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- PDB-3wa0: Crystal structure of merlin complexed with DCAF1/VprBP -

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Basic information

Entry
Database: PDB / ID: 3wa0
TitleCrystal structure of merlin complexed with DCAF1/VprBP
Components
  • (Protein VPRBP) x 4
  • Merlin
KeywordsCELL ADHESION / merlin FERM domain
Function / homology
Function and homology information


regulation of hippo signaling / RHO GTPases activate PAKs / cell competition in a multicellular organism / Schwann cell proliferation / regulation of gliogenesis / osteoblast proliferation / negative regulation of Schwann cell proliferation / negative regulation of osteoblast proliferation / Regulation of actin dynamics for phagocytic cup formation / ectoderm development ...regulation of hippo signaling / RHO GTPases activate PAKs / cell competition in a multicellular organism / Schwann cell proliferation / regulation of gliogenesis / osteoblast proliferation / negative regulation of Schwann cell proliferation / negative regulation of osteoblast proliferation / Regulation of actin dynamics for phagocytic cup formation / ectoderm development / lens fiber cell differentiation / regulation of neural precursor cell proliferation / regulation of stem cell proliferation / negative regulation of receptor signaling pathway via JAK-STAT / V(D)J recombination / cell-cell junction organization / regulation of protein localization to nucleus / Cul4-RING E3 ubiquitin ligase complex / negative regulation of cell-cell adhesion / cortical actin cytoskeleton / odontogenesis of dentin-containing tooth / cleavage furrow / mesoderm formation / regulation of neurogenesis / negative regulation of MAPK cascade / ubiquitin-like ligase-substrate adaptor activity / positive regulation of stress fiber assembly / ruffle / post-translational protein modification / B cell differentiation / hippocampus development / nuclear estrogen receptor binding / filopodium / adherens junction / positive regulation of cell differentiation / brain development / regulation of protein stability / fibrillar center / positive regulation of protein catabolic process / apical part of cell / MAPK cascade / Antigen processing: Ubiquitination & Proteasome degradation / lamellipodium / regulation of cell population proliferation / actin binding / cell body / actin cytoskeleton organization / regulation of apoptotic process / proteasome-mediated ubiquitin-dependent protein catabolic process / eukaryotic translation initiation factor 2alpha kinase activity / cytoskeleton / early endosome / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / regulation of cell cycle / neuron projection / protein ubiquitination / negative regulation of cell population proliferation / protein serine kinase activity / centrosome / nucleolus / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
VPRBP/DCAF1 family / 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 / Acyl-CoA Binding Protein - #10 / Ezrin/radixin/moesin-like ...VPRBP/DCAF1 family / 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 / Acyl-CoA Binding Protein - #10 / Ezrin/radixin/moesin-like / Lissencephaly type-1-like homology motif / 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 / LIS1 homology (LisH) motif profile. / LIS1 homology motif / 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 / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / PH-domain like / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Armadillo-like helical / PH-like domain superfamily / Armadillo-type fold / Ubiquitin-like domain superfamily / Roll / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Roll / Up-down Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Merlin / DDB1- and CUL4-associated factor 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å
AuthorsMori, T. / Gotoh, S. / Shirakawa, M. / Hakoshima, T.
CitationJournal: Genes Cells / Year: 2014
Title: Structural basis of DDB1-and-Cullin 4-associated Factor 1 (DCAF1) recognition by merlin/NF2 and its implication in tumorigenesis by CD44-mediated inhibition of merlin suppression of DCAF1 function.
Authors: Mori, T. / Gotoh, S. / Shirakawa, M. / Hakoshima, T.
History
DepositionApr 20, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 28, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 25, 2014Group: Database references / Structure summary
Revision 1.2Aug 24, 2022Group: Database references / Category: citation / database_2 / struct_ref_seq_dif
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
E: Merlin
F: Merlin
G: Protein VPRBP
H: Protein VPRBP
I: Protein VPRBP
J: Protein VPRBP
K: Protein VPRBP


Theoretical massNumber of molelcules
Total (without water)235,92211
Polymers235,92211
Non-polymers00
Water9,782543
1
A: Merlin
G: Protein VPRBP


Theoretical massNumber of molelcules
Total (without water)46,0042
Polymers46,0042
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Merlin
H: Protein VPRBP


Theoretical massNumber of molelcules
Total (without water)46,0042
Polymers46,0042
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Merlin
I: Protein VPRBP


Theoretical massNumber of molelcules
Total (without water)36,1322
Polymers36,1322
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Merlin


Theoretical massNumber of molelcules
Total (without water)35,5181
Polymers35,5181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Merlin
J: Protein VPRBP


Theoretical massNumber of molelcules
Total (without water)36,2172
Polymers36,2172
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Merlin
K: Protein VPRBP


Theoretical massNumber of molelcules
Total (without water)36,0472
Polymers36,0472
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.363, 135.760, 238.495
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 8 molecules ABCDEFGH

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


Mass: 35517.992 Da / Num. of mol.: 6 / Fragment: UNP residues 19-314
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: DH5a / Gene: Nf2 / Plasmid: pGEX-6P3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21Star(DE3) / References: UniProt: P46662
#2: Protein Protein VPRBP / DDB1- and CUL4-associated factor 1 / HIV-1 Vpr-binding protein / VprBP / Vpr-interacting protein


Mass: 10486.212 Da / Num. of mol.: 2 / Fragment: UNP residues 1417-1506
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Strain: DH5a / Gene: DCAF1 / Plasmid: pGEX-6P3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21Star(DE3) / References: UniProt: Q9Y4B6

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Protein/peptide , 3 types, 3 molecules IJK

#3: Protein/peptide Protein VPRBP


Mass: 613.749 Da / Num. of mol.: 1 / Fragment: UNP residues 1417-1506
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Strain: DH5a / Gene: DCAF1 / Plasmid: pGEX-6P3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21Star(DE3)
#4: Protein/peptide Protein VPRBP


Mass: 698.854 Da / Num. of mol.: 1 / Fragment: UNP residues 1417-1506
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Strain: DH5a / Gene: DCAF1 / Plasmid: pGEX-6P3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21Star(DE3)
#5: Protein/peptide Protein VPRBP


Mass: 528.644 Da / Num. of mol.: 1 / Fragment: UNP residues 1417-1506
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Strain: DH5a / Gene: DCAF1 / Plasmid: pGEX-6P3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21Star(DE3)

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Non-polymers , 1 types, 543 molecules

#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 543 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsSEQUENCE OF CHAIN G,H,I,J,K CORRESPONDS TO ISOFORM 2, Q9Y4B6-2. THE DEPOSITORS BELIEVE THAT CHAIN ...SEQUENCE OF CHAIN G,H,I,J,K CORRESPONDS TO ISOFORM 2, Q9Y4B6-2. THE DEPOSITORS BELIEVE THAT CHAIN I,J,K HAVE THE SAME SEQUENCE OF CHAIN G, H. BUT THEY COULD NOT ASSIGN TO A SPECIFIC SECTION OF THE SEQUENCE.

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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: 2.93 Å3/Da / Density % sol: 58 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: 0.2M ammonium fluoride, 23% PEG 3350, pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorDate: Jun 21, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→20.07 Å / Num. obs: 120906 / % possible obs: 99.7 %

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ISN

1isn


Resolution: 2.31→20.07 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.924 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / ESU R: 0.299 / ESU R Free: 0.228 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2638 6089 5 %RANDOM
Rwork0.2354 ---
obs0.2368 114487 98.77 %-
all-120906 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 143.79 Å2 / Biso mean: 60.9055 Å2 / Biso min: 21.6 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2--0.03 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.31→20.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14830 0 0 543 15373
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01915178
X-RAY DIFFRACTIONr_bond_other_d00.0214601
X-RAY DIFFRACTIONr_angle_refined_deg0.9981.9620485
X-RAY DIFFRACTIONr_angle_other_deg3.456333635
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.23751782
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.23524.19747
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.1152815
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9691589
X-RAY DIFFRACTIONr_chiral_restr0.0720.22213
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216787
X-RAY DIFFRACTIONr_gen_planes_other0.0030.023522
LS refinement shellResolution: 2.31→2.369 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 441 -
Rwork0.303 7723 -
all-8164 -
obs--92.71 %

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