SAXSdb — 3ctr

▼

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

Poly(A)-specific ribonuclease PARN

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	7-METHYL-GUANOSINE-5'-TRIPHOSPHATE × 1 water × 1	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 4	7-METHYL-GUANOSINE-5'-TRIPHOSPHATE × 4 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PARN_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 6–101； UniProt 445–540

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	3ctr
Deposition date deposition_date	2008-04-14
Structure title title	Crystal structure of the RRM-domain of the poly(A)-specific ribonuclease PARN bound to m7GTP
Keywords keywords	;PARN, Protein-RNA-complex, m7G-cap, m7GTP, RNA recognition motif, RRM, Exonuclease, Hydrolase, Magnesium, Metal-binding, Nonsense-mediated mRNA decay, Nuclease, Nucleus, Phosphoprotein, RNA-binding ;; HYDROLASE
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.

3ctr__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3ctr__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3ctr__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	22.93 Å
Rg (electron density)	21.50 Å
Total Rg	22.49 Å
Atom count	2540
Residues	300
Excluded volume	44512 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3ctr__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3ctr__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 (3)

Entity 1 Entity 1 polymer

Description description	Poly(A)-specific ribonuclease PARN
Molecular weight formula_weight	11822.2 kDa
EC 编号 ec_number	3.1.13.4
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	704

GPLGSDHVLHVTFPKEWKTSDLYQLFSAFGNIQISWIDDTSAFVSLSQPEQVKIAVNTSKYAESYRIQTYAEYMGRKQEEKQIKRKWTEDSWKEADSKRLN

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 non-polymer

Description description	7-METHYL-GUANOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	538.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	69

▼

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	3ctrA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	330 — RRM (RNA recognition motif) domain

▶

Unit-cell length a length_a	81.107 Å
Unit-cell length b length_b	81.107 Å
Unit-cell length c length_c	78.058 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	16

Space group space_group	I 41 2 2
Space-group number int_tables_number	98
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	15.000 Å
R factor r_factor	0.2112
R_work r_work	0.2096
R_free r_free	0.2429

Crystal structure of the RRM-domain of the poly(A)-specific ribonuclease PARN bound to m7GTP

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

Poly(A)-specific ribonuclease PARN

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

3ctr__assembly_2__model_1

3ctr__assembly_2__model_1 | I(q)

3ctr__assembly_2__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 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)

Crystal structure of the RRM-domain of the poly(A)-specific ribonuclease PARN bound to m7GTP

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

Poly(A)-specific ribonuclease PARN

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

3ctr__assembly_2__model_1

3ctr__assembly_2__model_1 | I(q)

3ctr__assembly_2__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 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)