5ehd

Crystal structure of human nucleophosmin-core in complex with cytochrome c

Method: X-RAY DIFFRACTION

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

Nucleophosmin

Homo sapiens

State in the Current Structure

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

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NPM_HUMAN
Isoform	P06748-2
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–116； UniProt 9–124 Author chain B； PDBConstruct 1–116； UniProt 9–124 Author chain C； PDBConstruct 1–116； UniProt 9–124 Author chain D； PDBConstruct 1–116； UniProt 9–124 Author chain E； PDBConstruct 1–116； UniProt 9–124 Author chain F； PDBConstruct 1–116； UniProt 9–124 Author chain G； PDBConstruct 1–116； UniProt 9–124 Author chain H； PDBConstruct 1–116； UniProt 9–124 Author chain I； PDBConstruct 1–116； UniProt 9–124 Author chain J； PDBConstruct 1–116； UniProt 9–124 Author chain a； PDBConstruct 1–116； UniProt 9–124 Author chain b； PDBConstruct 1–116； UniProt 9–124 Author chain c； PDBConstruct 1–116； UniProt 9–124 Author chain d； PDBConstruct 1–116； UniProt 9–124 Author chain e； PDBConstruct 1–116； UniProt 9–124 Author chain f； PDBConstruct 1–116； UniProt 9–124 Author chain g； PDBConstruct 1–116； UniProt 9–124 Author chain h； PDBConstruct 1–116； UniProt 9–124 Author chain i； PDBConstruct 1–116； UniProt 9–124 Author chain j； PDBConstruct 1–116； UniProt 9–124

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	5ehd
Deposition date deposition_date	2015-10-28
Structure title title	Crystal structure of human nucleophosmin-core in complex with cytochrome c
Keywords keywords	nucleolus, histone assembly, citochrome c, apoptosis, oxidoreductase; OXIDOREDUCTASE
Experimental Method method	X-RAY DIFFRACTION

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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.

5ehd__assembly_4__model_1

Assembly 4 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

5ehd__assembly_4__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5ehd__assembly_4__model_1 | P(r) · Pending

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

Rg（Guinier）	23.59 Å
Rg (electron density)	22.18 Å
Total Rg	23.09 Å
Atom count	4055
Residues	531
Excluded volume	72337 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5ehd__assembly_1__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5ehd__assembly_2__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`5ehd__assembly_3__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`5ehd__assembly_4__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Nucleophosmin
Molecular weight formula_weight	12673.4 kDa
Source method src_method	man
Copy count entity_count	20

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J,a,b,c,d,e,f,g,h,i,j
Atom count atom_count	16452

MSPLRPQNYLFGCELKADKDYHFKVDNDENEHQLSLRTVSLGAGAKDELHIVEAEAMNYEGSPIKVTLATLKMSVQPTVSLGGFEITPPVVLRLKCGSGPVHISGQHLVAVEEDAE

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 BL21(DE3)

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	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	235

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6. Fold Classification (SCOP + CATH) 30 domains

SCOP 2.08 (10 domains)

Domain ID domain_id	d5ehda_
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	d5ehdb_
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	d5ehdc_
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	d5ehdd_
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	d5ehde_
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	d5ehdf_
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	d5ehdg_
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	d5ehdh_
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	d5ehdi_
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	d5ehdj_
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 (20 domains)

Domain ID domain_id	5ehdA00
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	5ehdB00
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	5ehdC00
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	5ehdD00
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	5ehdE00
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	5ehdF00
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	5ehdG00
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	5ehdH00
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	5ehdI00
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	5ehdJ00
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	5ehda00
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	5ehdb00
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	5ehdc00
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	5ehdd00
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	5ehde00
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	5ehdf00
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	5ehdg00
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	5ehdh00
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	5ehdi00
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	5ehdj00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	340 — Nucleoplasmin core domain

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Unit-cell length a length_a	58.799 Å
Unit-cell length b length_b	179.720 Å
Unit-cell length c length_c	104.300 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	94.32 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	40

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

Resolution resolution	2.550 Å
Low-resolution limit resolution_low	45.526 Å
R factor r_factor	0.1668
R_work r_work	0.1636
R_free r_free	0.2291

Crystal structure of human nucleophosmin-core in complex with cytochrome c

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

5ehd__assembly_4__model_1

5ehd__assembly_4__model_1 | I(q)

5ehd__assembly_4__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) 30 domains

SCOP 2.08 (10 domains)

CATH v4.4 (20 domains)

7. Citations (1)

Crystal structure of human nucleophosmin-core in complex with cytochrome c

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

5ehd__assembly_4__model_1

5ehd__assembly_4__model_1 | I(q)

5ehd__assembly_4__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) 30 domains

SCOP 2.08 (10 domains)

CATH v4.4 (20 domains)

7. Citations (1)