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

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Basic information

Entry
Database: PDB / ID: 4wnd
TitleCrystal structure of the TPR domain of LGN in complex with Frmpd4/Preso1 at 1.5 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
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / THIOCYANATE ION / 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: 1.5 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)52,24021
Polymers50,7802
Non-polymers1,46019
Water5,368298
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7390 Å2
ΔGint-2 kcal/mol
Surface area16830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.487, 64.786, 69.118
Angle α, β, γ (deg.)90.000, 102.330, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 2 molecules AB

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


Mass: 44948.281 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: pRSFDUET-1 / 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: 5831.625 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: pGEX-6P-2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q14CM0

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Non-polymers , 5 types, 317 molecules

#3: Chemical
ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: CNS
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 298 / 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: 1.96 Å3/Da / Density % sol: 37.22 % / Mosaicity: 0.483 °
Crystal growTemperature: 293 K / Method: microbatch / pH: 7.5
Details: 0.1 M BisTrispropane (pH 7.5), 0.2 M potassium thiocyanate, 20% PEG 3350

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Apr 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 61319 / % possible obs: 98.8 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.037 / Rpim(I) all: 0.014 / Rrim(I) all: 0.04 / Rsym value: 0.037 / Χ2: 0.986 / Net I/av σ(I): 36.531 / Net I/σ(I): 21.9 / Num. measured all: 379458
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
1.5-1.5350.4462.72430130.9220.2190.4970.99297.7
1.53-1.555.10.42430210.9150.2070.4720.98598.1
1.55-1.585.10.35330230.9390.1730.3930.99298.1
1.58-1.625.10.330660.9570.1470.3340.95898.2
1.62-1.655.10.26330110.9640.1290.2930.96598.3
1.65-1.695.10.23330410.9690.1140.2590.98498.5
1.69-1.735.10.19630430.9820.0950.2180.96498.6
1.73-1.785.10.17130380.9840.0830.190.9598.6
1.78-1.835.10.13430660.9890.0650.1490.95199
1.83-1.895.10.11230920.9920.0550.1250.97498.9
1.89-1.965.10.09830590.9930.0480.1090.95799
1.96-2.045.10.08530650.9940.0420.0951.0199.3
2.04-2.135.10.06330660.9960.0310.070.92599.3
2.13-2.245.10.04930930.9980.0240.0540.97399.3
2.24-2.385.10.04431030.9980.0220.0491.03799.6
2.38-2.5670.04730880.9980.0180.050.94599.6
2.56-2.8210.30.05131100.9990.0170.0540.97199.8
2.82-3.2310.30.03831280.9990.0120.040.93699.8
3.23-4.0710.10.026312010.0090.0281.02599.8
4.07-509.40.021307310.0080.0231.13296.1

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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: 1.5→46.79 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.966 / WRfactor Rfree: 0.208 / WRfactor Rwork: 0.1869 / FOM work R set: 0.8847 / SU B: 1.189 / SU ML: 0.044 / SU R Cruickshank DPI: 0.0684 / SU Rfree: 0.0673 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.068 / ESU R Free: 0.067 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1824 3108 5.1 %RANDOM
Rwork0.1626 58188 --
obs0.1636 58188 98.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 81.59 Å2 / Biso mean: 24.126 Å2 / Biso min: 11.97 Å2
Baniso -1Baniso -2Baniso -3
1-0.42 Å20 Å2-0.45 Å2
2--0.97 Å20 Å2
3----1.17 Å2
Refinement stepCycle: final / Resolution: 1.5→46.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2767 0 90 298 3155
Biso mean--49.27 34.47 -
Num. residues----355
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0193118
X-RAY DIFFRACTIONr_bond_other_d0.0010.022920
X-RAY DIFFRACTIONr_angle_refined_deg1.1051.9614215
X-RAY DIFFRACTIONr_angle_other_deg0.69836739
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7275416
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.87424.583168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.74915532
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2011520
X-RAY DIFFRACTIONr_chiral_restr0.0750.2452
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023638
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02756
LS refinement shellResolution: 1.504→1.543 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 193 -
Rwork0.242 4005 -
all-4198 -
obs--91.54 %

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