2vtx

ACTIVATION OF NUCLEOPLASMIN, AN OLIGOMERIC HISTONE CHAPERONE, CHALLENGES ITS STABILITY

Method: X-RAY DIFFRACTION

▼

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

NPM-A PROTEIN

XENOPUS LAEVIS

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 5	water × 5	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 5	water × 5	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q6GQG6_XENLA
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 1–120； UniProt 1–120 Author chain B； PDBConstruct 1–120； UniProt 1–120 Author chain C； PDBConstruct 1–120； UniProt 1–120 Author chain D； PDBConstruct 1–120； UniProt 1–120 Author chain E； PDBConstruct 1–120； UniProt 1–120 Author chain G； PDBConstruct 1–120； UniProt 1–120 Author chain H； PDBConstruct 1–120； UniProt 1–120 Author chain I； PDBConstruct 1–120； UniProt 1–120 Author chain K； PDBConstruct 1–120； UniProt 1–120 Author chain J； PDBConstruct 1–120； UniProt 1–120

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	2vtx
Deposition date deposition_date	2008-05-16
Structure title title	ACTIVATION OF NUCLEOPLASMIN, AN OLIGOMERIC HISTONE CHAPERONE, CHALLENGES ITS STABILITY
Keywords keywords	NUCLEOPLASMIN, PHOSPHORYLATION, PROTEIN STABILITY, OLIGOMERIC PROTEIN, NUCLEAR PROTEIN; NUCLEAR 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.

2vtx__assembly_2__model_1

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

Download this curve (.dat)

2vtx__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2vtx__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	22.95 Å
Rg (electron density)	21.43 Å
Total Rg	22.26 Å
Atom count	3583
Residues	471
Excluded volume	64576 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2vtx__assembly_1__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2vtx__assembly_2__model_1`	pentameric （5）	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	NPM-A PROTEIN
Molecular weight formula_weight	13384.2 kDa
Source method src_method	man
Copy count entity_count	9

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,G,H,I,K
Atom count atom_count	7259

MADDVDNDDKLEKPVDLIWGCELNEQNKTFEFKVEDDEEKCEHQLALRTVCLGDKAKDEFHIVEIVDQEEGAEKSVPIATLKPSILPMATMVGIELDPPVTFRLKAGSGPLYISGQHVAM

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	ESCHERICHIA COLI

Entity 2 Entity 2 polymer

Description description	NPM-A PROTEIN
Molecular weight formula_weight	13396.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	J

MADDVDNDDKLEKPVDLIWGCELNEQNKTFEFKVEDDEEKCEHQLALRTVCLGDKAKDEFHIVEIVDQEEGAEKVVPIATLKPSILPMATMVGIELDPPVTFRLKAGSGPLYISGQHVAM

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	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	173

▼

6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (10 domains)

Domain ID domain_id	d2vtxa_
Class class	b — All beta proteins
Fold Fold fold	b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamily	b.121.3 — Nucleoplasmin-like core domain
Family Family family	b.121.3.1 — Nucleoplasmin-like core domain

Domain ID domain_id	d2vtxb_
Class class	b — All beta proteins
Fold Fold fold	b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamily	b.121.3 — Nucleoplasmin-like core domain
Family Family family	b.121.3.1 — Nucleoplasmin-like core domain

Domain ID domain_id	d2vtxc_
Class class	b — All beta proteins
Fold Fold fold	b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamily	b.121.3 — Nucleoplasmin-like core domain
Family Family family	b.121.3.1 — Nucleoplasmin-like core domain

Domain ID domain_id	d2vtxd_
Class class	b — All beta proteins
Fold Fold fold	b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamily	b.121.3 — Nucleoplasmin-like core domain
Family Family family	b.121.3.1 — Nucleoplasmin-like core domain

Domain ID domain_id	d2vtxe_
Class class	b — All beta proteins
Fold Fold fold	b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamily	b.121.3 — Nucleoplasmin-like core domain
Family Family family	b.121.3.1 — Nucleoplasmin-like core domain

Domain ID domain_id	d2vtxg_
Class class	b — All beta proteins
Fold Fold fold	b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamily	b.121.3 — Nucleoplasmin-like core domain
Family Family family	b.121.3.1 — Nucleoplasmin-like core domain

Domain ID domain_id	d2vtxh_
Class class	b — All beta proteins
Fold Fold fold	b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamily	b.121.3 — Nucleoplasmin-like core domain
Family Family family	b.121.3.1 — Nucleoplasmin-like core domain

Domain ID domain_id	d2vtxi_
Class class	b — All beta proteins
Fold Fold fold	b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamily	b.121.3 — Nucleoplasmin-like core domain
Family Family family	b.121.3.1 — Nucleoplasmin-like core domain

Domain ID domain_id	d2vtxj_
Class class	b — All beta proteins
Fold Fold fold	b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamily	b.121.3 — Nucleoplasmin-like core domain
Family Family family	b.121.3.1 — Nucleoplasmin-like core domain

Domain ID domain_id	d2vtxk_
Class class	b — All beta proteins
Fold Fold fold	b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamily	b.121.3 — Nucleoplasmin-like core domain
Family Family family	b.121.3.1 — Nucleoplasmin-like core domain

CATH v4.4 (10 domains)

Domain ID domain_id	2vtxA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	340 — Nucleoplasmin core domain

Domain ID domain_id	2vtxB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	340 — Nucleoplasmin core domain

Domain ID domain_id	2vtxC00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	340 — Nucleoplasmin core domain

Domain ID domain_id	2vtxD00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	340 — Nucleoplasmin core domain

Domain ID domain_id	2vtxE00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	340 — Nucleoplasmin core domain

Domain ID domain_id	2vtxG00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	340 — Nucleoplasmin core domain

Domain ID domain_id	2vtxH00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	340 — Nucleoplasmin core domain

Domain ID domain_id	2vtxI00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	340 — Nucleoplasmin core domain

Domain ID domain_id	2vtxJ00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	340 — Nucleoplasmin core domain

Domain ID domain_id	2vtxK00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	340 — Nucleoplasmin core domain

▶

Unit-cell length a length_a	67.034 Å
Unit-cell length b length_b	94.601 Å
Unit-cell length c length_c	176.100 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	36

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	40.000 Å
R factor r_factor	0.1870
R_work r_work	0.1820
R_free r_free	0.2690

ACTIVATION OF NUCLEOPLASMIN, AN OLIGOMERIC HISTONE CHAPERONE, CHALLENGES ITS STABILITY

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

NPM-A PROTEIN

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

2vtx__assembly_2__model_1

2vtx__assembly_2__model_1 | I(q)

2vtx__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (10 domains)

CATH v4.4 (10 domains)

7. Citations (1)

ACTIVATION OF NUCLEOPLASMIN, AN OLIGOMERIC HISTONE CHAPERONE, CHALLENGES ITS STABILITY

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

NPM-A 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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

2vtx__assembly_2__model_1

2vtx__assembly_2__model_1 | I(q)

2vtx__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (10 domains)

CATH v4.4 (10 domains)

7. Citations (1)