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6n8s

Crystal structure of the human cell polarity protein Lethal Giant Larvae 2 (Lgl2). aPKC phosphorylated, crystal form 3.

Method: X-RAY DIFFRACTION Dmax: 141.4 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Lethal(2) giant larvae protein homolog 2

Homo sapiens

UniProt Q6P1M3

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 13–978 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；295.15 K；1.4 M ammonium sulfate, 100 mM Hepes pH 7.5, 150 mM NaCl, 1.07% 1,6-hexanediol Resolution 3.90 Å R-free 0.298
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain D； UniProt 13–978 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；295.15 K；1.4 M ammonium sulfate, 100 mM Hepes pH 7.5, 150 mM NaCl, 1.07% 1,6-hexanediol Resolution 3.90 Å R-free 0.298

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 6N8S Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3WP0 Crystal structure of Dlg GK in complex with a phosphor-Lgl2 peptide Deposited 2014-01-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 640–654（15 aa） Fragment：UNP residues 640-654
Non-standard monomer：Yes (specific site not provided by mmCIF) GOL GLYCEROL × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；291 K；0.2M lithium chloride, 20% PEG3350, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.04 Å R-free 0.202
3WP1 Phosphorylation-dependent interaction between tumor suppressors Dlg and Lgl Deposited 2014-01-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 646–657（12 aa） Fragment：UNP residues 646-657
Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 4 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.80 Å R-free 0.268
6N8P Crystal structure of the human cell polarity protein Lethal Giant Larvae 2 (Lgl2). Unphosphorylated, crystal form 1. Deposited 2018-11-30 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 13–978（966 aa）
Not recorded CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；295.15 K；19.8 % PEG 3350, 0.29 M Na2SO4, 0.1 M bis-tris propane pH 7.5, 3% methanol
Resolution 3.19 Å R-free 0.250
6N8Q Crystal structure of the human cell polarity protein Lethal Giant Larvae 2 (Lgl2). Unphosphorylated, crystal form 2. Deposited 2018-11-30 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 13–978（966 aa）
Not recorded CL CHLORIDE ION × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；295.15 K；18-21 % PEG 2000 MME, 80-100 mM SPG pH 6.0
Resolution 2.20 Å R-free 0.226
6N8R Crystal structure of the human cell polarity protein Lethal Giant Larvae 2 (Lgl2). aPKC phosphorylated, crystal form 2. Deposited 2018-11-30 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 13–978（966 aa）
Not recorded CL CHLORIDE ION × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；295.15 K；25% PEG 1500, 100 mM SPG pH 8.0
Resolution 1.91 Å R-free 0.219
8R3X Crystal structure of aPKC Iota kinase domain with LLGL2 peptide Deposited 2023-11-10 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 641–660（20 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；300 K；Morpheus Condition: 25% (v/v) MPD, 25% (v/v) PEG 1000, 25% (v/v) PEG 3350, 0.3 M NaNO3, 0.3 M Na2HPO4, 0.3 M (NH4)2SO4, 0.1 M MES/imidazole pH 6.5
Resolution 2.59 Å R-free 0.269
8R3X Crystal structure of aPKC Iota kinase domain with LLGL2 peptide Deposited 2023-11-10 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 641–660（20 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；300 K；Morpheus Condition: 25% (v/v) MPD, 25% (v/v) PEG 1000, 25% (v/v) PEG 3350, 0.3 M NaNO3, 0.3 M Na2HPO4, 0.3 M (NH4)2SO4, 0.1 M MES/imidazole pH 6.5
Resolution 2.59 Å R-free 0.269
9EJK Lgl2 bound to the aPKCiota-Par6b complex in nucleotide-free form. Head sub-complex region subtracted Deposited 2024-11-28 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 13–978（966 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.08 Å
9EJL Lgl2 bound to the aPKCiota-Par6B complex in nucleotide-free form. Conformation with visible head sub-complex. Deposited 2024-11-28 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 13–978（966 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.48 Å
9EJM Lgl2 bound to the aPKCiota-Par6B complex in its ADP-bound form Deposited 2024-11-28 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 13–978（966 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.33 Å

9 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name L2GL2_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 2–967； UniProt 13–978 Author chain D； PDBConstruct 2–967； UniProt 13–978

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 6n8s

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6n8s
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6n8s
Deposition date deposition_date2018-11-30
Structure title titleCrystal structure of the human cell polarity protein Lethal Giant Larvae 2 (Lgl2). aPKC phosphorylated, crystal form 3.
Keywords keywordsLgl, Polarity, beta propeller, LIPID BINDING PROTEIN; LIPID BINDING PROTEIN
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier41.77 Å
Radius of gyration Rg (electron density) rg_electron41.33 Å
Forward intensity I(0) i0475803000.00
Molecular weight molecular_weight181570.0 kDa
Excluded volume excluded_volume228230 ų
Envelope volume envelope_volume303600 ų
Hydration-shell volume shell_volume61510 ų
Envelope diameter envelope_diameter150.6 Å
Shell Rg shell_rg46.28 Å
Envelope Rg envelope_rg41.23 Å
Shape Rg shape_rg41.35 Å
Total Rg total_rg41.50 Å
Total atoms total_atoms12829
Residues n_residues1664
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax141.4 Å
Rg (real space) rg_real41.82 Å
Rg uncertainty (real space) rg_real_error1.41 Å
I(0) (real space) i0_real4.7580e+08
I(0) uncertainty (real space) i0_real_error7.8840e+06
Rg (reciprocal space) rg_reciprocal41.77 Å
I(0) (reciprocal space) i0_reciprocal475800000.0000
Solution quality estimate total_estimate0.8081
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary52.1 Å
Skewness Skewness skewness0.371
Kurtosis Kurtosis kurtosis-0.286
Angular range angular_range— – 0.1900 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha311900000.0000
Real-space data points n_real_points39
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.836; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id6n8sA01
Class class2 — Mainly Beta
Architecture architecture130 — 7 Propeller
Topology topology10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily10 — YVTN repeat-like/Quinoprotein amine dehydrogenase
Domain ID domain_id6n8sD01
Class class2 — Mainly Beta
Architecture architecture130 — 7 Propeller
Topology topology10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily10 — YVTN repeat-like/Quinoprotein amine dehydrogenase
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8. Citations (1)

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9. Files and Curves (10)