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- PDB-6n8s: Crystal structure of the human cell polarity protein Lethal Giant... -

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Basic information

Entry
Database: PDB / ID: 6n8s
TitleCrystal structure of the human cell polarity protein Lethal Giant Larvae 2 (Lgl2). aPKC phosphorylated, crystal form 3.
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 / establishment or maintenance of epithelial cell apical/basal polarity / cortical actin cytoskeleton organization / cortical actin cytoskeleton / regulation of protein secretion / exocytosis ...establishment of spindle orientation / regulation of establishment or maintenance of cell polarity / L-leucine transport / regulation of Notch signaling pathway / myosin II binding / establishment or maintenance of epithelial cell apical/basal polarity / cortical actin cytoskeleton organization / cortical actin cytoskeleton / regulation of protein secretion / exocytosis / GTPase activator activity / PDZ domain binding / adherens junction / cell division / intracellular membrane-bounded organelle / plasma membrane / cytoplasm / cytosol
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 / MOLECULAR REPLACEMENT / Resolution: 3.9 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)218,5502
Polymers218,5502
Non-polymers00
Water00
1
A: Lethal(2) giant larvae protein homolog 2


Theoretical massNumber of molelcules
Total (without water)109,2751
Polymers109,2751
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Lethal(2) giant larvae protein homolog 2


Theoretical massNumber of molelcules
Total (without water)109,2751
Polymers109,2751
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)130.871, 130.871, 277.649
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 Lethal(2) giant larvae protein homolog 2 / HGL


Mass: 109275.109 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Human Lgl2(13-978) aPKC phosphorylated at S641, S645, S649, S653, S660, S663 and S680
Source: (gene. exp.) Homo sapiens (human) / Gene: LLGL2 / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q6P1M3
Compound detailsS641, S645, S649, S653, S660, S663 and S680 are all on an unstructured loop

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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: 2.72 Å3/Da / Density % sol: 54.78 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1.4 M ammonium sulfate, 100 mM Hepes pH 7.5, 150 mM NaCl, 1.07% 1,6-hexanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 3.9→39.66 Å / Num. obs: 22815 / % possible obs: 99.9 % / Redundancy: 13.1 % / CC1/2: 0.953 / Rmerge(I) obs: 1.246 / Net I/σ(I): 4
Reflection shellResolution: 3.9→4.21 Å / Redundancy: 13.8 % / Rmerge(I) obs: 4.841 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 4624 / CC1/2: 0.416 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.9→39.66 Å / SU ML: 0.57 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.52
RfactorNum. reflection% reflection
Rfree0.2978 1986 8.76 %
Rwork0.2515 --
obs0.2556 22670 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.9→39.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12829 0 0 0 12829
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00213167
X-RAY DIFFRACTIONf_angle_d0.45317965
X-RAY DIFFRACTIONf_dihedral_angle_d6.6347785
X-RAY DIFFRACTIONf_chiral_restr0.0422029
X-RAY DIFFRACTIONf_plane_restr0.0042329
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.9-3.99750.36961340.35431439X-RAY DIFFRACTION98
3.9975-4.10540.36391370.33831437X-RAY DIFFRACTION99
4.1054-4.22610.3751390.30221442X-RAY DIFFRACTION100
4.2261-4.36240.2871390.27221440X-RAY DIFFRACTION100
4.3624-4.51810.33171410.25791461X-RAY DIFFRACTION100
4.5181-4.69870.33021400.25171455X-RAY DIFFRACTION100
4.6987-4.91220.28871400.24211446X-RAY DIFFRACTION100
4.9122-5.17060.26851410.23351474X-RAY DIFFRACTION100
5.1706-5.49380.28381410.25731472X-RAY DIFFRACTION100
5.4938-5.91670.3341430.26281476X-RAY DIFFRACTION100
5.9167-6.50980.29881430.25121494X-RAY DIFFRACTION100
6.5098-7.44630.30891430.23341494X-RAY DIFFRACTION100
7.4463-9.36120.26481480.21231539X-RAY DIFFRACTION100
9.3612-39.66230.23121570.20631615X-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)
12.23830.4094-0.41035.3821-1.26960.84320.0792-0.29740.9967-0.064-0.09831.2328-0.0521-0.249-0.14250.80160.04250.0750.714-0.11820.873-28.198123.5154-49.3536
21.7360.55390.23044.8803-0.96372.3591-0.1605-0.08290.4247-0.0359-0.0234-0.9509-0.15250.18750.30820.7283-0.1441-0.07250.7049-0.0330.8357-6.024834.8647-52.8494
31.05460.95080.29891.90970.00340.6279-0.01690.2187-0.02360.00120.2776-0.38880.05820.0223-0.25340.71370.07780.14060.7292-0.13910.9354-11.9467-9.6366-52.4131
41.8264-0.93550.46065.2683-3.20095.15450.30190.2589-0.451-0.21120.60410.87430.68430.0416-0.83340.94780.0568-0.06170.8745-0.13811.0547-25.5166-31.6396-58.0627
53.75272.22771.20916.58130.46940.9092-0.28070.1423-0.2745-0.29070.36120.85480.40980.1224-0.120.8191-0.05860.08670.8363-0.12210.852-37.2309-14.344-50.5611
66.69396.14622.05675.63861.88640.6248-0.53840.2283-0.6734-0.58310.5377-0.16920.16370.0522-0.03181.1044-0.09740.02570.84320.13271.3173-61.3023-17.486-46.9138
77.8054-0.52950.38044.6568-0.51921.75680.29520.02040.3704-0.39160.2187-0.38880.35770.5277-0.60471.2478-0.15910.19280.7639-0.25281.0338-74.1783-44.0259-53.9511
80.09620.0846-0.4784.805-0.08622.2856-0.0457-0.0654-0.9883-0.2347-0.0917-0.6490.3098-0.61240.19940.9735-0.2074-0.16780.937-0.16261.0995-88.6368-24.8659-51.5717
93.11521.0591-0.54971.35550.07030.1690.2910.4190.7538-0.48180.25560.5547-0.1130.1253-0.10010.85050.1119-0.0530.85160.06650.625-78.32874.5671-48.83
104.90910.97990.53024.0524-1.09491.2597-0.11650.13321.164-0.2410.13410.3164-0.0828-0.15430.03760.95430.09310.09350.79790.12650.8822-65.125225.1704-54.9473
111.66033.1287-0.20528.0814-3.11123.4001-0.44050.58860.5376-1.75670.37720.12060.09480.81170.2420.7936-0.14330.16540.7121-0.01481.2279-55.96072.304-49.6846
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 12 through 146 )
2X-RAY DIFFRACTION2chain 'A' and (resid 147 through 354 )
3X-RAY DIFFRACTION3chain 'A' and (resid 355 through 608 )
4X-RAY DIFFRACTION4chain 'A' and (resid 609 through 749 )
5X-RAY DIFFRACTION5chain 'A' and (resid 750 through 926 )
6X-RAY DIFFRACTION6chain 'D' and (resid 12 through 107 )
7X-RAY DIFFRACTION7chain 'D' and (resid 108 through 227 )
8X-RAY DIFFRACTION8chain 'D' and (resid 228 through 375 )
9X-RAY DIFFRACTION9chain 'D' and (resid 376 through 523 )
10X-RAY DIFFRACTION10chain 'D' and (resid 524 through 857 )
11X-RAY DIFFRACTION11chain 'D' and (resid 858 through 926 )

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