SAXSdb — 2m09

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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 27–145	Fragment：UNP residues 27-145	No other associated polymer	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

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 2M09	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 experimental conditions	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 experimental conditions	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
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	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 method 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 method 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
4FXX Structure of SF1 coiled-coil domain Deposited 2012-07-03	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 26–132（107 aa） Fragment：UNP Residues 26-132	Not recorded	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
4FXX Structure of SF1 coiled-coil domain Deposited 2012-07-03	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 26–132（107 aa） Fragment：UNP Residues 26-132	Not recorded	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
4FXX Structure of SF1 coiled-coil domain Deposited 2012-07-03	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 26–132（107 aa） Fragment：UNP Residues 26-132	Not recorded	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
4FXX Structure of SF1 coiled-coil domain Deposited 2012-07-03	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 26–132（107 aa） Fragment：UNP Residues 26-132	Not recorded	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
4FXX Structure of SF1 coiled-coil domain Deposited 2012-07-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 5 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 26–132（107 aa） Fragment：UNP Residues 26-132 Chain B 26–132（107 aa） Fragment：UNP Residues 26-132	Not recorded	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
4FXX Structure of SF1 coiled-coil domain Deposited 2012-07-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 6 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 26–132（107 aa） Fragment：UNP Residues 26-132 Chain D 26–132（107 aa） Fragment：UNP Residues 26-132	Not recorded	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
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 experimental conditions	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 experimental conditions	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 14 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 3–121； UniProt 27–145

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	2m09
Deposition date deposition_date	2012-10-22
Structure title title	Structure, phosphorylation and U2AF65 binding of the Nterminal Domain of splicing factor 1 during 3 splice site Recognition
Keywords keywords	spliceosome assembly, SF1, UHM, ULM, RRM, TRANSCRIPTION; TRANSCRIPTION
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	19.17 Å
Radius of gyration Rg (electron density) rg_electron	18.73 Å
Forward intensity I(0) i0	284252000.00
Molecular weight molecular_weight	138020.0 kDa
Excluded volume excluded_volume	172350 Å³
Envelope volume envelope_volume	60990 Å³
Hydration-shell volume shell_volume	22707 Å³
Envelope diameter envelope_diameter	94.2 Å
Shell Rg shell_rg	29.37 Å
Envelope Rg envelope_rg	23.93 Å
Shape Rg shape_rg	18.70 Å
Total Rg total_rg	19.30 Å
Total atoms total_atoms	19550
Residues n_residues	1210
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	49.3 Å
Rg (real space) rg_real	18.16 Å
Rg uncertainty (real space) rg_real_error	0.07 Å
I(0) (real space) i0_real	2.7100e+08
I(0) uncertainty (real space) i0_real_error	2.1410e+06
Rg (reciprocal space) rg_reciprocal	19.28 Å
I(0) (reciprocal space) i0_reciprocal	284200000.0000
Solution quality estimate total_estimate	0.6851
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	19.9 Å
Skewness Skewness skewness	0.248
Kurtosis Kurtosis kurtosis	-0.607
Angular range angular_range	— – 0.4150 Å⁻¹
Current regularization parameter α current_alpha	3.1240
Highest regularization parameter α highest_alpha	411600.0000
Real-space data points n_real_points	73
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.001; Oscil: 1.000; Stabil: 0.976; Sysdev: 0.000; Positv: 1.000; Valcen: 0.979; Smooth: 0.000

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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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8. Citations (1)

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Description description	Splicing factor 1
Molecular weight formula_weight	13821.8 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	19550

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

fit	/app/data/saxs_computation/m0/2m09/2m09.fit
pddf	/app/data/pr_computation/m0/2m09/2m09.pr.out
profile	/app/data/saxs_computation/m0/2m09/2m09.dat

Structure, phosphorylation and U2AF65 binding of the Nterminal Domain of splicing factor 1 during 3 splice site Recognition

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

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)