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- PDB-6n8r: Crystal structure of the human cell polarity protein Lethal Giant... -

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Basic information

Entry
Database: PDB / ID: 6n8r
TitleCrystal structure of the human cell polarity protein Lethal Giant Larvae 2 (Lgl2). aPKC phosphorylated, crystal form 2.
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 / cytosol / cytoplasm
Similarity search - Function
Lethal(2) giant larvae protein / Lethal giant larvae homologue 2 / LLGL2 / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / 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: 1.91 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.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _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)109,4033
Polymers109,2751
Non-polymers1282
Water5,909328
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area390 Å2
ΔGint-8 kcal/mol
Surface area34470 Å2
Unit cell
Length a, b, c (Å)173.570, 46.562, 137.228
Angle α, β, γ (deg.)90.000, 115.840, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1001-

CL

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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
Details: Human Lgl2(13-978) aPKC phosphorylated at S641, S645, S649, S653, S660, S663 and S680. The phosphorylated residues are all positioned in an unstructered loop.
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 / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 328 / 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: 2.28 Å3/Da / Density % sol: 46.14 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 25% PEG 1500, 100 mM SPG pH 8.0

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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 PILATUS 6M / Detector: PIXEL / Date: Apr 29, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.91→39.05 Å / Num. obs: 66987 / % possible obs: 86.9 % / Redundancy: 6.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.047 / Rrim(I) all: 0.121 / Net I/σ(I): 7.9 / Num. measured all: 429153 / Scaling rejects: 2
Reflection shellResolution: 1.91→1.95 Å / Redundancy: 4.6 % / Rmerge(I) obs: 10.548 / Num. unique obs: 2420 / CC1/2: 0.117 / Rpim(I) all: 5.476 / Rrim(I) all: 11.922 / % possible all: 47.1

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 1.91→34.272 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.47
RfactorNum. reflection% reflection
Rfree0.2192 1888 5 %
Rwork0.1961 --
obs0.1973 37726 48.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 128.77 Å2 / Biso mean: 39.6811 Å2 / Biso min: 6.37 Å2
Refinement stepCycle: final / Resolution: 1.91→34.272 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6472 0 7 328 6807
Biso mean--30.65 34.73 -
Num. residues----831
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9102-1.96180.3937100.31231441543
1.9618-2.01950.365290.3512302394
2.0195-2.08470.3465240.30284574818
2.0847-2.15920.3018480.289279183914
2.1592-2.24560.3028970.28221567166428
2.2456-2.34780.32281100.30692156226639
2.3478-2.47160.3061440.27952542268645
2.4716-2.62640.28691560.2743008316453
2.6264-2.82910.29961790.25543651383065
2.8291-3.11360.27352560.24464526478280
3.1136-3.56370.22522820.19825397567995
3.5637-4.48840.16472980.15475602590098
4.4884-34.27780.18222750.1585767604298
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)
10.1069-0.0268-0.050.02680.06690.1662-0.0114-0.05230.0599-0.1164-0.1043-0.0069-0.20730.2225-0.06680.2303-0.1154-0.01780.1030.08960.1393126.9632-50.9747145.914
20.0209-0.03130.02780.0790.01280.0806-0.07020.00920.05830.08910.0609-0.1731-0.04640.27730.00070.2165-0.02920.01010.27620.02990.2095139.7048-57.5882171.6218
30.13770.0168-0.05480.0215-0.01810.0435-0.0624-0.1676-0.0030.0766-0.02140.041-0.06940.0018-0.02250.23270.006-0.01170.0915-0.00960.1372116.341-54.8752167.441
40.1610.00330.13410.165-0.10210.2091-0.0173-0.2262-0.00120.1593-0.0150.0774-0.2436-0.3389-0.00020.22020.05260.02810.2602-0.04830.214494.6512-54.3104151.6395
50.1524-0.0999-0.03390.1514-0.03920.4826-0.05070.0124-0.02970.1297-0.04140.0303-0.2344-0.6346-0.2327-0.05170.12040.04310.2706-0.04150.168989.5625-54.0663131.0781
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 126 )A1 - 126
2X-RAY DIFFRACTION2chain 'A' and (resid 127 through 285 )A127 - 285
3X-RAY DIFFRACTION3chain 'A' and (resid 286 through 375 )A286 - 375
4X-RAY DIFFRACTION4chain 'A' and (resid 376 through 551 )A376 - 551
5X-RAY DIFFRACTION5chain 'A' and (resid 552 through 926 )A552 - 926

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