SAXSdb — 1ejq

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

SYNDECAN-4

OrganismNot specified

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 171–198 Chain B； UniProt 171–198	Fragment：WHOLE CYTOPLASMIC DOMAIN (RESIDUES 171-198)	No other associated polymer	SOLUTION NMR NMR measurement conditions：pH 7.4；298 K；Ionic strength (raw mmCIF value) 50mM sodium phosphate；Pressure 1 NMR measurement conditions：pH 7.4；298 K；Ionic strength (raw mmCIF value) 50mM sodium phosphate；Pressure 1 NMR measurement conditions：pH 7.4；298 K；Ionic strength (raw mmCIF value) 50mM sodium phosphate；Pressure 1 NMR sample composition：2-4mM Syndecan-4 cytoplasmic domain;Molar ratio of 4:1(syndecan-4 peptide:PIP2);50mM sodium phosphate;90% H2O 10% D2O \| 90% H2O/10% D2O NMR sample composition：2-4mM Syndecan-4 cytoplasmic domain;Molar ratio of 4:1(syndecan-4 peptide:PIP2);50mM sodium phosphate;90% H2O 10% D2O \| 90% H2O/10% D2O NMR sample composition：2-4mM Syndecan-4 cytoplasmic domain;Molar ratio of 4:1(syndecan-4 peptide:PIP2);50mM sodium phosphate;90% H2O 10% 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 1EJQ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1EJP SOLUTION STRUCTURE OF THE SYNDECAN-4 WHOLE CYTOPLASMIC DOMAIN Deposited 2000-03-03	Different construct Different experimental conditions	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 171–198（28 aa） Fragment：WHOLE CYTOPLASMIC DOMAIN Chain B 171–198（28 aa） Fragment：WHOLE CYTOPLASMIC DOMAIN	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.4；298 K；Ionic strength (raw mmCIF value) 50mM sodium phosphate；Pressure 1 NMR measurement conditions pH 7.4；298 K；Ionic strength (raw mmCIF value) 50mM sodium phosphate；Pressure 1 NMR measurement conditions pH 7.4；298 K；Ionic strength (raw mmCIF value) 50mM sodium phosphate；Pressure 1 NMR sample composition 2-4mM Syndecan-4 peptide ; 50mM phosphate buffer; 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition 2-4mM Syndecan-4 peptide ; 50mM phosphate buffer; 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition 2-4mM Syndecan-4 peptide ; 50mM phosphate buffer; 100% D2O \| 100% D2O	Resolution not provided
1OBY Crystal structure of the complex of PDZ2 of syntenin with a syndecan-4 peptide. Deposited 2003-01-31	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain P 193–198（6 aa） Fragment：LAST 6 RESIDUES, RESIDUES 193-198 Chain Q 193–198（6 aa） Fragment：LAST 6 RESIDUES, RESIDUES 193-198	Not recorded	SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.8；SITTING DROP WITH 0.1 M HEPES, PH 6.8, 1.6 M AMMONIUM SULFATE, 20 MM COCL2, AND 0.2 MGSO4	Resolution 1.85 Å R-free 0.226
1YBO Crystal structure of the PDZ tandem of human syntenin with syndecan peptide Deposited 2004-12-21	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 182–198（17 aa） Chain D 182–198（17 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；20% PEG 3350, 0.2M NH4Cl, VAPOR DIFFUSION, SITTING DROP	Resolution 2.30 Å R-free 0.273
8BLV The PDZ domains of human SDCBP with a bound SDC4 C-terminal peptide Deposited 2022-11-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 191–198（8 aa）	Not recorded	SO4 SULFATE ION × 2 EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.3；293 K；200 mM sodium sulphate, 100 mM bis-tris-propane, 10% ethylene glycol, 20% PEG 3350	Resolution 1.50 Å R-free 0.222
8BLV The PDZ domains of human SDCBP with a bound SDC4 C-terminal peptide Deposited 2022-11-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 191–198（8 aa）	Not recorded	SO4 SULFATE ION × 1 EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.3；293 K；200 mM sodium sulphate, 100 mM bis-tris-propane, 10% ethylene glycol, 20% PEG 3350	Resolution 1.50 Å R-free 0.222

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

View Construct and Data Evidence

UniProt name	SDC4_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–28； UniProt 171–198 Author chain B； PDBConstruct 1–28； UniProt 171–198

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	1ejq
Deposition date deposition_date	2000-03-04
Structure title title	SOLUTION STRUCTURE OF THE SYNDECAN-4 WHOLE CYTOPLASMIC DOMAIN IN THE PRESENCE OF PHOSPHATIDYLINOSITOL 4,5-BISPHOSPHATE
Keywords keywords	Symmetric dimer, complexed with PIP2, SIGNALING PROTEIN; SIGNALING PROTEIN
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	20.82 Å
Radius of gyration Rg (electron density) rg_electron	19.94 Å
Forward intensity I(0) i0	133764000.00
Molecular weight molecular_weight	99326.0 kDa
Excluded volume excluded_volume	126410 Å³
Envelope volume envelope_volume	62630 Å³
Hydration-shell volume shell_volume	21181 Å³
Envelope diameter envelope_diameter	75.2 Å
Shell Rg shell_rg	31.60 Å
Envelope Rg envelope_rg	24.86 Å
Shape Rg shape_rg	19.87 Å
Total Rg total_rg	20.90 Å
Total atoms total_atoms	14220
Residues n_residues	840
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	71.7 Å
Rg (real space) rg_real	21.03 Å
Rg uncertainty (real space) rg_real_error	0.73 Å
I(0) (real space) i0_real	1.3380e+08
I(0) uncertainty (real space) i0_real_error	1.8030e+06
Rg (reciprocal space) rg_reciprocal	21.00 Å
I(0) (reciprocal space) i0_reciprocal	133800000.0000
Solution quality estimate total_estimate	0.7311
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	14.6 Å
Skewness Skewness skewness	0.310
Kurtosis Kurtosis kurtosis	-0.756
Angular range angular_range	— – 0.3800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	77630.0000
Real-space data points n_real_points	70
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.712; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.364; 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

SCOP 2.08 (2 domains)

Domain ID domain_id	d1ejqa_
Class class	j — Peptides
Fold Fold fold	j.80 — Syndecan-4 cytoplasmic domain
Superfamily Superfamily superfamily	j.80.1 — Syndecan-4 cytoplasmic domain
Family Family family	j.80.1.1 — Syndecan-4 cytoplasmic domain

Domain ID domain_id	d1ejqb_
Class class	j — Peptides
Fold Fold fold	j.80 — Syndecan-4 cytoplasmic domain
Superfamily Superfamily superfamily	j.80.1 — Syndecan-4 cytoplasmic domain
Family Family family	j.80.1.1 — Syndecan-4 cytoplasmic domain

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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	1

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

Description description	SYNDECAN-4
Molecular weight formula_weight	3314.8 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	14220

fit	/app/data/saxs_computation/ej/1ejq/1ejq.fit
pddf	/app/data/pr_computation/ej/1ejq/1ejq.pr.out
profile	/app/data/saxs_computation/ej/1ejq/1ejq.dat

SOLUTION STRUCTURE OF THE SYNDECAN-4 WHOLE CYTOPLASMIC DOMAIN IN THE PRESENCE OF PHOSPHATIDYLINOSITOL 4,5-BISPHOSPHATE

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

SYNDECAN-4

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

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)