SAXSdb — 4zrj

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Merlin

Homo sapiens

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–320 Chain B； UniProt 506–595	Fragment：FERM domain, UNP residues 1-320 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

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 4ZRJ	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 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 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 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
6CDS Human neurofibromin 2/merlin/schwannomin residues 1-339 in complex with PIP2 Deposited 2018-02-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–339（339 aa）	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
6CDS Human neurofibromin 2/merlin/schwannomin residues 1-339 in complex with PIP2 Deposited 2018-02-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–339（339 aa）	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
7LWH Human neurofibromin 2/merlin residues 1-339 in complex with LATS1 Deposited 2021-03-01	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 1–339（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 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	MERL_HUMAN
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 1–320； UniProt 1–320 Author chain B； PDBConstruct 1–90； UniProt 506–595

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	4zrj
Deposition date deposition_date	2015-05-12
Structure title title	Structure of Merlin-FERM and CTD
Keywords keywords	Merlin, FERM, CTD, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	23.79 Å
Radius of gyration Rg (electron density) rg_electron	22.65 Å
Forward intensity I(0) i0	31289300.00
Molecular weight molecular_weight	43915.0 kDa
Excluded volume excluded_volume	55378 Å³
Envelope volume envelope_volume	67254 Å³
Hydration-shell volume shell_volume	24929 Å³
Envelope diameter envelope_diameter	76.8 Å
Shell Rg shell_rg	29.33 Å
Envelope Rg envelope_rg	22.91 Å
Shape Rg shape_rg	22.60 Å
Total Rg total_rg	23.65 Å
Total atoms total_atoms	3093
Residues n_residues	379
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	73.8 Å
Rg (real space) rg_real	23.67 Å
Rg uncertainty (real space) rg_real_error	0.35 Å
I(0) (real space) i0_real	3.1290e+07
I(0) uncertainty (real space) i0_real_error	4.0730e+05
Rg (reciprocal space) rg_reciprocal	23.70 Å
I(0) (reciprocal space) i0_reciprocal	31290000.0000
Solution quality estimate total_estimate	0.9099
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	28.8 Å
Skewness Skewness skewness	0.159
Kurtosis Kurtosis kurtosis	-0.542
Angular range angular_range	— – 0.3350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5586000.0000
Real-space data points n_real_points	65
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.947; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.985

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Merlin
Molecular weight formula_weight	37730.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3200

MAGAIASRMSFSSLKRKQPKTFTVRIVTMDAEMEFNCEMKWKGKDLFDLVCRTLGLRETWFFGLQYTIKDTVAWLKMDKKVLDHDVSKEEPVTFHFLAKFYPENAEEELVQEITQHLFFLQVKKQILDEKIYCPPEASVLLASYAVQAKYGDYDPSVHKRGFLAQEELLPKRVINLYQMTPEMWEERITAWYAEHRGRARDEAEMEYLKIAQDLEMYGVNYFAIRNKKGTELLLGVDALGLHIYDPENRLTPKISFPWNEIRNISYSDKEFTIKPLDKKIDVFKFNSSKLRVNKLILQLCIGNHDLFMRRRKADSLEVQQ

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Merlin
Molecular weight formula_weight	10749.2 kDa
Mutation mutation	S518D, A585W
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

SFDFKDTDMKRLDMEIEKEKVEYMEKSKHLQEQLNELKTEIEALKLKERETALDILHNENSDRGGSSKHNTIKKLTLQSWKSRVAFFEEL

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	107

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d4zrja1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.1 — Ubiquitin-like
Family Family family	d.15.1.0 — automated matches

Domain ID domain_id	d4zrja2
Class class	a — All alpha proteins
Fold Fold fold	a.11 — Acyl-CoA binding protein-like
Superfamily Superfamily superfamily	a.11.2 — Second domain of FERM
Family Family family	a.11.2.0 — automated matches

Domain ID domain_id	d4zrja3
Class class	b — All beta proteins
Fold Fold fold	b.55 — PH domain-like barrel
Superfamily Superfamily superfamily	b.55.1 — PH domain-like
Family Family family	b.55.1.0 — automated matches

CATH v4.4 (3 domains)

Domain ID domain_id	4zrjA01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

Domain ID domain_id	4zrjA02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	80 — Acyl-CoA Binding Protein
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	4zrjA03
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	29 — PH-domain like
Homologous superfamily homologous superfamily	30 — Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)

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8. Citations (1)

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Unit-cell length a length_a	67.895 Å
Unit-cell length b length_b	68.202 Å
Unit-cell length c length_c	82.320 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	31.505 Å
R factor r_factor	0.1925
R_work r_work	0.1863
R_free r_free	0.2475

fit	/app/data/saxs_computation/zr/4zrj/4zrj.fit
pddf	/app/data/pr_computation/zr/4zrj/4zrj.pr.out
profile	/app/data/saxs_computation/zr/4zrj/4zrj.dat

Structure of Merlin-FERM and CTD

1. Protein Identity and Related Structures Protein Identity & Related Structures

Merlin

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)