SAXSdb — 2l5i

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

U1 small nuclear ribonucleoprotein 70 kDa

OrganismNot specified

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 131–151	Fragment：UNP residues 131-151	No other associated polymer	SOLUTION NMR NMR measurement conditions：pH 4；278 K；Ionic strength (raw mmCIF value) 0；Pressure ambient NMR sample composition：2 mM entity_1-1, 95% H2O/5% D2O \| 95% H2O/5% 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 2L5I	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2L5J structure of the spliceosomal phosphopeptide P140 (phosphorylated form) Deposited 2010-11-02	Different mutation/modification Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 131–151（21 aa） Fragment：UNP residues 131-151	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 4；278 K；Ionic strength (raw mmCIF value) 0；Pressure ambient NMR sample composition 2 mM entity-1, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
3CW1 Crystal Structure of Human Spliceosomal U1 snRNP Deposited 2008-04-21	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 9 PDB declaration: decameric	Chain K 1–216（216 aa） Fragment：residues 1-215	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.6；277 K；38-40% MPD, 0.3M KCl, 0.1M MES.KOH, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 5.49 Å
3CW1 Crystal Structure of Human Spliceosomal U1 snRNP Deposited 2008-04-21	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–RNA Heteromer；Protein × 9 PDB declaration: decameric	Chain 6 1–216（216 aa） Fragment：residues 1-215	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.6；277 K；38-40% MPD, 0.3M KCl, 0.1M MES.KOH, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 5.49 Å
3CW1 Crystal Structure of Human Spliceosomal U1 snRNP Deposited 2008-04-21	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein–RNA Heteromer；Protein × 9 PDB declaration: decameric	Chain 7 1–216（216 aa） Fragment：residues 1-215	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.6；277 K；38-40% MPD, 0.3M KCl, 0.1M MES.KOH, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 5.49 Å
3CW1 Crystal Structure of Human Spliceosomal U1 snRNP Deposited 2008-04-21	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 4 Protein–RNA Heteromer；Protein × 9 PDB declaration: decameric	Chain 8 1–216（216 aa） Fragment：residues 1-215	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.6；277 K；38-40% MPD, 0.3M KCl, 0.1M MES.KOH, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 5.49 Å
3PGW Crystal structure of human U1 snRNP Deposited 2010-11-02	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: undecameric	Chain S 1–437（437 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；277 K；8-10% PEG 4000, 0.1 M Trisodium citrate, 2 mM EDTA, 100 mM NaCl, 1-2% Anapoe X-305, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 4.40 Å R-free 0.348
3PGW Crystal structure of human U1 snRNP Deposited 2010-11-02	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 9 PDB declaration: undecameric	Chain L 1–437（437 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；277 K；8-10% PEG 4000, 0.1 M Trisodium citrate, 2 mM EDTA, 100 mM NaCl, 1-2% Anapoe X-305, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 4.40 Å R-free 0.348
4PJO Minimal U1 snRNP Deposited 2014-05-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 9 PDB declaration: Undecameric	Chain K 2–60（59 aa）	Mutation：M1G	ZN ZINC ION × 1 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 MG MAGNESIUM ION × 8 K POTASSIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.4；277 K；Minimal U1 snRNP at 4 mg/ml in 300mM KCl, 20mM KHepes, pH 7.5, 5mM MgCl2, 1mM DTT, 0.15 mM polyamine-9 mixed 1:1 with 7% MPD, 180mM KCl, 5mM MgSO4, 50mM NaHepes pH 6.4. Streak seeded.	Resolution 3.30 Å R-free 0.255
4PJO Minimal U1 snRNP Deposited 2014-05-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–RNA Heteromer；Protein × 9 PDB declaration: Undecameric	Chain k 2–60（59 aa）	Mutation：M1G	ZN ZINC ION × 1 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 MG MAGNESIUM ION × 5 K POTASSIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.4；277 K；Minimal U1 snRNP at 4 mg/ml in 300mM KCl, 20mM KHepes, pH 7.5, 5mM MgCl2, 1mM DTT, 0.15 mM polyamine-9 mixed 1:1 with 7% MPD, 180mM KCl, 5mM MgSO4, 50mM NaHepes pH 6.4. Streak seeded.	Resolution 3.30 Å R-free 0.255
4PJO Minimal U1 snRNP Deposited 2014-05-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein–RNA Heteromer；Protein × 9 PDB declaration: Undecameric	Chain N 2–60（59 aa）	Mutation：M1G	ZN ZINC ION × 1 MG MAGNESIUM ION × 4 K POTASSIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.4；277 K；Minimal U1 snRNP at 4 mg/ml in 300mM KCl, 20mM KHepes, pH 7.5, 5mM MgCl2, 1mM DTT, 0.15 mM polyamine-9 mixed 1:1 with 7% MPD, 180mM KCl, 5mM MgSO4, 50mM NaHepes pH 6.4. Streak seeded.	Resolution 3.30 Å R-free 0.255
4PJO Minimal U1 snRNP Deposited 2014-05-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 4 Protein–RNA Heteromer；Protein × 9 PDB declaration: Undecameric	Chain n 2–60（59 aa）	Mutation：M1G	ZN ZINC ION × 1 MG MAGNESIUM ION × 3 EOH ETHANOL × 1 CL CHLORIDE ION × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.4；277 K；Minimal U1 snRNP at 4 mg/ml in 300mM KCl, 20mM KHepes, pH 7.5, 5mM MgCl2, 1mM DTT, 0.15 mM polyamine-9 mixed 1:1 with 7% MPD, 180mM KCl, 5mM MgSO4, 50mM NaHepes pH 6.4. Streak seeded.	Resolution 3.30 Å R-free 0.255
4PKD U1-70k in complex with U1 snRNA stem-loops 1 and U1-A RRM in complex with stem-loop 2 Deposited 2014-05-14	Different construct Different mutation/modification 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: Dimeric	Chain B 60–215（156 aa）	Mutation：A2G	MG MAGNESIUM ION × 3 IMD IMIDAZOLE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.2；293 K；40% MPD, 0.15 M sodium chloride, 0.1 M sodium acetate, pH 4.2	Resolution 2.50 Å R-free 0.258
6QX9 Structure of a human fully-assembled precatalytic spliceosome (pre-B complex). Deposited 2019-03-07	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 65 PDB declaration: 71-meric	Chain 1K 1–437（437 aa）	Not recorded	ZN ZINC ION × 6 MG MAGNESIUM ION × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 IHP INOSITOL HEXAKISPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.28 Å
7B0Y Structure of a transcribing RNA polymerase II-U1 snRNP complex Deposited 2020-11-23	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 21 PDB declaration: 25-meric	Chain b 1–437（437 aa）	Not recorded	ZN ZINC ION × 8 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
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 O 1–437（437 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
8R08 Cryo-EM structure of the cross-exon pre-B+AMPPNP complex Deposited 2023-10-31	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 64 PDB declaration: 71-meric	Chain 1K 1–437（437 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.10 Å
9QEQ Structure of the transcribing Pol II-DSIF-SPT6-U1 snRNP complex Deposited 2025-03-10	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 24 PDB declaration: 28-meric	Chain b 1–437（437 aa）	Not recorded	ZN ZINC ION × 8 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；20 mM Hepes, 100 mM NaCl, 3 mM MgCl2, 0.5 mM TCEP cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å

10 other PDB entries and 17 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RU17_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–21； UniProt 131–151

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	2l5i
Deposition date deposition_date	2010-11-02
Structure title title	structure of the spliceosomal phosphopeptide P140 (non-phosphorylated form)
Keywords keywords	phosphorylation, HSC70, Lupus, SPLICING; SPLICING
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	7.37 Å
Radius of gyration Rg (electron density) rg_electron	7.52 Å
Forward intensity I(0) i0	6214670.00
Molecular weight molecular_weight	20504.0 kDa
Excluded volume excluded_volume	25921 Å³
Envelope volume envelope_volume	5498 Å³
Hydration-shell volume shell_volume	5745 Å³
Envelope diameter envelope_diameter	27.4 Å
Shell Rg shell_rg	13.61 Å
Envelope Rg envelope_rg	8.92 Å
Shape Rg shape_rg	7.43 Å
Total Rg total_rg	8.39 Å
Total atoms total_atoms	2888
Residues n_residues	168
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	21.7 Å
Rg (real space) rg_real	7.28 Å
Rg uncertainty (real space) rg_real_error	0.03 Å
I(0) (real space) i0_real	6.1170e+06
I(0) uncertainty (real space) i0_real_error	3.8330e+04
Rg (reciprocal space) rg_reciprocal	7.35 Å
I(0) (reciprocal space) i0_reciprocal	6215000.0000
Solution quality estimate total_estimate	0.7246
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	9.3 Å
Skewness Skewness skewness	0.164
Kurtosis Kurtosis kurtosis	-0.419
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	5.8610
Highest regularization parameter α highest_alpha	16740.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.966; Stabil: 0.961; Sysdev: 0.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.658

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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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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	1

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

Description description	U1 small nuclear ribonucleoprotein 70 kDa
Molecular weight formula_weight	2565.0 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2888

fit	/app/data/saxs_computation/l5/2l5i/2l5i.fit
pddf	/app/data/pr_computation/l5/2l5i/2l5i.pr.out
profile	/app/data/saxs_computation/l5/2l5i/2l5i.dat

structure of the spliceosomal phosphopeptide P140 (non-phosphorylated form)

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

U1 small nuclear ribonucleoprotein 70 kDa

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

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)