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- PDB-4p7i: Crystal structure of the Merlin FERM/DCAF1 complex -

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Basic information

Entry
Database: PDB / ID: 4p7i
TitleCrystal structure of the Merlin FERM/DCAF1 complex
Components
  • Merlin
  • Protein VPRBP
KeywordsSignaling Protein/Protein Binding / Signaling Protein-Protein Binding complex
Function / homology
Function and homology information


regulation of hippo signaling / regulation of neural precursor cell proliferation / RHO GTPases activate PAKs / regulation of organelle assembly / ectoderm development / cell competition in a multicellular organism / histone H2AT120 kinase activity / regulation of stem cell proliferation / positive regulation of early endosome to late endosome transport / Schwann cell proliferation ...regulation of hippo signaling / regulation of neural precursor cell proliferation / RHO GTPases activate PAKs / regulation of organelle assembly / ectoderm development / cell competition in a multicellular organism / histone H2AT120 kinase activity / regulation of stem cell proliferation / positive regulation of early endosome to late endosome transport / Schwann cell proliferation / regulation of gliogenesis / lens fiber cell differentiation / Regulation of actin dynamics for phagocytic cup formation / positive regulation of protein localization to early endosome / V(D)J recombination / cell-cell junction organization / negative regulation of receptor signaling pathway via JAK-STAT / regulation of protein localization to nucleus / odontogenesis of dentin-containing tooth / negative regulation of cell-cell adhesion / mesoderm formation / cortical actin cytoskeleton / Cul4-RING E3 ubiquitin ligase complex / cleavage furrow / regulation of neurogenesis / positive regulation of stress fiber assembly / ubiquitin-like ligase-substrate adaptor activity / negative regulation of MAPK cascade / ruffle / B cell differentiation / post-translational protein modification / nuclear estrogen receptor binding / hippocampus development / brain development / filopodium / adherens junction / positive regulation of cell differentiation / regulation of protein stability / negative regulation of cell growth / beta-catenin binding / integrin binding / fibrillar center / apical part of cell / positive regulation of protein catabolic process / regulation of cell population proliferation / regulation of cell shape / lamellipodium / Antigen processing: Ubiquitination & Proteasome degradation / actin cytoskeleton organization / actin binding / cell body / regulation of apoptotic process / early endosome / cytoskeleton / proteasome-mediated ubiquitin-dependent protein catabolic process / non-specific serine/threonine protein kinase / regulation of cell cycle / neuron projection / protein ubiquitination / negative regulation of cell population proliferation / protein domain specific binding / protein serine kinase activity / centrosome / nucleolus / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / protein-containing complex / DNA-templated transcription / nucleoplasm / ATP binding / nucleus / 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 / VPRBP/DCAF1 family / DCAF1 helical domain / DCAF1 fourth 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 / VPRBP/DCAF1 family / DCAF1 helical domain / DCAF1 fourth domain / Mahjong helical domain / DCAF1 N-terminal domain / Acyl-CoA Binding Protein - #10 / Acyl-CoA Binding Protein / Ezrin/radixin/moesin-like / Lissencephaly type-1-like homology motif / 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) / PH-domain like / 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) / Armadillo-like helical / PH-like domain superfamily / Armadillo-type fold / Roll / Ubiquitin-like domain superfamily / 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 / molecular replacement / Resolution: 2.6 Å
AuthorsWei, Z. / Li, Y. / Zhang, M.
Funding support Hong Kong, 1items
OrganizationGrant numberCountry
RGC of Hong Kong663610, 663811, 663812, HKUST6/CRF/10, SEG_HKUST06, AoE/M09/12, and T13-607/12R Hong Kong
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Structural basis of the binding of Merlin FERM domain to the E3 ubiquitin ligase substrate adaptor DCAF1.
Authors: Li, Y. / Wei, Z. / Zhang, J. / Yang, Z. / Zhang, M.
History
DepositionMar 27, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 9, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 23, 2014Group: Database references
Revision 1.2May 21, 2014Group: Data collection
Revision 1.3Oct 1, 2014Group: Database references
Revision 1.4Nov 22, 2017Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation
Revision 1.5Sep 27, 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 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Merlin
B: Merlin
C: Protein VPRBP
D: Protein VPRBP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,9425
Polymers88,8504
Non-polymers921
Water55831
1
A: Merlin
C: Protein VPRBP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5173
Polymers44,4252
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint-8 kcal/mol
Surface area16450 Å2
MethodPISA
2
B: Merlin
D: Protein VPRBP


Theoretical massNumber of molelcules
Total (without water)44,4252
Polymers44,4252
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area860 Å2
ΔGint-7 kcal/mol
Surface area16070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.104, 97.104, 224.339
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

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


Mass: 37245.086 Da / Num. of mol.: 2 / Fragment: FERM domain residues 1-313
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Nf2, Nf-2 / Plasmid: modified pET32a / Production host: Escherichia coli (E. coli) / Strain (production host): DE3 / References: UniProt: P46662
#2: Protein Protein VPRBP / DDB1- and CUL4-associated factor 1 / HIV-1 Vpr-binding protein / VprBP / Serine/threonine-protein ...DDB1- and CUL4-associated factor 1 / HIV-1 Vpr-binding protein / VprBP / Serine/threonine-protein kinase VPRBP / Vpr-interacting protein


Mass: 7180.022 Da / Num. of mol.: 2 / Fragment: UNP residues 998-1058
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VPRBP, DCAF1, KIAA0800, RIP / Plasmid: modified pET32a / Production host: Escherichia coli (E. coli) / Strain (production host): DE3
References: UniProt: Q9Y4B6, non-specific serine/threonine protein kinase
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 3.44 Å3/Da / Density % sol: 64.21 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 20% Isopropanol and 5% PEG8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 37859 / % possible obs: 98.2 % / Redundancy: 4.6 % / Biso Wilson estimate: 70.28 Å2 / Rmerge(I) obs: 0.079 / Χ2: 2.196 / Net I/av σ(I): 31.007 / Net I/σ(I): 13 / Num. measured all: 175045
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.6-2.644.80.92519131.38799.9
2.64-2.694.80.83618901.56999.8
2.69-2.744.80.81418741.41899.8
2.74-2.84.90.50418981.48699.9
2.8-2.864.80.4119011.57699.9
2.86-2.934.80.37518891.49999.9
2.93-34.80.32918911.57599.8
3-3.084.80.27218951.5799.8
3.08-3.174.80.19119121.82199.8
3.17-3.284.70.14719011.96399.7
3.28-3.394.70.12118892.15999.4
3.39-3.534.60.10419012.37399
3.53-3.694.50.08118922.46298.2
3.69-3.884.40.07318402.72394.7
3.88-4.134.60.06418982.84699.6
4.13-4.454.60.05719423.03799.2
4.45-4.894.40.05219423.17599.6
4.89-5.64.40.05219523.28199.7
5.6-7.054.30.05119843.32799.3
7.05-503.70.04816553.66378

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Blu-Icedata collection
HKL-2000data scaling
PDB_EXTRACT3.14data extraction
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ISN

1isn


Resolution: 2.6→31.47 Å / FOM work R set: 0.7848 / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2562 1880 4.98 %Random selection
Rwork0.2242 35837 --
obs0.2258 37717 97.9 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 213.67 Å2 / Biso mean: 96.18 Å2 / Biso min: 32.83 Å2
Refinement stepCycle: final / Resolution: 2.6→31.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5070 0 6 31 5107
Biso mean--74.92 60.75 -
Num. residues----608
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035191
X-RAY DIFFRACTIONf_angle_d0.6746998
X-RAY DIFFRACTIONf_chiral_restr0.049759
X-RAY DIFFRACTIONf_plane_restr0.003882
X-RAY DIFFRACTIONf_dihedral_angle_d12.171970
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6-2.67010.36711460.32022726287299
2.6701-2.74860.34981400.31942738287899
2.7486-2.83720.34311460.272727602906100
2.8372-2.93860.26921470.254727972944100
2.9386-3.05610.28641440.272730287499
3.0561-3.19510.28391430.256327842927100
3.1951-3.36340.24041440.22782760290499
3.3634-3.57380.27081460.22462775292199
3.5738-3.84930.26791440.21782678282296
3.8493-4.23590.22961490.20272814296399
4.2359-4.84690.2191500.18972812296299
4.8469-6.09930.26411500.212928693019100
6.0993-31.47270.24731310.23122594272586
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)
11.8171-0.2772-0.03811.92940.24720.36690.0136-0.2559-0.23190.3742-0.0212-0.22010.01070.05490.18530.7572-0.3958-0.06030.3275-0.00540.5845-35.66919.36021.6309
21.86720.5508-0.02392.8949-0.26452.31690.1011-0.12680.12910.21-0.08880.3306-0.0462-0.39690.06790.7111-0.4132-0.02090.2911-0.03260.3396-36.436340.0201-3.7852
30.0049-0.0033-0.00780.00220.00670.0190.33880.0012-0.0618-0.29850.1633-0.3256-0.0623-0.1315-0.00011.9555-0.33880.28271.28250.26731.2855-29.622365.5141-49.5749
40.0264-0.0227-0.03190.02450.0340.047-0.140.0213-0.0265-0.0423-0.212-0.1531-0.1473-0.13580.00011.5046-0.40240.18641.33020.29431.1556-28.975455.225-44.9892
50.02190.02780.01480.03630.00920.06010.10510.0081-0.1669-0.19880.13360.2627-0.037-0.3002-0.00021.34250.12970.14961.69950.14371.0021-37.53855.9571-55.8048
60.2223-0.0437-0.16510.20510.18690.2449-0.29540.31550.3841-0.7135-0.2183-0.4318-0.94050.5588-0.00081.6061-0.4728-0.06091.20160.24830.9404-36.850955.2413-39.5763
70.2699-0.0634-0.22070.02530.05210.3970.2460.07830.86850.078-0.09330.4887-1.3196-0.1401-0.00561.5438-0.2831-0.20740.73610.21481.0711-46.29860.4727-20.4851
80.0772-0.05850.04950.06960.01420.27240.37760.47720.2933-0.3557-0.39750.9267-0.9096-1.1345-0.00341.3072-0.004-0.16011.17420.08511.1364-53.654259.0431-17.6502
90.0575-0.0944-0.03690.15760.06170.02430.0808-0.32260.44870.27420.2389-0.3374-0.18770.57530.00621.1118-0.4622-0.04611.05470.15230.8585-37.349651.6978-22.8954
100.0796-0.0967-0.07110.49330.43830.3925-0.1030.8691-0.4064-0.5892-0.42770.4270.1017-0.637-0.03471.3791-0.3699-0.15861.4260.05030.8357-53.940542.7142-45.3411
110.04230.02590.03770.0453-0.02270.1180.08380.417-0.2627-0.5379-0.01850.14930.3988-0.13460.00041.2548-0.2343-0.00761.2776-0.05990.9311-49.324736.57-44.6545
120.1386-0.00170.00050.01610.04370.11120.10580.2891-0.2166-0.1755-0.1302-0.02310.4215-0.01720.00011.3039-0.26530.02921.3735-0.00091.1631-44.066637.2443-51.0224
130.0341-0.0088-0.03280.03070.01040.03160.07650.5168-0.1016-0.05-0.0753-0.02980.105-0.0115-0.00111.1056-0.0831-0.07120.63660.11151.3326-13.510725.5041-3.534
142.07721.90212.05292.04111.9022.03050.4608-0.9735-0.35460.2177-0.7503-0.469-0.24670.47620.36781.2799-0.1662-0.10071.1348-0.16081.3827-10.95229.283.134
150.0196-0.0047-0.01670.01540.01140.01810.00310.0285-0.1806-0.1093-0.0527-0.10480.05230.01270.00031.2852-0.0912-0.04181.84940.14580.9716-39.071534.3196-57.1381
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 19 through 111 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 112 through 312 )A0
3X-RAY DIFFRACTION3chain 'B' and (resid 21 through 42 )B0
4X-RAY DIFFRACTION4chain 'B' and (resid 43 through 67 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 68 through 83 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 84 through 127 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 128 through 170 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 171 through 195 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 196 through 213 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 214 through 236 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 237 through 267 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 268 through 312 )B0
13X-RAY DIFFRACTION13chain 'C' and (resid 1480 through 1485 )C0
14X-RAY DIFFRACTION14chain 'C' and (resid 1486 through 1506 )C0
15X-RAY DIFFRACTION15chain 'D' and (resid 1500 through 1506 )D0

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