SAXSdb — 1yvp

▼

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

60-kDa SS-A/Ro ribonucleoprotein

Xenopus laevis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Monomer	Protein 1 RNA 3	Y RNA sequence, first strand × 2 Y RNA sequence, second strand × 1 ACETATE ION × 1 MAGNESIUM ION × 1 water × 4	Consistent with all polymers
2	Protein–RNA	Monomer	Protein 1 RNA 3	Y RNA sequence, first strand × 2 Y RNA sequence, second strand × 1 ACETATE ION × 1 MAGNESIUM ION × 1 water × 4	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RO60_XENLA
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain A； PDBConstruct 1–538； UniProt 1–538 Author chain B； PDBConstruct 1–538； UniProt 1–538

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	1yvp
Deposition date deposition_date	2005-02-16
Structure title title	Ro autoantigen complexed with RNAs
Keywords keywords	HEAT repeat; von Willebrand Factor A; Rossmann fold; MIDAS motif; RNA duplex; ssRNA, 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.

1yvp__assembly_1__model_1

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

Download this curve (.dat)

1yvp__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1yvp__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	28.17 Å
Rg (electron density)	26.99 Å
Total Rg	27.87 Å
Atom count	4706
Residues	550
Excluded volume	82688 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1yvp__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1yvp__assembly_2__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Y RNA sequence, first strand
Molecular weight formula_weight	3318.8 kDa
Source method src_method	syn
Copy count entity_count	4

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	C,E,G,H
Atom count atom_count	9890

GCUGGUCCGA

Entity 2 Entity 2 polymer

Description description	Y RNA sequence, second strand
Molecular weight formula_weight	3515.6 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	D,F

UUGACUAGCC

Entity 3 Entity 3 polymer

Description description	60-kDa SS-A/Ro ribonucleoprotein
Molecular weight formula_weight	60772.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MEATMDQTQPLNEKQVPNSEGCYVWQVSDMNRLRRFLCFGSEGGTYYIEEKKLGQENAEALLRLIEDGKGCEVVQEIKTFSQEGRAAKQEPTLFALAVCSQCSDIKTKQAAFRAVPEVCRIPTHLFTFIQFKKDLKEGMKCGMWGRALRKAVSDWYNTKDALNLAMAVTKYKQRNGWSHKDLLRLSHIKPANEGLTMVAKYVSKGWKEVQEAYKEKELSPETEKVLKYLEATERVKRTKDELEIIHLIDEYRLVREHLLTIHLKSKEIWKSLLQDMPLTALLRNLGKMTADSVLAPASSEVSSVCERLTNEKLLKKARIHPFHILVALETYKKGHGNRGKLRWIPDTSIVEALDNAFYKSFKLVEPTGKRFLLAIDVSASMNQRVLGSILNASVVAAAMCMLVARTEKDSHMVAFSDEMLPCPITVNMLLHEVVEKMSDITMGSTDCALPMLWAQKTNTAADIFIVFTDCETNVEDVHPATALKQYREKMGIPAKLIVCAMTSNGFSIADPDDRGMLDICGFDSGALDVIRNFTLDLI

Source Source

Source organism organism	Xenopus laevis
Common name common_name	African clawed frog
NCBI taxonomy ID ncbi_taxonomy_id	8355
Host organism host_organism	Trichoplusia ni

Entity 4 Entity 4 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	408

▼

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1yvpa1
Class class	a — All alpha proteins
Fold Fold fold	a.118 — alpha-alpha superhelix
Superfamily Superfamily superfamily	a.118.25 — TROVE domain-like
Family Family family	a.118.25.1 — TROVE domain-like

Domain ID domain_id	d1yvpa2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.62 — vWA-like
Superfamily Superfamily superfamily	c.62.1 — vWA-like
Family Family family	c.62.1.5 — RoRNP C-terminal domain-like

Domain ID domain_id	d1yvpb1
Class class	a — All alpha proteins
Fold Fold fold	a.118 — alpha-alpha superhelix
Superfamily Superfamily superfamily	a.118.25 — TROVE domain-like
Family Family family	a.118.25.1 — TROVE domain-like

Domain ID domain_id	d1yvpb2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.62 — vWA-like
Superfamily Superfamily superfamily	c.62.1 — vWA-like
Family Family family	c.62.1.5 — RoRNP C-terminal domain-like

CATH v4.4 (2 domains)

Domain ID domain_id	1yvpA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	410 — von Willebrand factor, type A domain

Domain ID domain_id	1yvpB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	410 — von Willebrand factor, type A domain

▶

Unit-cell length a length_a	60.300 Å
Unit-cell length b length_b	153.650 Å
Unit-cell length c length_c	80.560 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	92.80 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2021
R_work r_work	0.2020
R_free r_free	0.2380

Ro autoantigen complexed with RNAs

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

60-kDa SS-A/Ro ribonucleoprotein

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

1yvp__assembly_1__model_1

1yvp__assembly_1__model_1 | I(q)

1yvp__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Ro autoantigen complexed with RNAs

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

60-kDa SS-A/Ro ribonucleoprotein

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

1yvp__assembly_1__model_1

1yvp__assembly_1__model_1 | I(q)

1yvp__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

CATH v4.4 (2 domains)

7. Citations (1)