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- PDB-6n8p: Crystal structure of the human cell polarity protein Lethal Giant... -

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Basic information

Entry
Database: PDB / ID: 6n8p
TitleCrystal structure of the human cell polarity protein Lethal Giant Larvae 2 (Lgl2). Unphosphorylated, crystal form 1.
ComponentsLethal(2) giant larvae protein homolog 2
KeywordsLIPID BINDING PROTEIN / Lgl / Polarity / beta propeller
Function / homology
Function and homology information


establishment of spindle orientation / regulation of establishment or maintenance of cell polarity / L-leucine transport / regulation of Notch signaling pathway / myosin II binding / Golgi to plasma membrane transport / establishment or maintenance of epithelial cell apical/basal polarity / cortical actin cytoskeleton organization / cortical actin cytoskeleton / exocytosis ...establishment of spindle orientation / regulation of establishment or maintenance of cell polarity / L-leucine transport / regulation of Notch signaling pathway / myosin II binding / Golgi to plasma membrane transport / establishment or maintenance of epithelial cell apical/basal polarity / cortical actin cytoskeleton organization / cortical actin cytoskeleton / exocytosis / GTPase activator activity / PDZ domain binding / adherens junction / cell division / intracellular membrane-bounded organelle / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Lethal(2) giant larvae protein / Lethal giant larvae homologue 2 / LLGL2 / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
LLGL scribble cell polarity complex component 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.193 Å
AuthorsAlmagor, L. / Weis, W.I.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)MH58570 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: Structural insights into the aPKC regulatory switch mechanism of the human cell polarity protein lethal giant larvae 2.
Authors: Almagor, L. / Ufimtsev, I.S. / Ayer, A. / Li, J. / Weis, W.I.
History
DepositionNov 30, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2019Provider: repository / Type: Initial release
Revision 1.1May 29, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jun 12, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 13, 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

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Assembly

Deposited unit
A: Lethal(2) giant larvae protein homolog 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,3112
Polymers109,2751
Non-polymers351
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area170 Å2
ΔGint-10 kcal/mol
Surface area34920 Å2
Unit cell
Length a, b, c (Å)78.699, 118.489, 126.639
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 Lethal(2) giant larvae protein homolog 2 / HGL


Mass: 109275.109 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LLGL2 / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q6P1M3
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl

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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: 2.7 Å3/Da / Density % sol: 54.47 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 19.8 % PEG 3350, 0.29 M Na2SO4, 0.1 M bis-tris propane pH 7.5, 3% methanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1.0055 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0055 Å / Relative weight: 1
ReflectionResolution: 3.19→39.35 Å / Num. obs: 20282 / % possible obs: 99.8 % / Redundancy: 6.5 % / CC1/2: 0.972 / Rmerge(I) obs: 0.419 / Net I/σ(I): 5.9
Reflection shellResolution: 3.19→3.41 Å / Redundancy: 6.8 % / Rmerge(I) obs: 2.097 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 3625 / CC1/2: 0.495 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
Aimlessdata scaling
RefinementResolution: 3.193→39.349 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.21
RfactorNum. reflection% reflection
Rfree0.2497 1989 9.84 %
Rwork0.2036 --
obs0.2081 20221 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.193→39.349 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6452 0 1 0 6453
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026624
X-RAY DIFFRACTIONf_angle_d0.4799030
X-RAY DIFFRACTIONf_dihedral_angle_d11.1263921
X-RAY DIFFRACTIONf_chiral_restr0.0421009
X-RAY DIFFRACTIONf_plane_restr0.0041173
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1934-3.27320.38341410.32661269X-RAY DIFFRACTION98
3.2732-3.36170.33041370.26731267X-RAY DIFFRACTION100
3.3617-3.46050.31661470.25811291X-RAY DIFFRACTION100
3.4605-3.57220.31981230.24731295X-RAY DIFFRACTION100
3.5722-3.69970.26161550.23541266X-RAY DIFFRACTION100
3.6997-3.84780.31681320.22171299X-RAY DIFFRACTION100
3.8478-4.02270.2741500.21441276X-RAY DIFFRACTION100
4.0227-4.23460.22551390.19021305X-RAY DIFFRACTION100
4.2346-4.49950.20941490.16721278X-RAY DIFFRACTION100
4.4995-4.84640.19231310.16271309X-RAY DIFFRACTION100
4.8464-5.3330.23311460.16281315X-RAY DIFFRACTION100
5.333-6.10220.24251380.19351324X-RAY DIFFRACTION100
6.1022-7.67880.25651410.20911332X-RAY DIFFRACTION100
7.6788-39.35250.20191600.18821406X-RAY DIFFRACTION99
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)
10.9696-0.09280.4312.48221.27142.42050.0043-0.2291-0.17640.0223-0.05770.4793-0.017-0.33390.07140.4169-0.00890.07680.52760.02220.6054-0.245264.538962.2552
23.15920.4176-0.98862.6656-1.44623.0189-0.1151-0.55070.1230.52850.04060.1681-0.36840.32650.05960.44440.0179-0.02550.4662-0.06340.402314.867282.884973.7856
30.750.46081.02980.58520.96972.4609-0.07760.0604-0.0399-0.2076-0.0345-0.0013-0.1170.15330.09890.47180.010.01060.5622-0.01580.475713.106771.927737.7569
41.10550.9582-0.31891.89850.01661.3263-0.11740.21220.1376-0.2730.07570.1438-0.2596-0.1870.02690.56320.0171-0.09620.6073-0.00530.5071-2.70166.09427.3713
51.73680.70732.49050.2821.00543.5558-0.0207-0.47590.04980.3369-0.01640.23760.1605-0.6676-0.00030.5594-0.0739-0.03510.76880.00910.6934-9.387655.544130.3379
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 18 through 159 )
2X-RAY DIFFRACTION2chain 'A' and (resid 160 through 291 )
3X-RAY DIFFRACTION3chain 'A' and (resid 292 through 523 )
4X-RAY DIFFRACTION4chain 'A' and (resid 524 through 822 )
5X-RAY DIFFRACTION5chain 'A' and (resid 823 through 926 )

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