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- PDB-5a7d: Tetrameric assembly of LGN with Inscuteable -

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Basic information

Entry
Database: PDB / ID: 5a7d
TitleTetrameric assembly of LGN with Inscuteable
Components
  • INSCUTEABLE
  • PINS
KeywordsCELL CYCLE / LGN / INSCUTEABLE / ASYMMETRIC CELL DIVISION
Function / homology
Function and homology information


G alpha (i) signalling events / Malpighian tubule tip cell differentiation / regulation of nervous system development / establishment of spindle orientation / basal protein localization / somatic muscle development / asymmetric protein localization involved in cell fate determination / neuroblast fate determination / regulation of asymmetric cell division / asymmetric cell division ...G alpha (i) signalling events / Malpighian tubule tip cell differentiation / regulation of nervous system development / establishment of spindle orientation / basal protein localization / somatic muscle development / asymmetric protein localization involved in cell fate determination / neuroblast fate determination / regulation of asymmetric cell division / asymmetric cell division / RNA localization / asymmetric neuroblast division / establishment of mitotic spindle localization / sensory organ development / apical cortex / cytoskeletal anchor activity / apical protein localization / peripheral nervous system development / GDP-dissociation inhibitor activity / establishment of mitotic spindle orientation / G-protein alpha-subunit binding / neuroblast proliferation / protein localization / cell cortex / defense response to Gram-negative bacterium / protein domain specific binding / membrane / cytoplasm
Similarity search - Function
Inscuteable / GoLoco motif / GoLoco motif / GoLoco/GPR motif profile. / LGN motif, putative GEFs specific for G-alpha GTPases / Tetratricopeptide repeat / Tetratricopeptide repeat / Tetratricopeptide repeat / Tetratricopeptide repeat domain / TPR repeat profile. ...Inscuteable / GoLoco motif / GoLoco motif / GoLoco/GPR motif profile. / LGN motif, putative GEFs specific for G-alpha GTPases / Tetratricopeptide repeat / Tetratricopeptide repeat / Tetratricopeptide repeat / Tetratricopeptide repeat domain / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Armadillo-like helical / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Inscuteable / LD33695p
Similarity search - Component
Biological speciesDROSOPHILA MELANOGASTER (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsCulurgioni, S. / Mari, S. / Bonetto, G. / Gallini, S. / Brennich, M. / Round, A. / Mapelli, M.
CitationJournal: To be Published
Title: The Structure of the Insc:Lgn Tetramer Reveals a New Function of Lgn in Promoting Asymmetric Cell Divisions
Authors: Culurgioni, S. / Mari, S. / Bonetto, G. / Gallini, S. / Brennich, M. / Round, A. / Mapelli, M.
History
DepositionJul 7, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 3, 2016Provider: repository / Type: Initial release
Revision 1.1May 23, 2018Group: Data collection / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: PINS
C: PINS
D: PINS
E: PINS
F: PINS
G: PINS
H: PINS
I: PINS
L: INSCUTEABLE
M: INSCUTEABLE
N: INSCUTEABLE
O: INSCUTEABLE
P: INSCUTEABLE
Q: INSCUTEABLE
R: INSCUTEABLE
S: INSCUTEABLE


Theoretical massNumber of molelcules
Total (without water)643,20516
Polymers643,20516
Non-polymers00
Water724
1
B: PINS
H: PINS
L: INSCUTEABLE
R: INSCUTEABLE


Theoretical massNumber of molelcules
Total (without water)160,8014
Polymers160,8014
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
E: PINS
G: PINS
O: INSCUTEABLE
Q: INSCUTEABLE


Theoretical massNumber of molelcules
Total (without water)160,8014
Polymers160,8014
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: PINS
F: PINS
M: INSCUTEABLE
P: INSCUTEABLE


Theoretical massNumber of molelcules
Total (without water)160,8014
Polymers160,8014
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: PINS
I: PINS
N: INSCUTEABLE
S: INSCUTEABLE


Theoretical massNumber of molelcules
Total (without water)160,8014
Polymers160,8014
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5180 Å2
ΔGint-29.7 kcal/mol
Surface area29200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.190, 212.580, 280.730
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
PINS


Mass: 42217.906 Da / Num. of mol.: 8 / Fragment: TPR DOMAIN, RESIDUES 25-406
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Plasmid: PGEX-6PI / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA / References: UniProt: Q9VB22
#2: Protein
INSCUTEABLE


Mass: 38182.758 Da / Num. of mol.: 8 / Fragment: ASYMMETRIC DOMAIN, RESIDUES 283-623
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Plasmid: PGEX-6PI / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA / References: UniProt: Q24367
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.95 Å3/Da / Density % sol: 58.3 % / Description: NONE
Crystal growpH: 7.8
Details: 13% PEG 3350, 0.1 M TRIS PH 7.8, 0.2 M K-THYOCIANATE, 2.5% 1-PROPANOL, 2.5% TACSIMATE PH 7.5

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1.00767
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00767 Å / Relative weight: 1
ReflectionResolution: 3.4→75.6 Å / Num. obs: 105973 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 14.9 % / Biso Wilson estimate: 84.49 Å2 / Rmerge(I) obs: 0.23 / Net I/σ(I): 12.7
Reflection shellResolution: 3.4→3.52 Å / Redundancy: 14.1 % / Rmerge(I) obs: 1.42 / Mean I/σ(I) obs: 2.15 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4A1S

4a1s


Resolution: 3.4→75.581 Å / SU ML: 0.42 / σ(F): 1.34 / Phase error: 25.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2497 5218 4.9 %
Rwork0.2088 --
obs0.2108 105843 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.4→75.581 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms38976 0 0 4 38980
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00339540
X-RAY DIFFRACTIONf_angle_d0.53353392
X-RAY DIFFRACTIONf_dihedral_angle_d16.03814410
X-RAY DIFFRACTIONf_chiral_restr0.0216044
X-RAY DIFFRACTIONf_plane_restr0.0027037
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4-3.43860.36221580.30383319X-RAY DIFFRACTION100
3.4386-3.47910.32581660.2943330X-RAY DIFFRACTION100
3.4791-3.52150.35341840.28413295X-RAY DIFFRACTION100
3.5215-3.56610.32541810.27823319X-RAY DIFFRACTION100
3.5661-3.6130.33521810.26283291X-RAY DIFFRACTION100
3.613-3.66250.32711560.26243380X-RAY DIFFRACTION100
3.6625-3.71480.27471710.25453265X-RAY DIFFRACTION100
3.7148-3.77030.30811940.24213343X-RAY DIFFRACTION100
3.7703-3.82920.26481760.23763311X-RAY DIFFRACTION100
3.8292-3.8920.29181540.23153368X-RAY DIFFRACTION100
3.892-3.95910.25141760.22193300X-RAY DIFFRACTION100
3.9591-4.03110.2441600.21253346X-RAY DIFFRACTION100
4.0311-4.10860.23811720.20673336X-RAY DIFFRACTION100
4.1086-4.19250.27011720.20593311X-RAY DIFFRACTION100
4.1925-4.28360.27131650.20963359X-RAY DIFFRACTION100
4.2836-4.38320.23491800.19873316X-RAY DIFFRACTION100
4.3832-4.49290.23741730.18763330X-RAY DIFFRACTION100
4.4929-4.61430.21331570.18923374X-RAY DIFFRACTION100
4.6143-4.75010.20371920.18493358X-RAY DIFFRACTION100
4.7501-4.90340.2751590.18913336X-RAY DIFFRACTION100
4.9034-5.07860.23771750.19583342X-RAY DIFFRACTION100
5.0786-5.28190.23881720.21173393X-RAY DIFFRACTION100
5.2819-5.52220.29631810.22553342X-RAY DIFFRACTION100
5.5222-5.81320.26231620.23513388X-RAY DIFFRACTION100
5.8132-6.17730.24761890.22433367X-RAY DIFFRACTION100
6.1773-6.6540.25471910.20413379X-RAY DIFFRACTION100
6.654-7.32310.23951750.19233405X-RAY DIFFRACTION100
7.3231-8.38160.20461800.1733421X-RAY DIFFRACTION100
8.3816-10.55530.15351760.13073459X-RAY DIFFRACTION100
10.5553-75.59990.2531900.2153542X-RAY DIFFRACTION98

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