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6cds

Human neurofibromin 2/merlin/schwannomin residues 1-339 in complex with PIP2

Method: X-RAY DIFFRACTION Dmax: 128.5 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Merlin

Homo sapiens

UniProt P35240

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 1–339 Mutation：G302E PIO [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate × 1 PO4 PHOSPHATE ION × 1 PEG DI(HYDROXYETHYL)ETHER × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；293.15 K；100 mM HEPES (pH 7.5), 50 mM MgCl2(H2O)6, 35 % PEG 550 monomethyl ether Resolution 2.62 Å R-free 0.237
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 1–339 Mutation：G302E PIO [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate × 1 PO4 PHOSPHATE ION × 1 PEG DI(HYDROXYETHYL)ETHER × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；293.15 K；100 mM HEPES (pH 7.5), 50 mM MgCl2(H2O)6, 35 % PEG 550 monomethyl ether Resolution 2.62 Å R-free 0.237

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 6CDS Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1H4R Crystal Structure of the FERM domain of Merlin, the Neurofibromatosis 2 Tumor Suppressor Protein. Deposited 2001-05-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–313（313 aa） Fragment：FERM DOMAIN RESIDUES 1-313
Chain B 1–313（313 aa） Fragment：FERM DOMAIN RESIDUES 1-313
Not recorded SO4 SULFATE ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；THE PROTEIN WAS CRYSTALLIZED USING HANGING-DROP VAPOR DIFFUSION WIHTH 56% AMMONIUM SULFATE, 2% DIOXANE, 100 MM CACODYLATE, PH 6.5. A 1:1 RATIO OF PROTEIN TO WELL SOLUTION WAS USED.
Resolution 1.80 Å R-free 0.227
3U8Z human merlin FERM domain Deposited 2011-10-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 18–312（295 aa） Fragment：FERM domain (UNP residues 20-312)
Chain C 18–312（295 aa） Fragment：FERM domain (UNP residues 20-312)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；protein in 50 mM Tris, pH 8.0, 300 mM sodium chloride, reservoir: 4.5% PEG4000, 0.2 M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.64 Å R-free 0.229
3U8Z human merlin FERM domain Deposited 2011-10-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain B 18–312（295 aa） Fragment：FERM domain (UNP residues 20-312)
Chain D 18–312（295 aa） Fragment：FERM domain (UNP residues 20-312)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；protein in 50 mM Tris, pH 8.0, 300 mM sodium chloride, reservoir: 4.5% PEG4000, 0.2 M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.64 Å R-free 0.229
4ZRI Crystal structure of Merlin-FERM and Lats2 Deposited 2015-05-12 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 1–320（320 aa） Fragment：FERM domain, UNP residues 1-320
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；18% iso-Propanol, 0.1M Tris, 5% PEG8000
Resolution 2.70 Å R-free 0.270
4ZRI Crystal structure of Merlin-FERM and Lats2 Deposited 2015-05-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–320（320 aa） Fragment：FERM domain, UNP residues 1-320
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；18% iso-Propanol, 0.1M Tris, 5% PEG8000
Resolution 2.70 Å R-free 0.270
4ZRJ Structure of Merlin-FERM and CTD Deposited 2015-05-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–320（320 aa） Fragment：FERM domain, UNP residues 1-320
Chain B 506–595（90 aa） Fragment：C terminal domain, UNP residues 506-595
Mutation：S518D, A585W GOL GLYCEROL × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；0.1 M Bis-Tris, 21% PEG 3000
Resolution 2.30 Å R-free 0.247
7LWH Human neurofibromin 2/merlin residues 1-339 in complex with LATS1 Deposited 2021-03-01 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 1–339（339 aa）
Not recorded IMD IMIDAZOLE × 3 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；600 mM imidazole (pH 6.5), 15% (w/v) polyethylene glycol 3,350
Resolution 1.61 Å R-free 0.233

5 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name MERL_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–339； UniProt 1–339 Author chain B； PDBConstruct 1–339； UniProt 1–339

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 6cds

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id6cds
Deposition date deposition_date2018-02-09
Structure title titleHuman neurofibromin 2/merlin/schwannomin residues 1-339 in complex with PIP2
Keywords keywordsNEUROFIBROMIN 2, SCHWANNOMIN, merlin, Tumor Suppressor protein, SIGNALING PROTEIN; SIGNALING 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_guinier36.46 Å
Radius of gyration Rg (electron density) rg_electron35.99 Å
Forward intensity I(0) i094672700.00
Molecular weight molecular_weight78175.0 kDa
Excluded volume excluded_volume98130 ų
Envelope volume envelope_volume143390 ų
Hydration-shell volume shell_volume34768 ų
Envelope diameter envelope_diameter140.1 Å
Shell Rg shell_rg39.98 Å
Envelope Rg envelope_rg36.28 Å
Shape Rg shape_rg35.90 Å
Total Rg total_rg36.62 Å
Total atoms total_atoms5491
Residues n_residues650
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 dmax128.5 Å
Rg (real space) rg_real36.67 Å
Rg uncertainty (real space) rg_real_error1.51 Å
I(0) (real space) i0_real9.4670e+07
I(0) uncertainty (real space) i0_real_error1.7360e+06
Rg (reciprocal space) rg_reciprocal36.54 Å
I(0) (reciprocal space) i0_reciprocal94660000.0000
Solution quality estimate total_estimate0.8523
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary35.9 Å
Skewness Skewness skewness0.403
Kurtosis Kurtosis kurtosis-0.454
Angular range angular_range— – 0.2150 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha7177000.0000
Real-space data points n_real_points44
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.814; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.722; Smooth: 0.912
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (6 domains)

Domain ID domain_idd6cdsa1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamilyd.15.1 — Ubiquitin-like
Family Family familyd.15.1.0 — automated matches
Domain ID domain_idd6cdsa2
Class classa — All alpha proteins
Fold Fold folda.11 — Acyl-CoA binding protein-like
Superfamily Superfamily superfamilya.11.2 — Second domain of FERM
Family Family familya.11.2.0 — automated matches
Domain ID domain_idd6cdsa3
Class classb — All beta proteins
Fold Fold foldb.55 — PH domain-like barrel
Superfamily Superfamily superfamilyb.55.1 — PH domain-like
Family Family familyb.55.1.0 — automated matches
Domain ID domain_idd6cdsb1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamilyd.15.1 — Ubiquitin-like
Family Family familyd.15.1.0 — automated matches
Domain ID domain_idd6cdsb2
Class classa — All alpha proteins
Fold Fold folda.11 — Acyl-CoA binding protein-like
Superfamily Superfamily superfamilya.11.2 — Second domain of FERM
Family Family familya.11.2.0 — automated matches
Domain ID domain_idd6cdsb3
Class classb — All beta proteins
Fold Fold foldb.55 — PH domain-like barrel
Superfamily Superfamily superfamilyb.55.1 — PH domain-like
Family Family familyb.55.1.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id6cdsA01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
Domain ID domain_id6cdsB01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
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8. Citations (1)

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9. Files and Curves (10)