SAXSdb — 9xoe

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

Pre-mRNA-splicing regulator WTAP

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 1–50 Chain C； UniProt 1–50	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；289.15 K；0.1M HEPES pH7.5, 40% v/v Polyethylene glycol 400	Resolution 1.65 Å R-free 0.256
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 1–50 Chain D； UniProt 1–50	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；289.15 K；0.1M HEPES pH7.5, 40% v/v Polyethylene glycol 400	Resolution 1.65 Å R-free 0.256

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 9XOE	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7VF2 Human m6A-METTL associated complex (WTAP, VIRMA, ZC3H13, and HAKAI) Deposited 2021-09-10	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 1–396（396 aa） Chain D 1–396（396 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
7VF5 Human m6A-METTL associated complex (WTAP, VIRMA, and HAKAI) Deposited 2021-09-10	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 1–396（396 aa） Chain D 1–396（396 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
7YFJ Crystal structure of human WTAP Deposited 2022-07-08	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 130–241（112 aa） Chain B 130–241（112 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291.15 K；MES, magnesium nitrate, sodium bromide, PEG6000, glycerol	Resolution 2.40 Å R-free 0.240
7YG4 Structure of WTAP-VIRMA in the m6A writer complex Deposited 2022-07-11	Different construct 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 1–273（273 aa） Chain E 1–273（273 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
9XOF Crystal structure of WTAP 150-245 Deposited 2025-11-13	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 150–245（96 aa） Chain D 150–245（96 aa） Chain H 150–245（96 aa） Chain I 150–245（96 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289.15 K；45% W/V Pentaerythritol Propoxylate (17/8 PO/OH), 100mM Tris pH 8.5.	Resolution 2.79 Å R-free 0.270
9XOF Crystal structure of WTAP 150-245 Deposited 2025-11-13	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain B 150–245（96 aa） Chain C 150–245（96 aa） Chain G 150–245（96 aa） Chain J 150–245（96 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289.15 K；45% W/V Pentaerythritol Propoxylate (17/8 PO/OH), 100mM Tris pH 8.5.	Resolution 2.79 Å R-free 0.270

5 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	FL2D_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–50； UniProt 1–50 Author chain B； PDBConstruct 1–50； UniProt 1–50 Author chain C； PDBConstruct 1–50； UniProt 1–50 Author chain D； PDBConstruct 1–50； UniProt 1–50

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	9xoe
Deposition date deposition_date	2025-11-13
最后修订 last_revision	2026-05-27
Structure title title	Crystal structure of WTAP 1-50
Keywords keywords	WTAP, Epigenetics, M6A writer complex, CELL CYCLE; CELL CYCLE
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	21.89 Å
Radius of gyration Rg (electron density) rg_electron	21.15 Å
Forward intensity I(0) i0	7937680.00
Molecular weight molecular_weight	21575.0 kDa
Excluded volume excluded_volume	27367 Å³
Envelope volume envelope_volume	34034 Å³
Hydration-shell volume shell_volume	14688 Å³
Envelope diameter envelope_diameter	75.0 Å
Shell Rg shell_rg	25.79 Å
Envelope Rg envelope_rg	21.43 Å
Shape Rg shape_rg	21.14 Å
Total Rg total_rg	21.91 Å
Total atoms total_atoms	1523
Residues n_residues	184
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	72.6 Å
Rg (real space) rg_real	22.06 Å
Rg uncertainty (real space) rg_real_error	0.71 Å
I(0) (real space) i0_real	7.9380e+06
I(0) uncertainty (real space) i0_real_error	1.1210e+05
Rg (reciprocal space) rg_reciprocal	22.03 Å
I(0) (reciprocal space) i0_reciprocal	7938000.0000
Solution quality estimate total_estimate	0.7694
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	17.3 Å
Skewness Skewness skewness	0.449
Kurtosis Kurtosis kurtosis	-0.423
Angular range angular_range	— – 0.3650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4094000.0000
Real-space data points n_real_points	68
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.771; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.687; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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8. Citations (1)

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Unit-cell length a length_a	76.173 Å
Unit-cell length b length_b	76.173 Å
Unit-cell length c length_c	75.414 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	32

Space group space_group	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	1.650 Å
Low-resolution limit resolution_low	43.830 Å
R factor r_factor	0.2301
R_work r_work	0.2287
R_free r_free	0.2559

Description description	Pre-mRNA-splicing regulator WTAP
Molecular weight formula_weight	5970.8 kDa
Source method src_method	man
Copy count entity_count	4

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	1584

Crystal structure of WTAP 1-50

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

Pre-mRNA-splicing regulator WTAP

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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

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 'BL21-Gold(DE3)pLysS AG' ;

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	56

fit	/app/data/saxs_computation/xo/9xoe/9xoe.fit
pddf	/app/data/pr_computation/xo/9xoe/9xoe.pr.out
profile	/app/data/saxs_computation/xo/9xoe/9xoe.dat