SAXSdb — 4fxx

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

Splicing factor 1

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 26–132	Fragment：UNP Residues 26-132	IMD IMIDAZOLE × 1 MLI MALONATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.5；277 K；1.34 M sodium malonate pH 6.0, 0.1 M imidazole maleate pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.48 Å R-free 0.270
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 26–132	Fragment：UNP Residues 26-132	IMD IMIDAZOLE × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.5；277 K；1.34 M sodium malonate pH 6.0, 0.1 M imidazole maleate pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.48 Å R-free 0.270
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 26–132	Fragment：UNP Residues 26-132	IMD IMIDAZOLE × 2 MLI MALONATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.5；277 K；1.34 M sodium malonate pH 6.0, 0.1 M imidazole maleate pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.48 Å R-free 0.270
4	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain D； UniProt 26–132	Fragment：UNP Residues 26-132	IMD IMIDAZOLE × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.5；277 K；1.34 M sodium malonate pH 6.0, 0.1 M imidazole maleate pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.48 Å R-free 0.270
5	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 26–132 Chain B； UniProt 26–132	Fragment：UNP Residues 26-132	IMD IMIDAZOLE × 3 MLI MALONATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.5；277 K；1.34 M sodium malonate pH 6.0, 0.1 M imidazole maleate pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.48 Å R-free 0.270
6	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 26–132 Chain D； UniProt 26–132	Fragment：UNP Residues 26-132	IMD IMIDAZOLE × 5 MLI MALONATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.5；277 K；1.34 M sodium malonate pH 6.0, 0.1 M imidazole maleate pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.48 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 4FXX	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1K1G STRUCTURAL BASIS FOR RECOGNITION OF THE INTRON BRANCH SITE RNA BY SPLICING FACTOR 1 Deposited 2001-09-25	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain A 133–260（128 aa） Fragment：Residues 133-260, KH-QUA2 region	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；295 K；Ionic strength (raw mmCIF value) 50 mM NaCl；Pressure ambient NMR measurement conditions pH 6.5；278 K；Ionic strength (raw mmCIF value) 50 mM NaCl；Pressure ambient NMR sample composition 1 mM U-15N,13C SF1 KH-QUA2/unlabeled BPS in 20 mM phosphate buffer NA pH 6.5, 50 mM NaCl, 2 mM DTT \| 90% H2O/10% D2O NMR sample composition 1 mM U-15N,13C SF1 KH-QUA2/unlabeled BPS in 20 mM phosphate buffer NA pH 6.5, 50 mM NaCl, 2 mM DTT \| 100% D2O NMR sample composition 1 mM U-15N SF1 KH-QUA2/unlabeled BPS in 20 mM phosphate buffer NA pH 6.5, 50 mM NaCl, 2 mM DTT \| 90% H2O/10% D2O	Resolution not provided
1OPI SOLUTION STRUCTURE OF THE THIRD RNA RECOGNITION MOTIF (RRM) OF U2AF65 IN COMPLEX WITH AN N-TERMINAL SF1 PEPTIDE Deposited 2003-03-05	Different construct 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 B 13–25（13 aa） Fragment：N-TERMINAL PEPTIDE	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.4；295 K；Ionic strength (raw mmCIF value) 50mM SALT；Pressure AMBIENT NMR sample composition 1MM 15N,13C U2AF65-RRM3 + 1MM UNLABELED SF1_10-25, 30MM PHOSPHATE BUFFER, 20MM NACL, 3MM DTT \| D2O	Resolution not provided
2M09 Structure, phosphorylation and U2AF65 binding of the Nterminal Domain of splicing factor 1 during 3 splice site Recognition Deposited 2012-10-22	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 27–145（119 aa） Fragment：UNP residues 27-145	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 70；Pressure ambient NMR sample composition 100-600 uM [U-15N] protein, 100-600 uM [U-13C; U-15N] entity, 100-600 uM [U-13C; U-15N; U-2H] entity, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2M0G Structure, phosphorylation and U2AF65 binding of the Nterminal Domain of splicing factor 1 during 3 splice site Recognition Deposited 2012-10-25	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 A 1–145（145 aa） Fragment：UNP residues 1-145	Mutation：S137C	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 70；Pressure ambient NMR sample composition 100-600 uM [U-15N] protein, 100-600 uM [U-13C; U-15N] entity, 100-600 uM [U-13C; U-15N; U-2H] entity, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
4FXW Structure of phosphorylated SF1 complex with U2AF65-UHM domain Deposited 2012-07-03	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 14–132（119 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；0.2 M Lithium sulfate, 20% PEG 3350 and 0.1 M Tris pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.29 Å R-free 0.281
4FXW Structure of phosphorylated SF1 complex with U2AF65-UHM domain Deposited 2012-07-03	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 14–132（119 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；0.2 M Lithium sulfate, 20% PEG 3350 and 0.1 M Tris pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.29 Å R-free 0.281
7VH9 Solution structure of the chimeric peptide of the first SURP domain of Human SF3A1 and the interacting region of SF1. Deposited 2021-09-21	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 295–327（33 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 20；Pressure 1 NMR sample composition 1.4 mM [U-99% 13C; U-99% 15N] protein, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
7VPX The cryo-EM structure of the human pre-A complex Deposited 2021-10-18	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 31 PDB declaration: 35-meric	Chain D 1–639（639 aa）	Not recorded	ZN ZINC ION × 6 SJT spliceostatin A (form II) × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
8PXX Structure of the WW domain tandem of PRPF40A in complex with SF1 Deposited 2023-07-24	Different construct 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 B 575–590（16 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；308 K；Ionic strength (raw mmCIF value) 133；Pressure 1 NMR sample composition 590 uM [U-100% 13C; U-100% 15N] PRPF40A, 590 uM SF1, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 590 uM [U-100% 13C; U-100% 15N] PRPF40A, 590 uM SF1, 100% D2O \| 100% D2O NMR sample composition 900 uM [U-100% 13C; U-100% 15N] SF1, 900 uM PRPF40A, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 900 uM [U-100% 13C; U-100% 15N] SF1, 900 uM PRPF40A, 100% D2O \| 100% D2O NMR sample composition 150 uM [U-100% 15N] PRPF40A, 150 uM SF1, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 150 uM [U-100% 15N] PRPF40A, 150 uM SF1, 10 mg/mL Pf1 phage, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided

8 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SF01_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 6–112； UniProt 26–132 Author chain B； PDBConstruct 6–112； UniProt 26–132 Author chain C； PDBConstruct 6–112； UniProt 26–132 Author chain D； PDBConstruct 6–112； UniProt 26–132

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	4fxx
Deposition date deposition_date	2012-07-03
Structure title title	Structure of SF1 coiled-coil domain
Keywords keywords	splicing factor 1, coiled-coil, pre-mRNA splicing, U2AF65-UHM binding, RNA binding protein; RNA BINDING PROTEIN
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	31.28 Å
Radius of gyration Rg (electron density) rg_electron	31.30 Å
Forward intensity I(0) i0	28990200.00
Molecular weight molecular_weight	41311.0 kDa
Excluded volume excluded_volume	51734 Å³
Envelope volume envelope_volume	79205 Å³
Hydration-shell volume shell_volume	23150 Å³
Envelope diameter envelope_diameter	107.1 Å
Shell Rg shell_rg	34.91 Å
Envelope Rg envelope_rg	30.54 Å
Shape Rg shape_rg	31.28 Å
Total Rg total_rg	31.77 Å
Total atoms total_atoms	2912
Residues n_residues	365
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	102.4 Å
Rg (real space) rg_real	31.46 Å
Rg uncertainty (real space) rg_real_error	0.87 Å
I(0) (real space) i0_real	2.8990e+07
I(0) uncertainty (real space) i0_real_error	4.8160e+05
Rg (reciprocal space) rg_reciprocal	31.39 Å
I(0) (reciprocal space) i0_reciprocal	28990000.0000
Solution quality estimate total_estimate	0.8786
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	34.1 Å
Skewness Skewness skewness	0.379
Kurtosis Kurtosis kurtosis	-0.433
Angular range angular_range	— – 0.2550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1758000.0000
Real-space data points n_real_points	52
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.944; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.859; Smooth: 0.727

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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 1
Molecular weight formula_weight	12762.5 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	2990

GPLGSTMEQKTVIPGMPTVIPPGLTREQERAYIVQLQIEDLTRKLRTGDLGIPPNPEDRSPSPEPIYNSEGKRLNTREFRTRKKLEEERHNLITEMVALNPDFKPPADYKPP

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	IMIDAZOLE
Molecular weight formula_weight	69.1 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 3 Entity 3 non-polymer

Description description	MALONATE ION
Molecular weight formula_weight	102.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	72

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	4fxxB01
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	1790 —

Domain ID domain_id	4fxxC01
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	1790 —

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8. Citations (1)

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Unit-cell length a length_a	96.030 Å
Unit-cell length b length_b	37.970 Å
Unit-cell length c length_c	144.680 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	107.38 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.480 Å
Low-resolution limit resolution_low	34.966 Å
R factor r_factor	0.2393
R_work r_work	0.2365
R_free r_free	0.2698

fit	/app/data/saxs_computation/fx/4fxx/4fxx.fit
pddf	/app/data/pr_computation/fx/4fxx/4fxx.pr.out
profile	/app/data/saxs_computation/fx/4fxx/4fxx.dat

Structure of SF1 coiled-coil domain

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

Splicing factor 1

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