SAXSdb — 1syx

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

Spliceosomal U5 snRNP-specific 15 kDa protein

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	CD2 antigen cytoplasmic tail-binding protein 2 × 1 （O95400） water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	CD2 antigen cytoplasmic tail-binding protein 2 × 1 （O95400） water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	CD2 antigen cytoplasmic tail-binding protein 2 × 1 （O95400） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TXN4A_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–142； UniProt 1–142 Author chain C； PDBConstruct 1–142； UniProt 1–142 Author chain E； PDBConstruct 1–142； UniProt 1–142

CD2 antigen cytoplasmic tail-binding protein 2

Homo sapiens

UniProt O95400

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Spliceosomal U5 snRNP-specific 15 kDa protein × 1 （P83876） water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Spliceosomal U5 snRNP-specific 15 kDa protein × 1 （P83876） water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	Spliceosomal U5 snRNP-specific 15 kDa protein × 1 （P83876） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CD2B2_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 7–86； UniProt 262–341 Author chain D； PDBConstruct 7–86； UniProt 262–341 Author chain F； PDBConstruct 7–86； UniProt 262–341

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	1syx
Deposition date deposition_date	2004-04-02
Structure title title	The crystal structure of a binary U5 snRNP complex
Keywords keywords	GYF-domain; thioredoxin-like; spliceosomal proteins, TRANSLATION-IMMUNE SYSTEM COMPLEX; TRANSLATION/IMMUNE SYSTEM
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.

1syx__assembly_1__model_1

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

Download this curve (.dat)

1syx__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1syx__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	18.88 Å
Rg (electron density)	17.98 Å
Total Rg	18.70 Å
Atom count	1630
Residues	197
Excluded volume	28956 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1syx__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1syx__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1syx__assembly_3__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	Spliceosomal U5 snRNP-specific 15 kDa protein
Molecular weight formula_weight	16807.3 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E
Atom count atom_count	5082

MSYMLPHLHNGWQVDQAILSEEDRVVVIRFGHDWDPTCMKMDEVLYSIAEKVKNFAVIYLVDITEVPDFNKMYELYDPCTVMFFFRNKHIMIDLGTGNNNKINWAMEDKQEMVDIIETVYRGARKGRGLVVSPKDYSTKYRY

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	CD2 antigen cytoplasmic tail-binding protein 2
Molecular weight formula_weight	9875.7 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D,F

AEEELETPTPTQRGEAESRGDGLVDVMWEYKWENTGDAELYGPFTSAQMQTWVSEGYFPDGVYCRKLDPPGGQFYNSKRIDFDLYT

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 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	192

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1syxa_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.47 — Thioredoxin fold
Superfamily Superfamily superfamily	c.47.1 — Thioredoxin-like
Family Family family	c.47.1.8 — spliceosomal protein U5-15Kd

Domain ID domain_id	d1syxb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.76 — GYF/BRK domain-like
Superfamily Superfamily superfamily	d.76.1 — GYF domain
Family Family family	d.76.1.1 — GYF domain

Domain ID domain_id	d1syxc_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.47 — Thioredoxin fold
Superfamily Superfamily superfamily	c.47.1 — Thioredoxin-like
Family Family family	c.47.1.8 — spliceosomal protein U5-15Kd

Domain ID domain_id	d1syxd_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.76 — GYF/BRK domain-like
Superfamily Superfamily superfamily	d.76.1 — GYF domain
Family Family family	d.76.1.1 — GYF domain

Domain ID domain_id	d1syxe_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.47 — Thioredoxin fold
Superfamily Superfamily superfamily	c.47.1 — Thioredoxin-like
Family Family family	c.47.1.8 — spliceosomal protein U5-15Kd

Domain ID domain_id	d1syxf_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.76 — GYF/BRK domain-like
Superfamily Superfamily superfamily	d.76.1 — GYF domain
Family Family family	d.76.1.1 — GYF domain

CATH v4.4 (6 domains)

Domain ID domain_id	1syxA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	30 — Glutaredoxin
Homologous superfamily homologous superfamily	10 — Glutaredoxin

Domain ID domain_id	1syxB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1490 — Dna Ligase; domain 1
Homologous superfamily homologous superfamily	40 — GYF domain

Domain ID domain_id	1syxC00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	30 — Glutaredoxin
Homologous superfamily homologous superfamily	10 — Glutaredoxin

Domain ID domain_id	1syxD00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1490 — Dna Ligase; domain 1
Homologous superfamily homologous superfamily	40 — GYF domain

Domain ID domain_id	1syxE00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	30 — Glutaredoxin
Homologous superfamily homologous superfamily	10 — Glutaredoxin

Domain ID domain_id	1syxF00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1490 — Dna Ligase; domain 1
Homologous superfamily homologous superfamily	40 — GYF domain

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Unit-cell length a length_a	135.726 Å
Unit-cell length b length_b	75.913 Å
Unit-cell length c length_c	77.027 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	94.27 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.345 Å
Low-resolution limit resolution_low	49.390 Å
R factor r_factor	0.2181
R_work r_work	0.2158
R_free r_free	0.2625

The crystal structure of a binary U5 snRNP complex

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

Spliceosomal U5 snRNP-specific 15 kDa protein

State in the Current Structure

Other States of the Same Protein in the Database

CD2 antigen cytoplasmic tail-binding protein 2

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

1syx__assembly_1__model_1

1syx__assembly_1__model_1 | I(q)

1syx__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)

The crystal structure of a binary U5 snRNP complex

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

Spliceosomal U5 snRNP-specific 15 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

CD2 antigen cytoplasmic tail-binding protein 2

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

1syx__assembly_1__model_1

1syx__assembly_1__model_1 | I(q)

1syx__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)