SAXSdb — 4wii

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

Splicing factor, proline- and glutamine-rich

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 276–535 Chain B； UniProt 276–535	Fragment：UNP RESIDUES 276-535	SO4 SULFATE ION × 1 EDO 1,2-ETHANEDIOL × 8	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；1.9 M AMMONIUM SULFATE, 0.1 M TRIS, 20% ETHYLENE GLYCOL (V/V), PH 8.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K	Resolution 2.05 Å R-free 0.235

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 4WII	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4WIJ HUMAN SPLICING FACTOR, CONSTRUCT 1 Deposited 2014-09-26	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 276–598（323 aa） Fragment：UNP RESIDUES 276-598 Chain B 276–598（323 aa） Fragment：UNP RESIDUES 276-598	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；26% (V/V) 1,4 DIOXANE, 0.05M MOPS, 50 MM MAGNESIUM CHLORIDE HEXAHYDRATE, 1 MM SPERMINE, PH 7.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K	Resolution 3.49 Å R-free 0.335
4WIK HUMAN SPLICING FACTOR, CONSTRUCT 2 Deposited 2014-09-26	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 369–598（230 aa） Fragment：UNP RESIDUES 369-598 Chain B 369–598（230 aa） Fragment：UNP RESIDUES 369-598	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M SODIUM PHOSPHATE DIBASIC DIHYDRATE, 22% (W/V) POLYETHYLENE GLYCOL 3350, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K	Resolution 3.00 Å R-free 0.291
5WPA Structure of human SFPQ/PSPC1 heterodimer Deposited 2017-08-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 276–535（260 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；25% PEG3350, 0.05 M MES, pH 5.5, 0.2 M sodium chloride, 3% aminohexanoic acid	Resolution 2.29 Å R-free 0.272
6NCQ The dimerization domain of human SFPQ in space group C2221 Deposited 2018-12-12	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 276–535（260 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M Tris-HCl (pH 8,5), 35-40% (v/v) MPD	Resolution 1.90 Å R-free 0.243
6OWJ Zn-mediated polymerization of human SFPQ Deposited 2019-05-10	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 276–535（260 aa） Fragment：UNP residues 276-535 Chain B 276–535（260 aa） Fragment：UNP residues 276-535	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；14% PEG4000, 0.2 M calcium chloride, 0.1 M MES, pH 6.0	Resolution 1.94 Å R-free 0.218
6WMZ Crystal structure of human SFPQ/NONO complex Deposited 2020-04-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 214–598（385 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M Tris-HCl (pH 8.5), 0.2 M ammonium sulfate, 19% PEG 3350	Resolution 2.85 Å R-free 0.283
6WMZ Crystal structure of human SFPQ/NONO complex Deposited 2020-04-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 214–598（385 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M Tris-HCl (pH 8.5), 0.2 M ammonium sulfate, 19% PEG 3350	Resolution 2.85 Å R-free 0.283
7LRQ Crystal structure of human SFPQ/NONO heterodimer, conserved DBHS region Deposited 2021-02-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 276–535（260 aa）	Not recorded	CL CHLORIDE ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；22.5% PEG3350, 0.4 M MgCl2, 0.1 M HEPES pH 7.5	Resolution 2.30 Å R-free 0.299
7LRU Crystal structure of SFPQ-NONO-SFPQ chimeric protein homodimer Deposited 2021-02-17	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 276–452（177 aa） Chain B 505–535（31 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；15%(v/v) Jeffamine ED-2003, 10% EtOH	Resolution 1.60 Å R-free 0.256
7PU5 Structure of SFPQ-NONO complex Deposited 2021-09-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 277–535（259 aa）	Not recorded	MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；25 mM Tris-HCl pH8.5, 14-16 % PEG 8K, 20 % w/v	Resolution 3.00 Å R-free 0.255
7PU5 Structure of SFPQ-NONO complex Deposited 2021-09-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 277–535（259 aa）	Not recorded	MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；25 mM Tris-HCl pH8.5, 14-16 % PEG 8K, 20 % w/v	Resolution 3.00 Å R-free 0.255
7PU5 Structure of SFPQ-NONO complex Deposited 2021-09-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 277–535（259 aa）	Not recorded	MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；25 mM Tris-HCl pH8.5, 14-16 % PEG 8K, 20 % w/v	Resolution 3.00 Å R-free 0.255
7PU5 Structure of SFPQ-NONO complex Deposited 2021-09-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 277–535（259 aa）	Not recorded	MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；25 mM Tris-HCl pH8.5, 14-16 % PEG 8K, 20 % w/v	Resolution 3.00 Å R-free 0.255
7PU5 Structure of SFPQ-NONO complex Deposited 2021-09-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain J 277–535（259 aa）	Not recorded	MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；25 mM Tris-HCl pH8.5, 14-16 % PEG 8K, 20 % w/v	Resolution 3.00 Å R-free 0.255
7PU5 Structure of SFPQ-NONO complex Deposited 2021-09-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain L 277–535（259 aa）	Not recorded	MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；25 mM Tris-HCl pH8.5, 14-16 % PEG 8K, 20 % w/v	Resolution 3.00 Å R-free 0.255
7SP0 Crystal structure of human SFPQ L534I mutant in complex with zinc Deposited 2021-11-01	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 276–535（260 aa） Chain B 276–535（260 aa）	Mutation：L534I Mutation：L534I	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；12% PEG4000, 0.2 M CALCIUM CHLORIDE, 0.1 M MES, PH 6.0	Resolution 1.83 Å R-free 0.216
7UJ1 Crystal structure of PSF-RNA complex Deposited 2022-03-30	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 214–598（385 aa） Chain B 214–598（385 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；295 K；0.1M Tris-HCl, pH 8.5, 5mM MgCl2, 1mM DTT, 26% SOKALAN CP 42.	Resolution 3.50 Å R-free 0.241
7UK1 Complex Structure of Human Polypyrimidine Splicing Factor (PSF/SFPQ) with Murine Virus-like 30S Transcript-1 (VS30-1) Reveals Cooperative Binding of RNA Deposited 2022-03-31	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 214–598（385 aa） Chain B 214–598（385 aa）	Not recorded	MG MAGNESIUM ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 7；285.15 K；0.1 M MgCl2, 0.1 M HEPES pH 7.0, 15% (w/v),PEG4000, or 15% (w/v) PEG3500, or 20% PEG2000MME	Resolution 2.70 Å R-free 0.291

12 other PDB entries and 18 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SFPQ_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–263； UniProt 276–535 Author chain B； PDBConstruct 4–263； UniProt 276–535

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	4wii
Deposition date deposition_date	2014-09-26
Structure title title	HUMAN SPLICING FACTOR, CONSTRUCT 3
Keywords keywords	RRM, TRANSCRIPTION; TRANSCRIPTION
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	26.64 Å
Radius of gyration Rg (electron density) rg_electron	25.63 Å
Forward intensity I(0) i0	57392500.00
Molecular weight molecular_weight	57688.0 kDa
Excluded volume excluded_volume	71861 Å³
Envelope volume envelope_volume	92922 Å³
Hydration-shell volume shell_volume	30630 Å³
Envelope diameter envelope_diameter	86.9 Å
Shell Rg shell_rg	32.50 Å
Envelope Rg envelope_rg	25.23 Å
Shape Rg shape_rg	25.63 Å
Total Rg total_rg	26.40 Å
Total atoms total_atoms	4060
Residues n_residues	498
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	81.8 Å
Rg (real space) rg_real	26.49 Å
Rg uncertainty (real space) rg_real_error	0.45 Å
I(0) (real space) i0_real	5.7390e+07
I(0) uncertainty (real space) i0_real_error	8.2780e+05
Rg (reciprocal space) rg_reciprocal	26.54 Å
I(0) (reciprocal space) i0_reciprocal	57390000.0000
Solution quality estimate total_estimate	0.9105
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	80.5 Å
Skewness Skewness skewness	0.112
Kurtosis Kurtosis kurtosis	-0.582
Angular range angular_range	— – 0.3000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	6506000.0000
Real-space data points n_real_points	61
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.954; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.973

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Splicing factor, proline- and glutamine-rich
Molecular weight formula_weight	30094.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	4264

GAMEGFKANLSLLRRPGEKTYTQRCRLFVGNLPADITEDEFKRLFAKYGEPGEVFINKGKGFGFIKLESRALAEIAKAELDDTPMRGRQLRVRFATHAAALSVRNLSPYVSNELLEEAFSQFGPIERAVVIVDDRGRSTGKGIVEFASKPAARKAFERCSEGVFLLTTTPRPVIVEPLEQLDDEDGLPEKLAQKNPMYQKERETPPRFAQHGTFEYEYSQRWKSLDEMEKQQREQVEKNMKDAKDKLESEMEDAYHEHQANLL

来源 Source

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

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	176

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7. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	4wiiA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	330 — RRM (RNA recognition motif) domain

Domain ID domain_id	4wiiA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	330 — RRM (RNA recognition motif) domain

Domain ID domain_id	4wiiA03
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	1170 —

Domain ID domain_id	4wiiB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	330 — RRM (RNA recognition motif) domain

Domain ID domain_id	4wiiB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	330 — RRM (RNA recognition motif) domain

Domain ID domain_id	4wiiB03
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	1170 —

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8. Citations (1)

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Unit-cell length a length_a	63.447 Å
Unit-cell length b length_b	67.611 Å
Unit-cell length c length_c	119.528 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	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.050 Å
Low-resolution limit resolution_low	19.520 Å
R factor r_factor	0.2010
R_work r_work	0.1990
R_free r_free	0.2350

fit	/app/data/saxs_computation/wi/4wii/4wii.fit
pddf	/app/data/pr_computation/wi/4wii/4wii.pr.out
profile	/app/data/saxs_computation/wi/4wii/4wii.dat

HUMAN SPLICING FACTOR, CONSTRUCT 3

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

Splicing factor, proline- and glutamine-rich

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