1xb9

The structure and function of Xenopus NO38-core, a histone chaperone in the nucleolus

Method: X-RAY DIFFRACTION

▼

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

Nucleophosmin

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	NPM_XENLA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 6–114； UniProt 16–124 Author chain B； PDBConstruct 6–114； UniProt 16–124 Author chain C； PDBConstruct 6–114； UniProt 16–124 Author chain D； PDBConstruct 6–114； UniProt 16–124 Author chain E； PDBConstruct 6–114； UniProt 16–124 Author chain F； PDBConstruct 6–114； UniProt 16–124 Author chain G； PDBConstruct 6–114； UniProt 16–124 Author chain H； PDBConstruct 6–114； UniProt 16–124 Author chain I； PDBConstruct 6–114； UniProt 16–124 Author chain J； PDBConstruct 6–114； UniProt 16–124

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	1xb9
Deposition date deposition_date	2004-08-30
Structure title title	The structure and function of Xenopus NO38-core, a histone chaperone in the nucleolus
Keywords keywords	NO38, drosophila Nucleoplasmin-like protein (dNLP), Nucleoplasmin (Np), histone binding, CHAPERONE; CHAPERONE
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.

1xb9__assembly_2__model_1

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

Download this curve (.dat)

1xb9__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1xb9__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	23.43 Å
Rg (electron density)	22.13 Å
Total Rg	23.16 Å
Atom count	4008
Residues	530
Excluded volume	71992 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1xb9__assembly_1__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1xb9__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 (2)

▼

6. Fold Classification (SCOP + CATH) 30 domains

SCOP 2.08 (20 domains)

Domain ID domain_id	d1xb9a1
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	d1xb9a2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d1xb9b1
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	d1xb9b2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d1xb9c1
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	d1xb9c2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d1xb9d1
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	d1xb9d2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d1xb9e1
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	d1xb9e2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d1xb9f1
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	d1xb9f2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d1xb9g1
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	d1xb9g2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d1xb9h1
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	d1xb9h2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d1xb9i1
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	d1xb9i2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d1xb9j1
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	d1xb9j2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (10 domains)

Domain ID domain_id	1xb9A00
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	1xb9B00
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	1xb9C00
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	1xb9D00
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	1xb9E00
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	1xb9F00
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	1xb9G00
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	1xb9H00
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	1xb9I00
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	1xb9J00
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	198.913 Å
Unit-cell length b length_b	64.549 Å
Unit-cell length c length_c	97.461 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	113.72 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	40

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

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	91.290 Å
R factor r_factor	0.2079
R_work r_work	0.2037
R_free r_free	0.2550

Description description	Nucleophosmin
Molecular weight formula_weight	12352.0 kDa
Source method src_method	man
Copy count entity_count	10

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J
Atom count atom_count	8337

The structure and function of Xenopus NO38-core, a histone chaperone in the nucleolus

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

Nucleophosmin

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

1xb9__assembly_2__model_1

1xb9__assembly_2__model_1 | I(q)

1xb9__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 30 domains

SCOP 2.08 (20 domains)

CATH v4.4 (10 domains)

7. Citations (1)

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 BL21(DE3)

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	305

The structure and function of Xenopus NO38-core, a histone chaperone in the nucleolus

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

Nucleophosmin

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

1xb9__assembly_2__model_1

1xb9__assembly_2__model_1 | I(q)

1xb9__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 30 domains

SCOP 2.08 (20 domains)

CATH v4.4 (10 domains)

7. Citations (1)