTION9( CHAIN B AND RESID 86:200 )B86 - 200
10X-RAY DIFFRACTION10( CHAIN B AND RESID 201:297 )B201 - 297
11X-RAY DIFFRACTION11( CHAIN B AND RESID 515:542 )B515 - 542
12X-RAY DIFFRACTION12( CHAIN B AND RESID 543:562 )B543 - 562
13X-RAY DIFFRACTION13( CHAIN B AND RESID 563:573 )B563 - 573
14X-RAY DIFFRACTION14( CHAIN B AND RESID 574:586 )B574 - 586

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