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- PDB-4wng: Crystal structure of the TPR domain of LGN in complex with Frmpd4... -

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Basic information

Entry
Database: PDB / ID: 4wng
TitleCrystal structure of the TPR domain of LGN in complex with Frmpd4/Preso1 at 2.1 Angstrom resolution
Components
  • FERM and PDZ domain-containing protein 4
  • G-protein-signaling modulator 2
KeywordsSIGNALING PROTEIN/PROTEIN BINDING / TETRATRICOPEPTIDE REPEAT / TPR / CELL POLARITY / CYTOPLASM AND CELL CORTEX / SIGNALING PROTEIN-PROTEIN BINDING COMPLEX
Function / homology
Function and homology information


lateral cell cortex / positive regulation of synapse structural plasticity / cell cortex region / maintenance of centrosome location / positive regulation of spindle assembly / response to light intensity / GDP-dissociation inhibitor activity / neurotransmitter receptor localization to postsynaptic specialization membrane / mitotic spindle pole / dynein complex binding ...lateral cell cortex / positive regulation of synapse structural plasticity / cell cortex region / maintenance of centrosome location / positive regulation of spindle assembly / response to light intensity / GDP-dissociation inhibitor activity / neurotransmitter receptor localization to postsynaptic specialization membrane / mitotic spindle pole / dynein complex binding / establishment of mitotic spindle orientation / lateral plasma membrane / G-protein alpha-subunit binding / positive regulation of protein localization to cell cortex / phosphatidylinositol-4,5-bisphosphate binding / regulation of mitotic spindle organization / mitotic spindle organization / cell cortex / G alpha (i) signalling events / dendritic spine / cytoskeleton / postsynaptic density / G protein-coupled receptor signaling pathway / protein domain specific binding / cell division / nucleotide binding / centrosome / protein-containing complex / identical protein binding / cytoplasm / cytosol
Similarity search - Function
FERM and PDZ domain-containing protein 1/3/4, FERM domain C-lobe / : / GoLoco motif / GoLoco motif / GoLoco/GPR motif profile. / LGN motif, putative GEFs specific for G-alpha GTPases / Tetratricopeptide repeat / : / FAK1/PYK2, FERM domain C-lobe / Tetratricopeptide repeat ...FERM and PDZ domain-containing protein 1/3/4, FERM domain C-lobe / : / GoLoco motif / GoLoco motif / GoLoco/GPR motif profile. / LGN motif, putative GEFs specific for G-alpha GTPases / Tetratricopeptide repeat / : / FAK1/PYK2, FERM domain C-lobe / Tetratricopeptide repeat / Tetratricopeptide repeat / FERM central domain / FERM/acyl-CoA-binding protein superfamily / Tetratricopeptide repeat domain / Tetratricopeptide repeat / FERM central domain / WW/rsp5/WWP domain profile. / WW domain / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / PDZ domain / Tetratricopeptide repeat / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / PH-like domain superfamily / Ubiquitin-like domain superfamily / Mainly Alpha
Similarity search - Domain/homology
G-protein-signaling modulator 2 / FERM and PDZ domain-containing protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å
AuthorsTakayanagi, H. / Yuzawa, S. / Sumimoto, H.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2015
Title: Structural basis for the recognition of the scaffold protein Frmpd4/Preso1 by the TPR domain of the adaptor protein LGN
Authors: Takayanagi, H. / Yuzawa, S. / Sumimoto, H.
History
DepositionOct 11, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 16, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2020Group: Data collection / Derived calculations / Refinement description
Category: diffrn_source / pdbx_struct_oper_list / software
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation / _software.name
Revision 1.2Nov 8, 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

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Assembly

Deposited unit
A: G-protein-signaling modulator 2
B: FERM and PDZ domain-containing protein 4


Theoretical massNumber of molelcules
Total (without water)51,8852
Polymers51,8852
Non-polymers00
Water1,11762
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2650 Å2
ΔGint-11 kcal/mol
Surface area16260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.527, 90.527, 177.067
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein G-protein-signaling modulator 2 / Mosaic protein LGN


Mass: 45061.441 Da / Num. of mol.: 1 / Fragment: N-terminal TPR domain, UNP residues 20-421
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GPSM2, LGN / Plasmid: pGEX-6P-2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P81274
#2: Protein FERM and PDZ domain-containing protein 4 / PDZ domain-containing protein 10 / PSD-95-interacting regulator of spine morphogenesis / Preso


Mass: 6823.635 Da / Num. of mol.: 1 / Fragment: FRMPD4-L, UNP residues 978-1025
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FRMPD4, KIAA0316, PDZD10, PDZK10 / Plasmid: pRSFDUET-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q14CM0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 2.02 Å3/Da / Density % sol: 39.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1 M BisTrispropane (pH 8.0), 0.2 M magnesium chloride, 20% PEG 3350

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 25343 / % possible obs: 99.9 % / Redundancy: 17.5 % / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.023 / Rrim(I) all: 0.096 / Χ2: 0.824 / Net I/av σ(I): 25.852 / Net I/σ(I): 8.2 / Num. measured all: 442380
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.1-2.1414.40.9512.30812270.9150.2570.9850.511100
2.14-2.1815.30.84412380.9420.2210.8730.529100
2.18-2.2216.50.78812240.9550.1980.8130.531100
2.22-2.2616.30.6412380.9650.1620.660.572100
2.26-2.3115.90.52312420.9770.1340.540.609100
2.31-2.3716.40.5112420.9770.1290.5260.615100
2.37-2.4218.20.45712510.9780.1090.470.645100
2.42-2.4918.20.37212330.9880.0890.3820.724100
2.49-2.5618.30.312400.9910.0720.3080.836100
2.56-2.6518.40.26312520.9920.0630.2710.914100
2.65-2.7418.50.22712510.9940.0540.2330.987100
2.74-2.8518.20.17912460.9950.0430.1841.053100
2.85-2.9817.30.15212700.9960.0370.1561.13100
2.98-3.1418.30.13312600.9970.0320.1371.034100
3.14-3.3318.30.1112760.9980.0260.1130.92599.9
3.33-3.5918.20.09212780.9980.0220.0940.987100
3.59-3.9519.40.0812830.9980.0190.0820.91100
3.95-4.5218.80.06813090.9990.0160.070.92399.9
4.52-5.716.90.0613330.9990.0150.0620.971100
5.7-5017.10.0414500.9990.010.0410.82199.2

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
MOLREP11.0.05phasing
Coot0.7-premodel building
REFMAC5.7.0029refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WNE

4wne


Resolution: 2.11→38.58 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.929 / WRfactor Rfree: 0.2773 / WRfactor Rwork: 0.2284 / FOM work R set: 0.8019 / SU B: 5.221 / SU ML: 0.139 / SU R Cruickshank DPI: 0.217 / SU Rfree: 0.1951 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.217 / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2712 1284 5.1 %RANDOM
Rwork0.2244 23962 --
obs0.2268 23962 98.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 128.04 Å2 / Biso mean: 56.444 Å2 / Biso min: 29.76 Å2
Baniso -1Baniso -2Baniso -3
1-1.14 Å21.14 Å20 Å2
2--1.14 Å20 Å2
3----3.7 Å2
Refinement stepCycle: final / Resolution: 2.11→38.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2607 0 0 62 2669
Biso mean---49.21 -
Num. residues----348
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0192658
X-RAY DIFFRACTIONr_bond_other_d0.0010.022396
X-RAY DIFFRACTIONr_angle_refined_deg1.0661.9433595
X-RAY DIFFRACTIONr_angle_other_deg0.70435468
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7735347
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.7624.453128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.92515408
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5851513
X-RAY DIFFRACTIONr_chiral_restr0.0580.2395
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023146
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02645
LS refinement shellResolution: 2.109→2.164 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 86 -
Rwork0.253 1550 -
all-1636 -
obs--89.16 %

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