SAXSdb — 9xof

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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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 150–245 Chain D； UniProt 150–245 Chain H； UniProt 150–245 Chain I； UniProt 150–245	Non-standard monomer：Yes (specific site not provided by mmCIF)	No other associated polymer	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
2	Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain B； UniProt 150–245 Chain C； UniProt 150–245 Chain G； UniProt 150–245 Chain J； UniProt 150–245	Non-standard monomer：Yes (specific site not provided by mmCIF)	No other associated polymer	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

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 9XOF	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 mutation/modification 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 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 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 mutation/modification Different oligomeric state 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 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 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
9XOE Crystal structure of WTAP 1-50 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 × 2 PDB declaration: dimeric	Chain A 1–50（50 aa） Chain C 1–50（50 aa）	Not recorded	No recorded non-water small molecule	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
9XOE Crystal structure of WTAP 1-50 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 × 2 PDB declaration: dimeric	Chain B 1–50（50 aa） Chain D 1–50（50 aa）	Not recorded	No recorded non-water small molecule	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

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 5–100； UniProt 150–245 Author chain B； PDBConstruct 5–100； UniProt 150–245 Author chain C； PDBConstruct 5–100； UniProt 150–245 Author chain D； PDBConstruct 5–100； UniProt 150–245 Author chain G； PDBConstruct 5–100； UniProt 150–245 Author chain H； PDBConstruct 5–100； UniProt 150–245 Author chain I； PDBConstruct 5–100； UniProt 150–245 Author chain J； PDBConstruct 5–100； UniProt 150–245

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	9xof
Deposition date deposition_date	2025-11-13
最后修订 last_revision	2026-05-27
Structure title title	Crystal structure of WTAP 150-245
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	46.98 Å
Radius of gyration Rg (electron density) rg_electron	48.59 Å
Forward intensity I(0) i0	123546000.00
Molecular weight molecular_weight	85018.0 kDa
Excluded volume excluded_volume	104270 Å³
Envelope volume envelope_volume	156400 Å³
Hydration-shell volume shell_volume	32602 Å³
Envelope diameter envelope_diameter	211.4 Å
Shell Rg shell_rg	41.03 Å
Envelope Rg envelope_rg	49.17 Å
Shape Rg shape_rg	48.66 Å
Total Rg total_rg	47.98 Å
Total atoms total_atoms	5859
Residues n_residues	714
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	126.7 Å
Rg (real space) rg_real	42.97 Å
Rg uncertainty (real space) rg_real_error	0.48 Å
I(0) (real space) i0_real	1.1740e+08
I(0) uncertainty (real space) i0_real_error	1.7140e+06
Rg (reciprocal space) rg_reciprocal	46.99 Å
I(0) (reciprocal space) i0_reciprocal	123300000.0000
Solution quality estimate total_estimate	0.6747
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	41.0 Å
Skewness Skewness skewness	0.411
Kurtosis Kurtosis kurtosis	-0.620
Angular range angular_range	— – 0.1700 Å⁻¹
Current regularization parameter α current_alpha	0.8033
Highest regularization parameter α highest_alpha	3826000.0000
Real-space data points n_real_points	35
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.004; Oscil: 0.983; Stabil: 0.986; Sysdev: 0.000; Positv: 1.000; Valcen: 0.870; 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	47.621 Å
Unit-cell length b length_b	104.618 Å
Unit-cell length c length_c	101.601 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.22 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	P 1 2 1
Space-group number int_tables_number	3
Crystal system crystal_system	—

Resolution resolution	2.785 Å
Low-resolution limit resolution_low	47.621 Å
R factor r_factor	0.2186
R_work r_work	0.2158
R_free r_free	0.2704

Description description	Pre-mRNA-splicing regulator WTAP
Molecular weight formula_weight	11604.5 kDa
Source method src_method	man
Copy count entity_count	8

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,G,H,I,J
Atom count atom_count	5864

Crystal structure of WTAP 150-245

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	5

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