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- PDB-4a1s: Crystallographic structure of the Pins:Insc complex -

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Basic information

Entry
Database: PDB / ID: 4a1s
TitleCrystallographic structure of the Pins:Insc complex
Components
  • PARTNER OF INSCUTEABLE
  • RE60102P
KeywordsCELL CYCLE / LGN / MITOTIC SPINDLE ORIENTATION / ASYMMETRIC CELL DIVISIONS
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
RE60102p / Partner of Inscuteable / LD33695p / Inscuteable
Similarity search - Component
Biological speciesDROSOPHILA MELANOGASTER (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsCulurgioni, S. / Alfieri, A. / Pendolino, V. / Laddomada, F. / Mapelli, M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Inscuteable and Numa Proteins Bind Competitively to Leu-Gly- Asn Repeat-Enriched Protein (Lgn) During Asymmetric Cell Divisions.
Authors: Culurgioni, S. / Alfieri, A. / Pendolino, V. / Laddomada, F. / Mapelli, M.
History
DepositionSep 19, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 28, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 7, 2012Group: Database references
Revision 1.2Oct 16, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_status ...exptl_crystal_grow / pdbx_database_status / reflns / reflns_shell
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp ..._exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.status_code_sf / _reflns.pdbx_Rmerge_I_obs / _reflns_shell.Rmerge_I_obs
Revision 1.3May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: PARTNER OF INSCUTEABLE
B: PARTNER OF INSCUTEABLE
C: RE60102P
E: RE60102P


Theoretical massNumber of molelcules
Total (without water)96,8814
Polymers96,8814
Non-polymers00
Water8,737485
1
B: PARTNER OF INSCUTEABLE
E: RE60102P


Theoretical massNumber of molelcules
Total (without water)48,4402
Polymers48,4402
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3740 Å2
ΔGint-17.7 kcal/mol
Surface area16890 Å2
MethodPISA
2
A: PARTNER OF INSCUTEABLE
C: RE60102P


Theoretical massNumber of molelcules
Total (without water)48,4402
Polymers48,4402
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3820 Å2
ΔGint-18.1 kcal/mol
Surface area17220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)160.200, 64.232, 107.599
Angle α, β, γ (deg.)90.00, 117.90, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 39:368 OR RESSEQ 375:386 )
211CHAIN B AND (RESSEQ 39:368 OR RESSEQ 375:386 )
112CHAIN C AND (RESSEQ 7:34 )
212CHAIN E AND (RESSEQ 7:34 )

NCS ensembles :
ID
1
2

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Components

#1: Protein PARTNER OF INSCUTEABLE / PINS


Mass: 43777.938 Da / Num. of mol.: 2 / Fragment: TPR-REGION, RESIDUES 1-406
Source method: isolated from a genetically manipulated source
Details: RESIDUES 369-386 ARE BUILT AS POLYALANINE / Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): ROSETTA / References: UniProt: Q9NH88, UniProt: Q9VB22*PLUS
#2: Protein/peptide RE60102P / INSC


Mass: 4662.351 Da / Num. of mol.: 2 / Fragment: PINS-BINDING PEPTIDE, RESIDUES 301-340
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): ROSETTA / References: UniProt: Q5BIH3, UniProt: Q9W2R4*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 485 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUE 369-386 ARE BUILT AS POLYALANINE. THE SEQUENCE OF THIS REGION IS ...RESIDUE 369-386 ARE BUILT AS POLYALANINE. THE SEQUENCE OF THIS REGION IS KELHDPVGESTARVNISDLRKLLGMPDSEPSPTEEEAR

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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: 2.44 Å3/Da / Density % sol: 49 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M MAGNESIUM CLORIDE, 15% PEG 4000, 0.1 M TRIS-HCL PH 8.5

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.979
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 28, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.1→25 Å / Num. obs: 56295 / % possible obs: 98.7 % / Observed criterion σ(I): 3 / Redundancy: 3.2 % / Biso Wilson estimate: 35.31 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 12.5
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.224 / Mean I/σ(I) obs: 2.3 / % possible all: 96.7

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
HKL-2000data reduction
SCALEPACKdata scaling
SHELXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.1→23.132 Å / SU ML: 0.81 / σ(F): 1.34 / Phase error: 25.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2559 2270 4.2 %
Rwork0.2081 --
obs0.2101 54632 96.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.536 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.9158 Å20 Å24.9348 Å2
2---2.2706 Å20 Å2
3---0.3548 Å2
Refinement stepCycle: LAST / Resolution: 2.1→23.132 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5755 0 0 485 6240
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0195854
X-RAY DIFFRACTIONf_angle_d1.5897877
X-RAY DIFFRACTIONf_dihedral_angle_d15.012126
X-RAY DIFFRACTIONf_chiral_restr0.113826
X-RAY DIFFRACTIONf_plane_restr0.0071056
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2636X-RAY DIFFRACTIONPOSITIONAL
12B2636X-RAY DIFFRACTIONPOSITIONAL0.207
21C224X-RAY DIFFRACTIONPOSITIONAL
22E224X-RAY DIFFRACTIONPOSITIONAL0.096
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.14560.39251410.32052999X-RAY DIFFRACTION89
2.1456-2.19550.30591420.29123147X-RAY DIFFRACTION94
2.1955-2.25040.35841370.27683157X-RAY DIFFRACTION95
2.2504-2.31120.30551250.24463293X-RAY DIFFRACTION96
2.3112-2.37910.25961450.21613266X-RAY DIFFRACTION96
2.3791-2.45580.24151420.21063264X-RAY DIFFRACTION97
2.4558-2.54350.28381270.20943270X-RAY DIFFRACTION97
2.5435-2.64520.28391270.20393286X-RAY DIFFRACTION98
2.6452-2.76540.27171190.21223358X-RAY DIFFRACTION98
2.7654-2.91090.2891450.20123321X-RAY DIFFRACTION98
2.9109-3.09290.22711580.19313325X-RAY DIFFRACTION99
3.0929-3.33110.22141410.20753343X-RAY DIFFRACTION99
3.3311-3.66510.23531450.19753392X-RAY DIFFRACTION99
3.6651-4.19270.24391750.18543366X-RAY DIFFRACTION99
4.1927-5.2720.22181540.18793307X-RAY DIFFRACTION97
5.272-23.13360.2771470.21823268X-RAY DIFFRACTION93
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.5765-0.9104-2.2480.13760.28872.0914-0.0437-0.091-0.0103-0.0323-0.0995-0.02540.09960.22660.13720.33720.01690.0410.17870.02920.208158.92882.7171-14.7606
23.11271.9383-1.11524.3891-2.26012.8021-0.34690.2334-0.0503-0.26830.1992-0.00350.2128-0.11710.15190.18620.02810.02970.2546-0.01910.1974.451388.5456-38.2486
33.61081.018-1.05013.41060.45114.06070.14890.02831.54330.24790.28220.1273-0.7331-0.1648-0.39350.44560.1094-0.06260.33260.05111.023676.8756116.7091-40.3059
44.9255-3.0531.55513.2199-1.3091.83340.06370.2830.0383-0.2776-0.1560.14510.15990.12320.08750.2006-0.0042-0.00940.28-0.00050.155628.31758.6781-35.3845
51.89210.9567-0.30115.1685-2.27272.79110.1627-0.04910.09530.4572-0.3481-0.1851-0.21720.22520.18370.22760.0063-0.04380.2450.01140.161838.238146.5827-13.5146
62.69221.42381.39996.54011.08352.552-0.01310.1543-0.66510.2217-0.17341.20810.3922-0.67550.15980.3724-0.15180.12180.4765-0.18340.581421.26924.5248-6.6267
76.92612.9928-3.31162.0053-8.78182.0070.3678-0.4330.66890.6066-0.09680.1918-0.3978-0.0579-0.28810.35350.0723-0.01990.2925-0.07180.295283.6229103.5636-33.7548
82.00012.0002-3.512.0001-3.515.72630.28550.13690.5778-0.08920.11630.1178-0.68-0.0277-0.3970.4318-0.08340.1160.28-0.06010.289970.593190.7616-32.2897
93.46933.4276-2.49578.0357-8.91782.00010.06190.8664-0.1726-0.5581-0.0008-0.0433-0.0265-0.3954-0.06240.54040.18380.20140.60960.12110.505660.913684.1916-25.8006
102.0018.3085-8.72837.4635-6.80076.3011-0.47072.3882-1.1532-0.57850.3207-0.15670.4894-0.5090.1290.5140.01660.11660.4419-0.08460.348349.87277.8155-18.4313
110.7747-1.63081.36433.8034-3.53413.3368-0.13960.22090.0970.28190.21090.0936-0.0355-0.2871-0.08080.20120.0019-0.00160.374-0.00130.225830.586942.6219-20.2392
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 44:186)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 187:315)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 316:391)
4X-RAY DIFFRACTION4CHAIN B AND (RESSEQ 44:186)
5X-RAY DIFFRACTION5CHAIN B AND (RESSEQ 187:295)
6X-RAY DIFFRACTION6CHAIN B AND (RESSEQ 296:391)
7X-RAY DIFFRACTION7CHAIN C AND (RESSEQ 6:19)
8X-RAY DIFFRACTION8CHAIN C AND (RESSEQ 20:24)
9X-RAY DIFFRACTION9CHAIN C AND (RESSEQ 25:29)
10X-RAY DIFFRACTION10CHAIN C AND (RESSEQ 30:35)
11X-RAY DIFFRACTION11CHAIN E

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