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- PDB-7edr: The crystal structure of the FERM and C-terminal domain complex o... -

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Basic information

Entry
Database: PDB / ID: 7edr
TitleThe crystal structure of the FERM and C-terminal domain complex of Drosophila Merlin
Components(Moesin/ezrin/radixin homolog 2) x 2
KeywordsPROTEIN BINDING / NF2/Merlin / close conformation / lipid binding / membrane localization
Function / homology
Function and homology information


Nebenkern / Kibra-Ex-Mer complex / regulation of compound eye retinal cell programmed cell death / axis specification / apicomedial cortex / subapical part of cell / RHO GTPases activate PAKs / male meiosis cytokinesis / R8 cell fate specification / cytoplasmic side of apical plasma membrane ...Nebenkern / Kibra-Ex-Mer complex / regulation of compound eye retinal cell programmed cell death / axis specification / apicomedial cortex / subapical part of cell / RHO GTPases activate PAKs / male meiosis cytokinesis / R8 cell fate specification / cytoplasmic side of apical plasma membrane / pole plasm mRNA localization / compound eye photoreceptor cell differentiation / Regulation of actin dynamics for phagocytic cup formation / compound eye morphogenesis / meiotic chromosome separation / sperm individualization / epithelial structure maintenance / positive regulation of hippo signaling / positive regulation of cell-cell adhesion / negative regulation of organ growth / hippo signaling / endocytic recycling / negative regulation of glial cell proliferation / regulation of cell differentiation / regulation of signal transduction / protein localization to plasma membrane / regulation of cell growth / adherens junction / endocytosis / apical part of cell / cell-cell signaling / actin binding / regulation of cell population proliferation / cell cortex / spermatogenesis / cytoskeleton / positive regulation of protein phosphorylation / positive regulation of apoptotic process / apical plasma membrane / negative regulation of cell population proliferation / identical protein binding / membrane / plasma membrane / 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 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 ...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 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 / PH-like domain superfamily / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Moesin/ezrin/radixin homolog 2
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.527 Å
AuthorsZhang, F. / Long, J. / Zhou, H.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31870750 China
National Natural Science Foundation of China (NSFC)31670758 China
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2021
Title: The crystal structure of the FERM and C-terminal domain complex of Drosophila Merlin.
Authors: Zhang, F. / Liu, B. / Gao, Y. / Long, J. / Zhou, H.
History
DepositionMar 16, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 14, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Moesin/ezrin/radixin homolog 2
C: Moesin/ezrin/radixin homolog 2
B: Moesin/ezrin/radixin homolog 2
D: Moesin/ezrin/radixin homolog 2


Theoretical massNumber of molelcules
Total (without water)101,5524
Polymers101,5524
Non-polymers00
Water6,918384
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12470 Å2
ΔGint-69 kcal/mol
Surface area43730 Å2
Unit cell
Length a, b, c (Å)86.464, 100.366, 163.593
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11D-726-

HOH

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Components

#1: Protein Moesin/ezrin/radixin homolog 2 / Ezrin-moesin-radixin 2 / Merlin / dMerlin


Mass: 36555.598 Da / Num. of mol.: 2 / Fragment: UNP residues 8-314
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Mer, EMR2, CG14228 / Production host: Escherichia coli (E. coli) / References: UniProt: Q24564
#2: Protein Moesin/ezrin/radixin homolog 2 / Ezrin-moesin-radixin 2 / Merlin / dMerlin


Mass: 14220.535 Da / Num. of mol.: 2 / Fragment: UNP residues 510-635
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Mer, EMR2, CG14228 / Production host: Escherichia coli (E. coli) / References: UniProt: Q24564
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 384 / 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: 3.5 Å3/Da / Density % sol: 64.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Sodium cacodylate/Hydrochloric acid, pH 6.5, 1.0 M sodium citrate tribasic

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9778 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 2.527→50 Å / Num. obs: 48350 / % possible obs: 100 % / Redundancy: 6.4 % / Rpim(I) all: 0.047 / Net I/σ(I): 14.2
Reflection shellResolution: 2.53→2.57 Å / Num. unique obs: 2354 / CC1/2: 0.892

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZRJ

4zrj


Resolution: 2.527→47.976 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.235 2265 4.91 %
Rwork0.1841 43871 -
obs0.1866 46136 95.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 95.05 Å2 / Biso mean: 39.0684 Å2 / Biso min: 12.72 Å2
Refinement stepCycle: final / Resolution: 2.527→47.976 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6997 0 0 384 7381
Biso mean---37.87 -
Num. residues----849
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097145
X-RAY DIFFRACTIONf_angle_d0.9339642
X-RAY DIFFRACTIONf_chiral_restr0.0521040
X-RAY DIFFRACTIONf_plane_restr0.0051243
X-RAY DIFFRACTIONf_dihedral_angle_d17.2824320
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5275-2.58240.24471070.2315191868
2.5824-2.64250.31131210.2372228580
2.6425-2.70860.28191300.2287247187
2.7086-2.78180.3231430.2374264993
2.7818-2.86360.30971310.236280498
2.8636-2.9560.29741350.23472843100
2.956-3.06170.28081610.23632815100
3.0617-3.18420.26721280.21462879100
3.1842-3.32910.23931570.20182860100
3.3291-3.50460.25481610.18442831100
3.5046-3.72410.23411260.17072887100
3.7241-4.01150.20661420.1542884100
4.0115-4.41490.19221440.14612900100
4.4149-5.05320.18151510.13722901100
5.0532-6.36420.24561650.17582911100
6.3642-47.9760.18651630.1717303398

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