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- PDB-3sf4: Crystal structure of the complex between the conserved cell polar... -

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Basic information

Entry
Database: PDB / ID: 3sf4
TitleCrystal structure of the complex between the conserved cell polarity proteins Inscuteable and LGN
Components
  • G-protein-signaling modulator 2
  • Protein inscuteable homolog
KeywordsSIGNALING PROTEIN/PROTEIN BINDING / tetratricopeptide repeat / TPR / cell polarity / asymmetric cell division / mitotic spindle orientation / 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 / asymmetric cell division / 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 / asymmetric cell division / 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 / mitotic spindle organization / regulation of protein stability / : / protein-macromolecule adaptor activity / nervous system development / cell cortex / G alpha (i) signalling events / cell differentiation / G protein-coupled receptor signaling pathway / cell division / protein domain specific binding / nucleotide binding / centrosome / protein-containing complex / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Inscuteable LGN-binding domain / Protein inscuteable homologue, LGN-binding domain / Protein inscuteable homologue, LGN-binding domain superfamily / Inscuteable LGN-binding domain / Inscuteable / Defensin A-like / GoLoco motif / GoLoco motif / GoLoco/GPR motif profile. / LGN motif, putative GEFs specific for G-alpha GTPases ...Inscuteable LGN-binding domain / Protein inscuteable homologue, LGN-binding domain / Protein inscuteable homologue, LGN-binding domain superfamily / Inscuteable LGN-binding domain / Inscuteable / Defensin A-like / GoLoco motif / GoLoco motif / GoLoco/GPR motif profile. / LGN motif, putative GEFs specific for G-alpha GTPases / Tetratricopeptide repeat / Tetratricopeptide repeat / Tetratricopeptide repeat / Other non-globular / Tetratricopeptide repeat domain / Tetratricopeptide repeat / Armadillo/beta-catenin-like repeats / Armadillo / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Special / Armadillo-like helical / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
G-protein-signaling modulator 2 / Protein inscuteable homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsYuzawa, S. / Kamakura, S. / Iwakiri, Y. / Hayase, J. / Sumimoto, H.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Structural basis for interaction between the conserved cell polarity proteins Inscuteable and Leu-Gly-Asn repeat-enriched protein (LGN)
Authors: Yuzawa, S. / Kamakura, S. / Iwakiri, Y. / Hayase, J. / Sumimoto, H.
History
DepositionJun 12, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Nov 1, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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: G-protein-signaling modulator 2
C: G-protein-signaling modulator 2
D: Protein inscuteable homolog
E: Protein inscuteable homolog
F: Protein inscuteable homolog


Theoretical massNumber of molelcules
Total (without water)151,6376
Polymers151,6376
Non-polymers00
Water3,747208
1
A: G-protein-signaling modulator 2
D: Protein inscuteable homolog


Theoretical massNumber of molelcules
Total (without water)50,5462
Polymers50,5462
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4300 Å2
ΔGint-20 kcal/mol
Surface area18690 Å2
MethodPISA
2
B: G-protein-signaling modulator 2
E: Protein inscuteable homolog


Theoretical massNumber of molelcules
Total (without water)50,5462
Polymers50,5462
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4110 Å2
ΔGint-18 kcal/mol
Surface area18130 Å2
MethodPISA
3
C: G-protein-signaling modulator 2
F: Protein inscuteable homolog


Theoretical massNumber of molelcules
Total (without water)50,5462
Polymers50,5462
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4240 Å2
ΔGint-20 kcal/mol
Surface area17750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.815, 124.815, 233.851
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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


Mass: 44948.281 Da / Num. of mol.: 3 / Fragment: N-terminal TPR domain (residues in UNP 20-421)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LGN / Plasmid: pRSFDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P81274
#2: Protein Protein inscuteable homolog


Mass: 5597.461 Da / Num. of mol.: 3 / Fragment: LGN-binding domain (residues in UNP 70-116)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INSC / Plasmid: pGEX-6p / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q1MX18
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 208 / 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 Å3/Da / Density % sol: 59.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris HCl, 15% PEG 3350, 0.2M MgCL2, 4% 2,2,2-Trifluoroethanol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 8, 2010
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. all: 57538 / Num. obs: 57538 / % possible obs: 100 % / Redundancy: 12.1 % / Biso Wilson estimate: 46.8 Å2 / Rmerge(I) obs: 0.096
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 10.4 % / Rmerge(I) obs: 0.422 / Mean I/σ(I) obs: 6.17 / Num. unique all: 2791 / % possible all: 100

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Processing

Software
NameVersionClassification
MOLREPphasing
PHASERphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2FO7, 2WQH, 1NA0

2fo7

2wqh

1na0


Resolution: 2.6→48.72 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 3108570.8 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.262 2918 5.1 %RANDOM
Rwork0.216 ---
obs0.216 57419 99.8 %-
all-57538 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 35.5476 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 47.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.95 Å20 Å20 Å2
2---0.95 Å20 Å2
3---1.91 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2.6→48.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9122 0 0 208 9330
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1
X-RAY DIFFRACTIONc_dihedral_angle_d17.2
X-RAY DIFFRACTIONc_improper_angle_d0.71
X-RAY DIFFRACTIONc_mcbond_it1.381.5
X-RAY DIFFRACTIONc_mcangle_it2.352
X-RAY DIFFRACTIONc_scbond_it2.222
X-RAY DIFFRACTIONc_scangle_it3.372.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.316 476 5.1 %
Rwork0.273 8855 -
obs--99 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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