SAXSdb — 2dk1

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

WW domain-binding protein 4

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 124–163	Fragment：WW domain	No other associated polymer	SOLUTION NMR NMR measurement conditions：pH 7；298 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient NMR sample composition：0.8mM U-15N/13C; 20mM phosphate buffer NA; 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O \| 90% H2O/10% 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 2DK1	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2JXW Solution Structure of the Tandem WW Domains of FBP21 Deposited 2007-11-30	Different construct Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 122–196（75 aa） Fragment：WW Domian	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；293 K；Pressure 1 NMR measurement conditions pH 6.5；298 K；Pressure 1 NMR sample composition 1.0mM [U-99% 13C; U-99% 15N] FBP21; 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.5mM [U-99% 15N] FBP21; 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
5O9Z Cryo-EM structure of a pre-catalytic human spliceosome primed for activation (B complex) Deposited 2017-06-20	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 57-meric	Chain Q 1–376（376 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.50 Å
6AHD The Cryo-EM Structure of Human Pre-catalytic Spliceosome (B complex) at 3.8 angstrom resolution Deposited 2018-08-17	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 58 PDB declaration: 63-meric	Chain X 1–376（376 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
7OS1 Cryo-EM structure of Brr2 in complex with Fbp21 Deposited 2021-06-07	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 199–376（178 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
8H6K Cryo-EM structure of human exon-defined spliceosome in the mature B state. Deposited 2022-10-18	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 58 PDB declaration: 63-meric	Chain 4I 1–376（376 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.70 Å
8H6L Cryo-EM structure of human exon-defined spliceosome in the early B state. Deposited 2022-10-18	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 59-meric	Chain 4I 1–376（376 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.60 Å
8Q7N cryo-EM structure of the human spliceosomal B complex protomer (tri-snRNP core region) Deposited 2023-08-16	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 17 PDB declaration: 21-meric	Chain X 1–376（376 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
8QO9 Cryo-EM structure of a human spliceosomal B complex protomer Deposited 2023-09-28	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 66 PDB declaration: 71-meric	Chain X 1–376（376 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 5.29 Å
8QPE Cryo-EM Structure of Pre-B-like Complex (core part) Deposited 2023-10-01	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 15 PDB declaration: 20-meric	Chain X 1–376（376 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
8QZS Cryo-EM structure of the cross-exon B-like complex Deposited 2023-10-29	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 61 PDB declaration: 68-meric	Chain X 1–376（376 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.10 Å

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

View Construct and Data Evidence

UniProt name	WBP4_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 8–44； UniProt 124–163

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	2dk1
Deposition date deposition_date	2006-04-06
Structure title title	Solution structure of WW domain in WW domain binding protein 4 (WBP-4)
Keywords keywords	;WW domain, WW domain-binding protein 4, WBP-4, Formin-binding protein 21, Structural Genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI, GENE REGULATION ;; GENE REGULATION
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	13.03 Å
Radius of gyration Rg (electron density) rg_electron	12.57 Å
Forward intensity I(0) i0	180915000.00
Molecular weight molecular_weight	106250.0 kDa
Excluded volume excluded_volume	129910 Å³
Envelope volume envelope_volume	27127 Å³
Hydration-shell volume shell_volume	13820 Å³
Envelope diameter envelope_diameter	54.1 Å
Shell Rg shell_rg	22.58 Å
Envelope Rg envelope_rg	17.84 Å
Shape Rg shape_rg	12.49 Å
Total Rg total_rg	13.19 Å
Total atoms total_atoms	14300
Residues n_residues	1000
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	50.4 Å
Rg (real space) rg_real	13.11 Å
Rg uncertainty (real space) rg_real_error	0.48 Å
I(0) (real space) i0_real	1.8090e+08
I(0) uncertainty (real space) i0_real_error	2.2320e+06
Rg (reciprocal space) rg_reciprocal	13.11 Å
I(0) (reciprocal space) i0_reciprocal	180900000.0000
Solution quality estimate total_estimate	0.8061
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	14.7 Å
Skewness Skewness skewness	0.481
Kurtosis Kurtosis kurtosis	0.058
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	74740.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.619; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.622; Smooth: 0.995

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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) 4 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d2dk1a1
Class class	b — All beta proteins
Fold Fold fold	b.72 — WW domain-like
Superfamily Superfamily superfamily	b.72.1 — WW domain
Family Family family	b.72.1.1 — WW domain

Domain ID domain_id	d2dk1a2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2dk1a3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (1 domains)

Domain ID domain_id	2dk1A00
Class class	2 — Mainly Beta
Architecture architecture	20 — Single Sheet
Topology topology	70 — Ubiquitin Ligase Nedd4; Chain: W;
Homologous superfamily homologous superfamily	10 —

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8. Citations (1)

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Description description	WW domain-binding protein 4
Molecular weight formula_weight	5336.6 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	14300

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	Cell free synthesis

fit	/app/data/saxs_computation/dk/2dk1/2dk1.fit
pddf	/app/data/pr_computation/dk/2dk1/2dk1.pr.out
profile	/app/data/saxs_computation/dk/2dk1/2dk1.dat

Solution structure of WW domain in WW domain binding protein 4 (WBP-4)

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

WW domain-binding protein 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

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (3 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)