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- PDB-5a6c: Concomitant binding of Afadin to LGN and F-actin directs planar s... -

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Basic information

Entry
Database: PDB / ID: 5a6c
TitleConcomitant binding of Afadin to LGN and F-actin directs planar spindle orientation
ComponentsG-PROTEIN-SIGNALING MODULATOR 2, AFADIN
KeywordsCELL ADHESION / MITOTIC SPINDLE ORIENTATION / LGN / AFADIN
Function / homology
Function and homology information


lateral cell cortex / cell cortex region / maintenance of centrosome location / establishment of protein localization to plasma membrane / positive regulation of cell-cell adhesion mediated by cadherin / pore complex assembly / establishment of endothelial intestinal barrier / positive regulation of cell-cell adhesion / positive regulation of spindle assembly / cell-cell adhesion mediated by cadherin ...lateral cell cortex / cell cortex region / maintenance of centrosome location / establishment of protein localization to plasma membrane / positive regulation of cell-cell adhesion mediated by cadherin / pore complex assembly / establishment of endothelial intestinal barrier / positive regulation of cell-cell adhesion / positive regulation of spindle assembly / cell-cell adhesion mediated by cadherin / bicellular tight junction assembly / cell-cell contact zone / Adherens junctions interactions / tight junction / GDP-dissociation inhibitor activity / dynein complex binding / pore complex / 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 / cell adhesion molecule binding / mitotic spindle organization / negative regulation of cell migration / adherens junction / small GTPase binding / regulation of protein localization / actin filament binding / cell-cell junction / cell junction / cell-cell signaling / cell cortex / G alpha (i) signalling events / cell adhesion / nuclear speck / cadherin binding / G protein-coupled receptor signaling pathway / protein domain specific binding / cell division / nucleotide binding / centrosome / positive regulation of gene expression / signal transduction / protein-containing complex / nucleoplasm / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
: / Afadin, cargo binding domain / : / GoLoco motif / GoLoco motif / GoLoco/GPR motif profile. / LGN motif, putative GEFs specific for G-alpha GTPases / Tetratricopeptide repeat / Ras association (RalGDS/AF-6) domain / Tetratricopeptide repeat ...: / Afadin, cargo binding domain / : / GoLoco motif / GoLoco motif / GoLoco/GPR motif profile. / LGN motif, putative GEFs specific for G-alpha GTPases / Tetratricopeptide repeat / Ras association (RalGDS/AF-6) domain / Tetratricopeptide repeat / Dilute domain / DIL domain / Dilute domain profile. / DIL / Ras-associating (RA) domain profile. / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain / Tetratricopeptide repeat / Forkhead associated domain / FHA domain / Forkhead-associated (FHA) domain / Tetratricopeptide repeat domain / Tetratricopeptide repeat / SMAD/FHA domain superfamily / 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 / Ubiquitin-like domain superfamily / Mainly Alpha
Similarity search - Domain/homology
Afadin / G-protein-signaling modulator 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.901 Å
AuthorsCarminati, M. / Gallini, S. / Pirovano, L. / Alfieri, A. / Bisi, S. / Mapelli, M.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2016
Title: Concomitant Binding of Afadin to Lgn and F-Actin Directs Planar Spindle Orientation.
Authors: Carminati, M. / Gallini, S. / Pirovano, L. / Alfieri, A. / Bisi, S. / Mapelli, M.
History
DepositionJun 25, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 30, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2016Group: Database references
Revision 1.2Jan 27, 2016Group: Structure summary
Revision 1.3Mar 2, 2016Group: Database references
Revision 1.4Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: G-PROTEIN-SIGNALING MODULATOR 2, AFADIN
B: G-PROTEIN-SIGNALING MODULATOR 2, AFADIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,2885
Polymers83,0002
Non-polymers2883
Water00
1
B: G-PROTEIN-SIGNALING MODULATOR 2, AFADIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5962
Polymers41,5001
Non-polymers961
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: G-PROTEIN-SIGNALING MODULATOR 2, AFADIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6923
Polymers41,5001
Non-polymers1922
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)169.880, 169.880, 169.880
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213

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Components

#1: Protein G-PROTEIN-SIGNALING MODULATOR 2, AFADIN


Mass: 41500.105 Da / Num. of mol.: 2
Fragment: LGN TPR DOMAIN RESIDUES 15-350, AFADIN RESIDUES 1719-1756
Source method: isolated from a genetically manipulated source
Details: FUSION PROTEIN SPANNING RESIDUES 15-350 OF HUMAN LGN AND RESIDUES 1709-1746 OF AFADIN
Source: (gene. exp.) HOMO SAPIENS (human) / Gene: GPSM2, LGN, MLLT4, AF6 / Plasmid: PGEX-6PI / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA / References: UniProt: P81274, UniProt: P55196
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
Sequence detailsP81274 P55196

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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: 4.66 Å3/Da / Density % sol: 73.6 % / Description: NONE
Crystal growpH: 8.25 / Details: 1.5 M AMMONIUM SULPHATE, 0.1 M TRIS-HCL PH 8.25

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00883
DetectorType: PILATUS / Detector: PIXEL / Date: Apr 5, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00883 Å / Relative weight: 1
ReflectionResolution: 2.9→45.4 Å / Num. obs: 34817 / % possible obs: 96.3 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Biso Wilson estimate: 77.8 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.6
Reflection shellResolution: 2.9→2.98 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 1.5 / % possible all: 95.8

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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 3RO2

3ro2


Resolution: 2.901→45.402 Å / SU ML: 0.46 / σ(F): 1.37 / Phase error: 25.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2523 1750 5 %
Rwork0.2059 --
obs0.2082 34817 95.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.901→45.402 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5732 0 15 0 5747
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015848
X-RAY DIFFRACTIONf_angle_d1.147894
X-RAY DIFFRACTIONf_dihedral_angle_d17.6372110
X-RAY DIFFRACTIONf_chiral_restr0.046847
X-RAY DIFFRACTIONf_plane_restr0.0041045
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9011-2.97950.36151440.33882543X-RAY DIFFRACTION96
2.9795-3.06710.3031410.29082519X-RAY DIFFRACTION97
3.0671-3.16610.33741470.27842607X-RAY DIFFRACTION99
3.1661-3.27930.31581400.26092584X-RAY DIFFRACTION99
3.2793-3.41050.29411320.25112605X-RAY DIFFRACTION99
3.4105-3.56570.24661310.2082587X-RAY DIFFRACTION98
3.5657-3.75360.26671350.20732603X-RAY DIFFRACTION98
3.7536-3.98860.24031330.19352533X-RAY DIFFRACTION97
3.9886-4.29640.25071330.17982483X-RAY DIFFRACTION93
4.2964-4.72830.1981350.17262541X-RAY DIFFRACTION95
4.7283-5.41160.24341180.21142546X-RAY DIFFRACTION95
5.4116-6.81430.27161240.22052487X-RAY DIFFRACTION92
6.8143-45.40790.22071370.16932429X-RAY DIFFRACTION87
Refinement TLS params.Method: refined / Origin x: -12.5507 Å / Origin y: 35.7585 Å / Origin z: -8.5509 Å
111213212223313233
T0.5562 Å20.0131 Å2-0.1226 Å2-0.4351 Å20.0008 Å2--0.6082 Å2
L0.8918 °2-0.4598 °20.2499 °2-0.555 °2-0.4402 °2--1.2146 °2
S0.1583 Å °0.1271 Å °-0.2468 Å °-0.2044 Å °0.0345 Å °0.1941 Å °0.2695 Å °-0.2714 Å °-0.1825 Å °
Refinement TLS groupSelection details: ALL

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