3kur

Crystal structure of the MLLE domain of poly(A)-binding protein

Method: X-RAY DIFFRACTION

▼

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

Polyadenylate-binding protein 1

Homo sapiens

UniProt P11940

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	CHLORIDE ION × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	CHLORIDE ION × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
5	Protein monomer	Monomer	Protein 1	CHLORIDE ION × 1 water × 1	Consistent with protein count
6	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
7	Protein monomer	Monomer	Protein 1	CHLORIDE ION × 1 water × 1	Consistent with protein count
8	Protein monomer	Monomer	Protein 1	CHLORIDE ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PABP1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 6–79； UniProt 544–617 Author chain B； PDBConstruct 6–79； UniProt 544–617 Author chain C； PDBConstruct 6–79； UniProt 544–617 Author chain D； PDBConstruct 6–79； UniProt 544–617 Author chain E； PDBConstruct 6–79； UniProt 544–617 Author chain F； PDBConstruct 6–79； UniProt 544–617 Author chain G； PDBConstruct 6–79； UniProt 544–617 Author chain H； PDBConstruct 6–79； UniProt 544–617

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	3kur
Deposition date deposition_date	2009-11-27
Structure title title	Crystal structure of the MLLE domain of poly(A)-binding protein
Keywords keywords	;all-helical domain, Methylation, mRNA processing, mRNA splicing, Nucleus, Phosphoprotein, RNA-binding, Spliceosome, RNA BINDING PROTEIN ;; RNA BINDING PROTEIN
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.

3kur__assembly_2__model_1

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

Download this curve (.dat)

3kur__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3kur__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	13.44 Å
Rg (electron density)	12.03 Å
Total Rg	13.39 Å
Atom count	553
Residues	73
Excluded volume	10023 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3kur__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3kur__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3kur__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`3kur__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`3kur__assembly_5__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`3kur__assembly_6__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
7	1	`3kur__assembly_7__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
8	1	`3kur__assembly_8__model_1`	monomeric （1）	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	Polyadenylate-binding protein 1
Molecular weight formula_weight	8493.9 kDa
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H
Atom count atom_count	4501

GPLGSPLTASMLASAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESPESLRSKVDEAVAVLQAH

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	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	107

▼

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d3kura_
Class class	a — All alpha proteins
Fold Fold fold	a.144 — PABP domain-like
Superfamily Superfamily superfamily	a.144.1 — PABC (PABP) domain
Family Family family	a.144.1.1 — PABC (PABP) domain

Domain ID domain_id	d3kurb_
Class class	a — All alpha proteins
Fold Fold fold	a.144 — PABP domain-like
Superfamily Superfamily superfamily	a.144.1 — PABC (PABP) domain
Family Family family	a.144.1.1 — PABC (PABP) domain

Domain ID domain_id	d3kurc_
Class class	a — All alpha proteins
Fold Fold fold	a.144 — PABP domain-like
Superfamily Superfamily superfamily	a.144.1 — PABC (PABP) domain
Family Family family	a.144.1.1 — PABC (PABP) domain

Domain ID domain_id	d3kurd_
Class class	a — All alpha proteins
Fold Fold fold	a.144 — PABP domain-like
Superfamily Superfamily superfamily	a.144.1 — PABC (PABP) domain
Family Family family	a.144.1.1 — PABC (PABP) domain

Domain ID domain_id	d3kure_
Class class	a — All alpha proteins
Fold Fold fold	a.144 — PABP domain-like
Superfamily Superfamily superfamily	a.144.1 — PABC (PABP) domain
Family Family family	a.144.1.1 — PABC (PABP) domain

Domain ID domain_id	d3kurf_
Class class	a — All alpha proteins
Fold Fold fold	a.144 — PABP domain-like
Superfamily Superfamily superfamily	a.144.1 — PABC (PABP) domain
Family Family family	a.144.1.1 — PABC (PABP) domain

Domain ID domain_id	d3kurg_
Class class	a — All alpha proteins
Fold Fold fold	a.144 — PABP domain-like
Superfamily Superfamily superfamily	a.144.1 — PABC (PABP) domain
Family Family family	a.144.1.1 — PABC (PABP) domain

Domain ID domain_id	d3kurh_
Class class	a — All alpha proteins
Fold Fold fold	a.144 — PABP domain-like
Superfamily Superfamily superfamily	a.144.1 — PABC (PABP) domain
Family Family family	a.144.1.1 — PABC (PABP) domain

CATH v4.4 (8 domains)

Domain ID domain_id	3kurA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1900 — c-terminal domain of poly(a) binding protein
Homologous superfamily homologous superfamily	10 — c-terminal domain of poly(a) binding protein

Domain ID domain_id	3kurB01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1900 — c-terminal domain of poly(a) binding protein
Homologous superfamily homologous superfamily	10 — c-terminal domain of poly(a) binding protein

Domain ID domain_id	3kurC01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1900 — c-terminal domain of poly(a) binding protein
Homologous superfamily homologous superfamily	10 — c-terminal domain of poly(a) binding protein

Domain ID domain_id	3kurD01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1900 — c-terminal domain of poly(a) binding protein
Homologous superfamily homologous superfamily	10 — c-terminal domain of poly(a) binding protein

Domain ID domain_id	3kurE01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1900 — c-terminal domain of poly(a) binding protein
Homologous superfamily homologous superfamily	10 — c-terminal domain of poly(a) binding protein

Domain ID domain_id	3kurF01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1900 — c-terminal domain of poly(a) binding protein
Homologous superfamily homologous superfamily	10 — c-terminal domain of poly(a) binding protein

Domain ID domain_id	3kurG01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1900 — c-terminal domain of poly(a) binding protein
Homologous superfamily homologous superfamily	10 — c-terminal domain of poly(a) binding protein

Domain ID domain_id	3kurH01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1900 — c-terminal domain of poly(a) binding protein
Homologous superfamily homologous superfamily	10 — c-terminal domain of poly(a) binding protein

▶

Unit-cell length a length_a	146.977 Å
Unit-cell length b length_b	146.977 Å
Unit-cell length c length_c	83.055 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	64

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.2184
R_work r_work	0.2157
R_free r_free	0.2722

Crystal structure of the MLLE domain of poly(A)-binding protein

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

Polyadenylate-binding 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

3kur__assembly_2__model_1

3kur__assembly_2__model_1 | I(q)

3kur__assembly_2__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 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Crystal structure of the MLLE domain of poly(A)-binding protein

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

Polyadenylate-binding 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

3kur__assembly_2__model_1

3kur__assembly_2__model_1 | I(q)

3kur__assembly_2__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 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)