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

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Basic information

Entry
Database: PDB / ID: 4wne
TitleCrystal structure of the TPR domain of LGN in complex with Frmpd4/Preso1 at 2.0 Angstrom resolution
Components
  • G-protein-signaling modulator 2
  • Peptide from FERM and PDZ domain-containing protein 4
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 / positive regulation of protein localization to cell cortex ...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 / positive regulation of protein localization to cell cortex / G-protein alpha-subunit binding / lateral plasma membrane / 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 / cell division / protein domain specific binding / 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 / Tetratricopeptide repeat / FERM/acyl-CoA-binding protein superfamily / 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 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: Peptide from FERM and PDZ domain-containing protein 4


Theoretical massNumber of molelcules
Total (without water)47,9802
Polymers47,9802
Non-polymers00
Water1,910106
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2820 Å2
ΔGint-13 kcal/mol
Surface area15840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.784, 91.784, 176.783
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/peptide Peptide from FERM and PDZ domain-containing protein 4 / / PDZ domain-containing protein 10 / PSD-95-interacting regulator of spine morphogenesis / Preso


Mass: 3031.391 Da / Num. of mol.: 1 / Fragment: FRMPD4-S, UNP residues 987-1011 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q14CM0
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 2.24 Å3/Da / Density % sol: 45.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.25
Details: 0.1 M BisTrispropane (pH 7.25), 0.2 M sodium bromide, 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: Jun 17, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 30371 / % possible obs: 99.2 % / Redundancy: 9.4 % / Rmerge(I) obs: 0.079 / Χ2: 0.8 / Net I/av σ(I): 20.168 / Net I/σ(I): 9.1 / Num. measured all: 286743
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2-2.039.60.8812.05914840.47999.1
2.03-2.079.10.63414840.51199.6
2.07-2.119.50.51714730.51299.3
2.11-2.1510.10.38614930.5399.6
2.15-2.210.10.34414860.5699.6
2.2-2.2510.10.28714860.60799.5
2.25-2.31100.24115040.64299.6
2.31-2.37100.22514950.65699.7
2.37-2.449.80.19515020.69999.7
2.44-2.529.70.15315010.80199.8
2.52-2.619.30.1315140.96799.8
2.61-2.718.70.11615131.01399.9
2.71-2.849.30.09915160.92699.8
2.84-2.998.90.08615231.042100
2.99-3.179.70.08315430.96199.8
3.17-3.429.80.07515191.09299
3.42-3.769.50.0715320.99698.6
3.76-4.318.90.06415271.01696.9
4.31-5.438.30.05815821.03398.6
5.43-508.70.04816941.03496.9

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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: 3SF4

3sf4


Resolution: 2→39.78 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.935 / WRfactor Rfree: 0.2332 / WRfactor Rwork: 0.2125 / FOM work R set: 0.8269 / SU B: 3.981 / SU ML: 0.11 / SU R Cruickshank DPI: 0.1676 / SU Rfree: 0.1493 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.168 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2379 1533 5.1 %RANDOM
Rwork0.2104 28795 --
obs0.2119 28795 99.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 119.81 Å2 / Biso mean: 50.965 Å2 / Biso min: 27.08 Å2
Baniso -1Baniso -2Baniso -3
1-1.41 Å21.41 Å20 Å2
2--1.41 Å20 Å2
3----4.58 Å2
Refinement stepCycle: final / Resolution: 2→39.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2616 0 0 106 2722
Biso mean---48.18 -
Num. residues----345
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0192668
X-RAY DIFFRACTIONr_bond_other_d0.0010.022412
X-RAY DIFFRACTIONr_angle_refined_deg1.0291.9453606
X-RAY DIFFRACTIONr_angle_other_deg0.71735511
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6075344
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.28524.351131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.57115418
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8731514
X-RAY DIFFRACTIONr_chiral_restr0.0590.2394
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023143
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02651
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 98 -
Rwork0.277 2092 -
all-2190 -
obs--99.14 %

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