SAXSdb — 5yi4

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

Disrupted in schizophrenia 1 homolog,Nuclear distribution protein nudE-like 1

Mus musculus

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Insufficient information Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 765–852	Fragment：UNP residues 765-852,UNP residues 238-284	No other associated polymer	SOLUTION NMR NMR measurement conditions：pH 6.5；303 K；Ionic strength (raw mmCIF value) 50 NaCl；Pressure 1 NMR sample composition：0.8 mM [U-99% 13C; U-99% 15N] DISC1_Ndel1, 100% D2O \| 100% D2O NMR sample composition：0.8 mM [U-99% 15N] DISC1_Ndel1, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition：0.8 mM [U-99% 13C; U-99% 15N] DISC1_Ndel1, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition：0.8 mM no labelling DISC1_Ndel1, 100% D2O \| 100% D2O	Resolution not provided

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 5YI4	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6IRR Solution structure of DISC1/ATF4 complex Deposited 2018-11-14	Different construct Different experimental conditions	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 763–850（88 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；303 K；Ionic strength (raw mmCIF value) 100mM potassium phosphate；Pressure ambient NMR sample composition 0.8 mM [U-100% 13C; U-100% 15N] DISC1/ATF4 complex, 1 mM DTT, 1 mM EDTA, 100 mM potassium phosphate, 100% D2O \| 100% D2O NMR sample composition 0.8 mM [U-99% 15N] DISC1/ATF4 complex, 1 mM DTT, 1 mM EDTA, 100 mM potassium phosphate, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.8 mM DISC1/ATF4 complex, 1 mM DTT, 1 mM EDTA, 100 mM potassium phosphate, 100% D2O \| 100% D2O	Resolution not provided
9RUX Cryo-EM structure of DISC1 core Deposited 2025-07-05	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 322–722（401 aa） Chain B 322–722（401 aa） Chain C 322–722（401 aa） Chain D 322–722（401 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 Å

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	DISC1_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–92； UniProt 765–852

Disrupted in schizophrenia 1 homolog,Nuclear distribution protein nudE-like 1

Mus musculus

UniProt Q9ERR1

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Insufficient information Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 238–284	Fragment：UNP residues 765-852,UNP residues 238-284	No other associated polymer	SOLUTION NMR NMR measurement conditions：pH 6.5；303 K；Ionic strength (raw mmCIF value) 50 NaCl；Pressure 1 NMR sample composition：0.8 mM [U-99% 13C; U-99% 15N] DISC1_Ndel1, 100% D2O \| 100% D2O NMR sample composition：0.8 mM [U-99% 15N] DISC1_Ndel1, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition：0.8 mM [U-99% 13C; U-99% 15N] DISC1_Ndel1, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition：0.8 mM no labelling DISC1_Ndel1, 100% D2O \| 100% D2O	Resolution not provided

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 5YI4	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6KZJ Crystal structure of Ankyrin B/NdeL1 complex Deposited 2019-09-24	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 238–284（47 aa） Chain C 238–284（47 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5.6；289 K；1.9M ammonium sulfate, 0.16M potassium sodium tartrate tetrahydrate, 0.1M sodium citrate tribasic dehydrate pH 5.6	Resolution 1.50 Å R-free 0.211

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	NDEL1_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 99–145； UniProt 238–284

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	5yi4
Deposition date deposition_date	2017-10-02
Structure title title	Solution Structure of the DISC1/Ndel1 complex
Keywords keywords	DISC1, Ndel1, coiled coil, psychiatric disorder, PROTEIN BINDING; PROTEIN BINDING
Experimental Method method	SOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier	23.55 Å
Radius of gyration Rg (electron density) rg_electron	23.27 Å
Forward intensity I(0) i0	1374050000.00
Molecular weight molecular_weight	308670.0 kDa
Excluded volume excluded_volume	384870 Å³
Envelope volume envelope_volume	87679 Å³
Hydration-shell volume shell_volume	25920 Å³
Envelope diameter envelope_diameter	100.4 Å
Shell Rg shell_rg	34.95 Å
Envelope Rg envelope_rg	30.18 Å
Shape Rg shape_rg	23.33 Å
Total Rg total_rg	23.32 Å
Total atoms total_atoms	43460
Residues n_residues	2900
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	90.5 Å
Rg (real space) rg_real	24.01 Å
Rg uncertainty (real space) rg_real_error	1.09 Å
I(0) (real space) i0_real	1.3740e+09
I(0) uncertainty (real space) i0_real_error	1.9200e+07
Rg (reciprocal space) rg_reciprocal	23.90 Å
I(0) (reciprocal space) i0_reciprocal	1374000000.0000
Solution quality estimate total_estimate	0.6993
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	18.4 Å
Skewness Skewness skewness	0.665
Kurtosis Kurtosis kurtosis	-0.125
Angular range angular_range	— – 0.3350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1054000.0000
Real-space data points n_real_points	65
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.336; Stabil: 0.996; Sysdev: 1.000; Positv: 1.000; Valcen: 0.093; Smooth: 0.996

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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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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Description description	Disrupted in schizophrenia 1 homolog,Nuclear distribution protein nudE-like 1
Molecular weight formula_weight	15455.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	43460

来源生物 organism	Mus musculus
通用名 common_name	Mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Solution Structure of the DISC1/Ndel1 complex

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

Disrupted in schizophrenia 1 homolog,Nuclear distribution protein nudE-like 1

State in the Current Structure

Other States of the Same Protein in the Database

Disrupted in schizophrenia 1 homolog,Nuclear distribution protein nudE-like 1

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

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

fit	/app/data/saxs_computation/yi/5yi4/5yi4.fit
pddf	/app/data/pr_computation/yi/5yi4/5yi4.pr.out
profile	/app/data/saxs_computation/yi/5yi4/5yi4.dat