SAXSdb — 4pyu

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

Ubiquitin-like protein 5

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	U4/U6.U5 tri-snRNP-associated protein 1 × 1 （O43290） water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	U4/U6.U5 tri-snRNP-associated protein 1 × 1 （O43290） water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	U4/U6.U5 tri-snRNP-associated protein 1 × 1 （O43290） water × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	U4/U6.U5 tri-snRNP-associated protein 1 × 1 （O43290） water × 2	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 2	U4/U6.U5 tri-snRNP-associated protein 1 × 1 （O43290） water × 2	Consistent with protein count
6	Protein heterocomplex	Heteromer	Protein 2	U4/U6.U5 tri-snRNP-associated protein 1 × 1 （O43290） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UBL5_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–76； UniProt 1–73 Author chain B； PDBConstruct 4–76； UniProt 1–73 Author chain G； PDBConstruct 4–76； UniProt 1–73 Author chain K； PDBConstruct 4–76； UniProt 1–73 Author chain O； PDBConstruct 4–76； UniProt 1–73 Author chain S； PDBConstruct 4–76； UniProt 1–73

U4/U6.U5 tri-snRNP-associated protein 1

OrganismNot specified

UniProt O43290

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Ubiquitin-like protein 5 × 1 （Q9BZL1） water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Ubiquitin-like protein 5 × 1 （Q9BZL1） water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	Ubiquitin-like protein 5 × 1 （Q9BZL1） water × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	Ubiquitin-like protein 5 × 1 （Q9BZL1） water × 2	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 2	Ubiquitin-like protein 5 × 1 （Q9BZL1） water × 2	Consistent with protein count
6	Protein heterocomplex	Heteromer	Protein 2	Ubiquitin-like protein 5 × 1 （Q9BZL1） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SNUT1_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–19； UniProt 117–135 Author chain D； PDBConstruct 1–19； UniProt 117–135 Author chain H； PDBConstruct 1–19； UniProt 117–135 Author chain L； PDBConstruct 1–19； UniProt 117–135 Author chain P； PDBConstruct 1–19； UniProt 117–135 Author chain T； PDBConstruct 1–19； UniProt 117–135

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	4pyu
Deposition date deposition_date	2014-03-28
Structure title title	The conserved ubiquitin-like protein hub1 plays a critical role in splicing in human cells
Keywords keywords	UBIQUITIN-LIKE, PRE-MRNA SPLICING, PROTEIN BINDING-ALLERGEN COMPLEX; PROTEIN BINDING/ALLERGEN
Experimental Method method	X-RAY DIFFRACTION

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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.

4pyu__assembly_1__model_1

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

Download this curve (.dat)

4pyu__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4pyu__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	13.66 Å
Rg (electron density)	12.36 Å
Total Rg	13.64 Å
Atom count	746
Residues	95
Excluded volume	13420 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4pyu__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4pyu__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`4pyu__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`4pyu__assembly_4__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`4pyu__assembly_5__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`4pyu__assembly_6__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Ubiquitin-like protein 5
Molecular weight formula_weight	8843.2 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,G,K,O,S
Atom count atom_count	4741

GSHMIEVVCNDRLGKKVRVKCNTDDTIGDLKKLIAAQTGTRWNKIVLKKWYTIFKDHVSLGDYEIHDGMNLELYYQ

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 2 Entity 2 polymer

Description description	U4/U6.U5 tri-snRNP-associated protein 1
Molecular weight formula_weight	2114.5 kDa
Source method src_method	syn
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D,H,L,P,T

SLSIEETNKLRAKLGLKPL

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	287

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6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	4pyuA00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

Domain ID domain_id	4pyuB00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

Domain ID domain_id	4pyuG00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

Domain ID domain_id	4pyuK00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

Domain ID domain_id	4pyuO00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

Domain ID domain_id	4pyuS00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

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Unit-cell length a length_a	87.510 Å
Unit-cell length b length_b	103.630 Å
Unit-cell length c length_c	67.000 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	24

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	19.970 Å
R factor r_factor	0.1890
R_work r_work	0.1860
R_free r_free	0.2460

The conserved ubiquitin-like protein hub1 plays a critical role in splicing in human cells

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

Ubiquitin-like protein 5

State in the Current Structure

Other States of the Same Protein in the Database

U4/U6.U5 tri-snRNP-associated protein 1

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

4pyu__assembly_1__model_1

4pyu__assembly_1__model_1 | I(q)

4pyu__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)

The conserved ubiquitin-like protein hub1 plays a critical role in splicing in human cells

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

Ubiquitin-like protein 5

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.U5 tri-snRNP-associated protein 1

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

4pyu__assembly_1__model_1

4pyu__assembly_1__model_1 | I(q)

4pyu__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)