SAXSdb — 2ozb

▼

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

U4/U6.U5 tri-snRNP 15.5 kDa protein

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 2 RNA 1	;RNA comprising the 5' Stem-Loop RNA of U4snRNA ; × 1 U4/U6 small nuclear ribonucleoprotein Prp31 × 1 （Q8WWY3） CALCIUM ION × 2 water × 3	Consistent with all polymers
2	Protein–RNA	Heteromer	Protein 2 RNA 1	;RNA comprising the 5' Stem-Loop RNA of U4snRNA ; × 1 U4/U6 small nuclear ribonucleoprotein Prp31 × 1 （Q8WWY3） CALCIUM ION × 1 water × 3	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NH2L1_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 3–130； UniProt 1–128 Author chain D； PDBConstruct 3–130； UniProt 1–128

U4/U6 small nuclear ribonucleoprotein Prp31

Homo sapiens

UniProt Q8WWY3

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 2 RNA 1	;RNA comprising the 5' Stem-Loop RNA of U4snRNA ; × 1 U4/U6.U5 tri-snRNP 15.5 kDa protein × 1 （P55769） CALCIUM ION × 2 water × 3	Consistent with all polymers
2	Protein–RNA	Heteromer	Protein 2 RNA 1	;RNA comprising the 5' Stem-Loop RNA of U4snRNA ; × 1 U4/U6.U5 tri-snRNP 15.5 kDa protein × 1 （P55769） CALCIUM ION × 1 water × 3	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PRP31_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain B； PDBConstruct 5–260； UniProt 78–333 Author chain E； PDBConstruct 5–260； UniProt 78–333

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	2ozb
Deposition date deposition_date	2007-02-26
Structure title title	Structure of a human Prp31-15.5K-U4 snRNA complex
Keywords keywords	;RNA-protein complex, ribonucleoprotein particle (RNP), pre-mRNA splicing, U4/U6 di-snRNA, U4/U6 di-snRNP, hierarchical assembly, Nop domain, RNP-binding domain, RNA BINDING PROTEIN-RNA COMPLEX ;; RNA BINDING PROTEIN/RNA
Experimental Method method	X-RAY DIFFRACTION

▼

3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

2ozb__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2ozb__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2ozb__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	28.47 Å
Rg (electron density)	28.73 Å
Total Rg	29.08 Å
Atom count	3558
Residues	398
Excluded volume	61133 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2ozb__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2ozb__assembly_2__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	;RNA comprising the 5' Stem-Loop RNA of U4snRNA ;
Molecular weight formula_weight	10626.3 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	C,F
Atom count atom_count	7375

AUCGUAGCCAAUGAGGUUUAUCCGAGGCGCGAU

Entity 2 Entity 2 polymer

Description description	U4/U6.U5 tri-snRNP 15.5 kDa protein
Molecular weight formula_weight	14335.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,D

GSMTEADVNPKAYPLADAHLTKKLLDLVQQSCNYKQLRKGANEATKTLNRGISEFIVMAADAEPLEIILHLPLLCEDKNVPYVFVRSKQALGRACGVSRPVIACSVTIKEGSQLKQQIQSIQQSIERLLV

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 polymer

Description description	U4/U6 small nuclear ribonucleoprotein Prp31
Molecular weight formula_weight	28881.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,E

GPLGSEVMGPVEAAPEYRVIVDANNLTVEIENELNIIHKFIRDKYSKRFPELESLVPNALDYIRTVKELGNSLDKCKNNENLQQILTNATIMVVSVTASTTQGQQLSEEELERLEEACDMALELNASKHRIYEYVESRMSFIAPNLSIIIGASTAAKIMGVAGGLTNLSKMPACNIMLLGAQRKTLSGFSSTSVLPHTGYIYHSDIVQSLPPDLRRKAARLVAAKCTLAARVDSFHESTEGKVGYELKDEIERKFDKWQE

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	228

▼

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2ozba1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.79 — Bacillus chorismate mutase-like
Superfamily Superfamily superfamily	d.79.3 — L30e-like
Family Family family	d.79.3.1 — L30e/L7ae ribosomal proteins

Domain ID domain_id	d2ozbb1
Class class	a — All alpha proteins
Fold Fold fold	a.183 — Nop domain
Superfamily Superfamily superfamily	a.183.1 — Nop domain
Family Family family	a.183.1.1 — Nop domain

Domain ID domain_id	d2ozbd1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.79 — Bacillus chorismate mutase-like
Superfamily Superfamily superfamily	d.79.3 — L30e-like
Family Family family	d.79.3.1 — L30e/L7ae ribosomal proteins

Domain ID domain_id	d2ozbe_
Class class	a — All alpha proteins
Fold Fold fold	a.183 — Nop domain
Superfamily Superfamily superfamily	a.183.1 — Nop domain
Family Family family	a.183.1.1 — Nop domain

CATH v4.4 (6 domains)

Domain ID domain_id	2ozbA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1330 — 60s Ribosomal Protein L30; Chain: A;
Homologous superfamily homologous superfamily	30 — Ribosomal protein L30/S12

Domain ID domain_id	2ozbB01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	4070 —

Domain ID domain_id	2ozbB02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily	90 — Nop domain

Domain ID domain_id	2ozbD00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1330 — 60s Ribosomal Protein L30; Chain: A;
Homologous superfamily homologous superfamily	30 — Ribosomal protein L30/S12

Domain ID domain_id	2ozbE01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	4070 —

Domain ID domain_id	2ozbE02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily	90 — Nop domain

▶

Unit-cell length a length_a	83.555 Å
Unit-cell length b length_b	99.896 Å
Unit-cell length c length_c	169.645 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	2.600 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2078
R_work r_work	0.2057
R_free r_free	0.2476

Structure of a human Prp31-15.5K-U4 snRNA complex

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

U4/U6.U5 tri-snRNP 15.5 kDa protein

State in the Current Structure

Other States of the Same Protein in the Database

U4/U6 small nuclear ribonucleoprotein Prp31

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

2ozb__assembly_1__model_1

2ozb__assembly_1__model_1 | I(q)

2ozb__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Structure of a human Prp31-15.5K-U4 snRNA complex

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

U4/U6.U5 tri-snRNP 15.5 kDa protein

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

U4/U6 small nuclear ribonucleoprotein Prp31

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

2ozb__assembly_1__model_1

2ozb__assembly_1__model_1 | I(q)

2ozb__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

CATH v4.4 (6 domains)

7. Citations (1)