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- PDB-4wnf: Crystal structure of the oxidized TPR domain of LGN in complex wi... -

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Basic information

Entry
Database: PDB / ID: 4wnf
TitleCrystal structure of the oxidized TPR domain of LGN in complex with Frmpd4/Preso1 at 2.9 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 / cell cortex region / maintenance of centrosome location / positive regulation of synapse structural plasticity / positive regulation of spindle assembly / GDP-dissociation inhibitor activity / dynein complex binding / mitotic spindle pole / establishment of mitotic spindle orientation / lateral plasma membrane ...lateral cell cortex / cell cortex region / maintenance of centrosome location / positive regulation of synapse structural plasticity / positive regulation of spindle assembly / GDP-dissociation inhibitor activity / dynein complex binding / mitotic spindle pole / establishment of mitotic spindle orientation / lateral plasma membrane / G-protein alpha-subunit binding / positive regulation of protein localization to cell cortex / regulation of mitotic spindle organization / phosphatidylinositol-4,5-bisphosphate binding / mitotic spindle organization / : / cell cortex / G alpha (i) signalling events / dendritic spine / cytoskeleton / G protein-coupled receptor signaling pathway / protein domain specific binding / cell division / nucleotide binding / centrosome / protein-containing complex / identical protein binding / cytosol / cytoplasm
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 / 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 / Tetratricopeptide repeat / : / FAK1/PYK2, FERM domain C-lobe / Tetratricopeptide repeat / Tetratricopeptide repeat domain / FERM central domain / FERM/acyl-CoA-binding protein superfamily / Tetratricopeptide repeat / WW/rsp5/WWP domain profile. / WW domain / FERM central 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 / Tetratricopeptide repeat / PDZ domain / 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: 2.9 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)50,7802
Polymers50,7802
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
ΔGint-11 kcal/mol
Surface area12990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.599, 92.599, 175.238
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: 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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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / 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: Dec 12, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 10385 / % possible obs: 99.3 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.075 / Χ2: 0.998 / Net I/av σ(I): 18.174 / Net I/σ(I): 15 / Num. measured all: 74336
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2.9-2.957.60.5022.7284961.081100
2.95-37.40.4455050.969100
3-3.067.40.4754990.976100
3.06-3.127.50.355110.994100
3.12-3.197.40.2965101.05100
3.19-3.277.50.2545000.91999.8
3.27-3.357.50.1935170.994100
3.35-3.447.20.2185110.996100
3.44-3.547.10.1645091.106100
3.54-3.656.90.1365120.97299.6
3.65-3.786.80.1654970.95599
3.78-3.946.50.1345100.96698.8
3.94-4.117.40.0685230.963100
4.11-4.337.20.0595241.03100
4.33-4.67.30.0495290.92599.6
4.6-4.967.20.0495200.949100
4.96-5.467.10.0465421.09599.8
5.46-6.247.10.0395390.957100
6.24-7.866.90.0275551.199.3
7.86-506.10.0225760.95391.6

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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: 2.9→39.12 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.908 / WRfactor Rfree: 0.2832 / WRfactor Rwork: 0.2379 / FOM work R set: 0.7607 / SU B: 17.097 / SU ML: 0.315 / SU R Cruickshank DPI: 0.8202 / SU Rfree: 0.382 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.82 / ESU R Free: 0.382 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2802 513 5 %RANDOM
Rwork0.237 9777 --
obs0.2391 9777 98.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 202.88 Å2 / Biso mean: 88.325 Å2 / Biso min: 50.24 Å2
Baniso -1Baniso -2Baniso -3
1-3.13 Å23.13 Å20 Å2
2--3.13 Å20 Å2
3----10.16 Å2
Refinement stepCycle: final / Resolution: 2.9→39.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2065 0 0 0 2065
Num. residues----273
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0192100
X-RAY DIFFRACTIONr_bond_other_d0.0010.021923
X-RAY DIFFRACTIONr_angle_refined_deg1.1381.952834
X-RAY DIFFRACTIONr_angle_other_deg0.6853.0014406
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5225270
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.50124.706102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.49615337
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7791510
X-RAY DIFFRACTIONr_chiral_restr0.0580.2312
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022453
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02493
LS refinement shellResolution: 2.903→2.978 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 47 -
Rwork0.316 692 -
all-739 -
obs--99.73 %

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