SAXSdb — 1x4q

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

U4/U6 small nuclear ribonucleoprotein Prp3

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 1–79	Fragment：PWI domain	No other associated polymer	SOLUTION NMR NMR measurement conditions：pH 7；298 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient NMR sample composition：0.8mM U-15, 13C; 20mM phosphate buffer NA; 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 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 1X4Q	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3JCR 3D structure determination of the humanU4/U6.U5 tri-snRNP complex Deposited 2016-01-21	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 33 PDB declaration: 36-meric	Chain K 1–683（683 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 20 mM HEPES, pH 7.9, 100 mM KCl, 5 mM MgCl2, 0.1 mM EDTA；pH 7.9；20 mM HEPES, pH 7.9, 100 mM KCl, 5 mM MgCl2, 0.1 mM EDTA cryo-EM vitrification conditions Cryogen ETHANE；Plunged into liquid ethane (FEI VITROBOT MARK IV).	Resolution 7.00 Å
5O9Z Cryo-EM structure of a pre-catalytic human spliceosome primed for activation (B complex) Deposited 2017-06-20	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 57-meric	Chain E 1–683（683 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.50 Å
6AH0 The Cryo-EM Structure of the Precusor of Human Pre-catalytic Spliceosome (pre-B complex) Deposited 2018-08-15	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 57-meric	Chain J 1–683（683 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 5.70 Å
6AHD The Cryo-EM Structure of Human Pre-catalytic Spliceosome (B complex) at 3.8 angstrom resolution Deposited 2018-08-17	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 58 PDB declaration: 63-meric	Chain J 1–683（683 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
6QW6 Structure of the human U5.U4/U6 tri-snRNP at 2.9A resolution. Deposited 2019-03-05	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 36 PDB declaration: 39-meric	Chain 4A 1–683（683 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 1 MG MAGNESIUM ION × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE；Wait 30s, blot for 2s to 3s.	Resolution 2.92 Å
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 4A 1–683（683 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
8H6E Cryo-EM structure of human exon-defined spliceosome in the late pre-B state. Deposited 2022-10-17	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 56 PDB declaration: 61-meric	Chain 4B 1–683（683 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 1 MG MAGNESIUM ION × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
8H6J Cryo-EM structure of human exon-defined spliceosome in the mature pre-B state. Deposited 2022-10-18	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 56 PDB declaration: 61-meric	Chain 4B 1–683（683 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 1 MG MAGNESIUM ION × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.25 Å
8H6K Cryo-EM structure of human exon-defined spliceosome in the mature B state. Deposited 2022-10-18	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 58 PDB declaration: 63-meric	Chain 4B 1–683（683 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.70 Å
8H6L Cryo-EM structure of human exon-defined spliceosome in the early B state. Deposited 2022-10-18	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 59-meric	Chain 4B 1–683（683 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.60 Å
8Q7N cryo-EM structure of the human spliceosomal B complex protomer (tri-snRNP core region) Deposited 2023-08-16	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 17 PDB declaration: 21-meric	Chain J 1–683（683 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
8QO9 Cryo-EM structure of a human spliceosomal B complex protomer Deposited 2023-09-28	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 66 PDB declaration: 71-meric	Chain J 1–683（683 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 5.29 Å
8QOZ Cryo-EM Structure of Pre-B+5'ss+ATPgammaS Complex (core part) Deposited 2023-09-29	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 13 PDB declaration: 17-meric	Chain J 1–683（683 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
8QP8 Cryo-EM Structure of Pre-B Complex (core part) Deposited 2023-09-30	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 12 PDB declaration: 15-meric	Chain J 1–683（683 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
8QP9 Cryo-EM Structure of Pre-B+AMPPNP Complex (core part) Deposited 2023-09-30	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 13 PDB declaration: 16-meric	Chain J 1–683（683 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.10 Å
8QPA Cryo-EM Structure of Pre-B+5'ssLNG Complex (core part) Deposited 2023-10-01	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 13 PDB declaration: heptadecameric	Chain J 1–683（683 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å
8QPB Cryo-EM Structure of Pre-B+ATP Complex (core part) Deposited 2023-10-01	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 13 PDB declaration: 17-meric	Chain J 1–683（683 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å
8QPE Cryo-EM Structure of Pre-B-like Complex (core part) Deposited 2023-10-01	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 15 PDB declaration: 20-meric	Chain J 1–683（683 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
8QXD Cryo-EM structure of the cross-exon pre-B complex Deposited 2023-10-24	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 56 PDB declaration: 61-meric	Chain J 1–683（683 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 9.60 Å
8QZS Cryo-EM structure of the cross-exon B-like complex Deposited 2023-10-29	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 61 PDB declaration: 68-meric	Chain J 1–683（683 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.10 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 J 1–683（683 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
8R09 Cryo-EM structure of the cross-exon pre-B+5'ss+ATPgammaS 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 × 54 PDB declaration: 60-meric	Chain J 1–683（683 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.30 Å
8R0A Cryo-EM structure of the cross-exon pre-B+5'ss 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 × 56 PDB declaration: 62-meric	Chain J 1–683（683 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 5.80 Å
8R0B Cryo-EM structure of the cross-exon pre-B+ATP 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 × 54 PDB declaration: 60-meric	Chain J 1–683（683 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.40 Å
8RM5 Cryo-EM structure of the cross-exon pre-B+5'ssLNG+ATPyS complex Deposited 2024-01-05	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 60-meric	Chain J 1–683（683 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.90 Å
8Y6O Cryo-EM Structure of the human minor pre-B complex (pre-precatalytic spliceosome) U11 and tri-snRNP part Deposited 2024-02-02	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 41 PDB declaration: 46-meric	Chain N 1–683（683 aa）	Not recorded	MG MAGNESIUM ION × 2 IHP INOSITOL HEXAKISPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 3.38 Å

26 other PDB entries and 26 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PRPF3_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 8–86； UniProt 1–79

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	1x4q
Deposition date deposition_date	2005-05-14
Structure title title	Solution structure of PWI domain in U4/U6 small nuclear ribonucleoprotein Prp3(hPrp3)
Keywords keywords	;PWI domain, Structural Genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI, RNA BINDING PROTEIN ;; RNA BINDING PROTEIN
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	14.67 Å
Radius of gyration Rg (electron density) rg_electron	13.88 Å
Forward intensity I(0) i0	572788000.00
Molecular weight molecular_weight	197590.0 kDa
Excluded volume excluded_volume	246200 Å³
Envelope volume envelope_volume	41330 Å³
Hydration-shell volume shell_volume	18127 Å³
Envelope diameter envelope_diameter	61.0 Å
Shell Rg shell_rg	25.74 Å
Envelope Rg envelope_rg	20.40 Å
Shape Rg shape_rg	13.87 Å
Total Rg total_rg	14.24 Å
Total atoms total_atoms	27880
Residues n_residues	1840
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	54.5 Å
Rg (real space) rg_real	14.72 Å
Rg uncertainty (real space) rg_real_error	0.53 Å
I(0) (real space) i0_real	5.7280e+08
I(0) uncertainty (real space) i0_real_error	7.6800e+06
Rg (reciprocal space) rg_reciprocal	14.71 Å
I(0) (reciprocal space) i0_reciprocal	572800000.0000
Solution quality estimate total_estimate	0.7096
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	15.9 Å
Skewness Skewness skewness	0.475
Kurtosis Kurtosis kurtosis	0.092
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	292500.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.460; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.841; 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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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	1x4qA01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1390 — PWI domain
Homologous superfamily homologous superfamily	10 — PWI domain

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8. Citations (1)

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Description description	U4/U6 small nuclear ribonucleoprotein Prp3
Molecular weight formula_weight	9911.3 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	27880

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606

fit	/app/data/saxs_computation/x4/1x4q/1x4q.fit
pddf	/app/data/pr_computation/x4/1x4q/1x4q.pr.out
profile	/app/data/saxs_computation/x4/1x4q/1x4q.dat

Solution structure of PWI domain in U4/U6 small nuclear ribonucleoprotein Prp3(hPrp3)

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

U4/U6 small nuclear ribonucleoprotein Prp3

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

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)