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- PDB-3u8z: human merlin FERM domain -

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Basic information

Entry
Database: PDB / ID: 3u8z
Titlehuman merlin FERM domain
ComponentsMerlin
KeywordsSIGNALING PROTEIN / neurofibromatosis / tumor suppressor
Function / homology
Function and homology information


regulation of hippo signaling / regulation of organelle assembly / regulation of gliogenesis / positive regulation of early endosome to late endosome transport / Schwann cell proliferation / osteoblast proliferation / negative regulation of Schwann cell proliferation / negative regulation of osteoblast proliferation / negative regulation of tyrosine phosphorylation of STAT protein / ectoderm development ...regulation of hippo signaling / regulation of organelle assembly / regulation of gliogenesis / positive regulation of early endosome to late endosome transport / Schwann cell proliferation / osteoblast proliferation / negative regulation of Schwann cell proliferation / negative regulation of osteoblast proliferation / negative regulation of tyrosine phosphorylation of STAT protein / ectoderm development / lens fiber cell differentiation / positive regulation of protein localization to early endosome / regulation of neural precursor cell proliferation / regulation of stem cell proliferation / negative regulation of receptor signaling pathway via JAK-STAT / cell-cell junction organization / filopodium membrane / regulation of protein localization to nucleus / negative regulation of cell-matrix adhesion / cortical actin cytoskeleton / negative regulation of MAPK cascade / negative regulation of cell-cell adhesion / odontogenesis of dentin-containing tooth / RHO GTPases activate PAKs / cleavage furrow / mesoderm formation / positive regulation of stress fiber assembly / negative regulation of cell migration / filopodium / hippocampus development / positive regulation of cell differentiation / adherens junction / regulation of protein stability / Regulation of actin dynamics for phagocytic cup formation / ruffle membrane / MAPK cascade / integrin binding / apical part of cell / lamellipodium / cell body / actin binding / regulation of cell shape / actin cytoskeleton organization / regulation of apoptotic process / cytoskeleton / early endosome / regulation of cell cycle / neuron projection / negative regulation of cell population proliferation / nucleolus / perinuclear region of cytoplasm / membrane / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Acyl-CoA Binding Protein - #60 / 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 / Acyl-CoA Binding Protein - #10 / Ezrin/radixin/moesin-like ...Acyl-CoA Binding Protein - #60 / 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 / Acyl-CoA Binding Protein - #10 / Ezrin/radixin/moesin-like / Acyl-CoA Binding Protein / 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) / FERM central domain / PH-domain like / 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 / 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: 2.64 Å
AuthorsYogesha, S.D. / Sharff, A.J. / Giovannini, M. / Bricogne, G. / Izard, T.
CitationJournal: Protein Sci. / Year: 2011
Title: Unfurling of the band 4.1, ezrin, radixin, moesin (FERM) domain of the merlin tumor suppressor.
Authors: Yogesha, S.D. / Sharff, A.J. / Giovannini, M. / Bricogne, G. / Izard, T.
History
DepositionOct 17, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2011Group: Database references / Derived calculations ...Database references / Derived calculations / Experimental preparation / Source and taxonomy / Structure summary
Revision 1.2Nov 30, 2011Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Sep 13, 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 / software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name / _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: Merlin
B: Merlin
C: Merlin
D: Merlin


Theoretical massNumber of molelcules
Total (without water)141,7764
Polymers141,7764
Non-polymers00
Water9,674537
1
A: Merlin
C: Merlin


Theoretical massNumber of molelcules
Total (without water)70,8882
Polymers70,8882
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5580 Å2
ΔGint-19.2 kcal/mol
Surface area26660 Å2
MethodPISA
2
B: Merlin
D: Merlin


Theoretical massNumber of molelcules
Total (without water)70,8882
Polymers70,8882
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3360 Å2
ΔGint-12.3 kcal/mol
Surface area26350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.446, 105.446, 329.997
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein
Merlin / / Moesin-ezrin-radixin-like protein / Neurofibromin-2 / Schwannomerlin / Schwannomin


Mass: 35443.957 Da / Num. of mol.: 4 / Fragment: FERM domain (UNP residues 20-312)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NF2, SCH / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL / References: UniProt: P35240
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 537 / 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: 3.28 Å3/Da / Density % sol: 62.45 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: protein in 50 mM Tris, pH 8.0, 300 mM sodium chloride, reservoir: 4.5% PEG4000, 0.2 M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.99999 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 16, 2008
RadiationMonochromator: Kohzu Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 2.64→105.45 Å / Num. all: 55821 / Num. obs: 52570 / % possible obs: 95.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.2 % / Biso Wilson estimate: 65.13 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 19.9
Reflection shellResolution: 2.64→2.78 Å / Redundancy: 2 % / Rmerge(I) obs: 0.377 / Mean I/σ(I) obs: 1.9 / Num. unique all: 6182 / % possible all: 79.7

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Processing

Software
NameVersionClassification
MD2data collection
PHASERphasing
BUSTER2.13.0refinement
autoPROCdata scaling
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1H4R

1h4r


Resolution: 2.64→26.36 Å / Cor.coef. Fo:Fc: 0.9246 / Cor.coef. Fo:Fc free: 0.903 / SU R Cruickshank DPI: 0.403 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.443 / SU Rfree Blow DPI: 0.26 / SU Rfree Cruickshank DPI: 0.256 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2294 2666 5.08 %RANDOM
Rwork0.2003 ---
all0.2017 55821 --
obs0.2017 52476 94.14 %-
Displacement parametersBiso mean: 64.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.6162 Å20 Å20 Å2
2--0.6162 Å20 Å2
3----1.2324 Å2
Refine analyzeLuzzati coordinate error obs: 0.353 Å
Refinement stepCycle: LAST / Resolution: 2.64→26.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8540 0 0 537 9077
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d4132SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes223HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1246HARMONIC5
X-RAY DIFFRACTIONt_it8736HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1099SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact9706SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d8736HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg11757HARMONIC20.87
X-RAY DIFFRACTIONt_omega_torsion5.91
X-RAY DIFFRACTIONt_other_torsion3.03
LS refinement shellResolution: 2.64→2.71 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2703 128 4.65 %
Rwork0.234 2626 -
all0.2356 2754 -
obs-2754 94.14 %
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)
10.8179-0.37360.44291.0991-0.66211.5243-0.0120.0672-0.1069-0.07330.02580.03480.0614-0.0665-0.0138-0.16280.03170.0027-0.0116-0.0592-0.06083.630617.7124-24.4327
22.48110.70750.78441.91840.91332.1727-0.06260.4587-0.5881-0.09050.1295-0.20580.19140.4747-0.0669-0.26490.02570.023-0.0594-0.0251-0.1372-4.689915.689-57.242
31.611-0.64790.86471.5437-0.87031.4660.11590.2791-0.1976-0.0611-0.1188-0.21110.2870.29450.0029-0.13960.1248-0.0085-0.0837-0.1101-0.072423.6601-4.0069-9.993
43.42560.33210.16524.7911.5582.1127-0.0899-0.1928-0.25680.3211-0.31570.63170.3369-0.38040.4056-0.1971-0.23190.0854-0.268-0.1689-0.05-28.9615-9.9213-69.5178
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A20 - 312
2X-RAY DIFFRACTION2{ B|* }B20 - 312
3X-RAY DIFFRACTION3{ C|* }C20 - 312
4X-RAY DIFFRACTION4{ D|* }D20 - 312

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