SAXSdb — 6k09

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

Nucleosome Assembly Protein

Caenorhabditis elegans

UniProt Q19007

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 3	Histone H2B 1,Histone H2A × 1 （P04255,P09588） water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q19007_CAEEL
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 22–308； UniProt 10–296 Author chain B； PDBConstruct 22–308； UniProt 10–296

Histone H2B 1,Histone H2A

Caenorhabditis elegans

UniProt P04255

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 3	Nucleosome Assembly Protein × 2 （Q19007） water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H2B1_CAEEL
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain D； PDBConstruct 3–94； UniProt 30–121

Histone H2B 1,Histone H2A

Caenorhabditis elegans

UniProt P09588

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 3	Nucleosome Assembly Protein × 2 （Q19007） water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H2A_CAEEL
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain D； PDBConstruct 95–207； UniProt 9–121

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	6k09
Deposition date deposition_date	2019-05-05
Structure title title	Crystal structure B of ceNAP1-H2A-H2B complex
Keywords keywords	NAP1, H2A-H2B, CHAPERONE; CHAPERONE
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.

6k09__assembly_1__model_1

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

Download this curve (.dat)

6k09__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6k09__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	30.12 Å
Rg (electron density)	29.15 Å
Total Rg	30.00 Å
Atom count	5600
Residues	715
Excluded volume	99730 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6k09__assembly_1__model_1`	trimeric （3）	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	Nucleosome Assembly Protein
Molecular weight formula_weight	34989.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	5716

MGSSHHHHHHSSGENLYFQHMGLLSTNFDMIQALPLNVKQRVCALKNLQMKTIQIESDFYKRVHELEIEFEGKFKSTFDQRKAIVAGEVEPTKEQIDTPILEGLEGDQLAELYKAAEADPSAKGIKDFWLTALRTHDLVAEAIEEHDVPILSYLTDVTTAASKDPAGFKIEFHFATNPYFKNQVLTKTYLLGFDPDAEAPLQFDGPHVIRAVGDTIEWEDGKNVTKKAVKKKQKKGANAGKFLTKTVKADSFFNFFEPPKSKDERNEDEDDEQAEEFLELDYEMGQAIRDTIIPRAVLFYTGELQSDD

Source Source

Source organism organism	Caenorhabditis elegans
NCBI taxonomy ID ncbi_taxonomy_id	6239
Host organism host_organism	Escherichia coli K-12

Entity 2 Entity 2 polymer

Description description	Histone H2B 1,Histone H2A
Molecular weight formula_weight	22653.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

HMRKESYSVYIYRVLKQVHPDTGVSSKAMSIMNSFVNDVFERIAAEASRLAHYNKRSTISSREIQTAVRLILPGELAKHAVSEGTKAVTKYTSSKAKTGGKAKSRSSRAGLQFPVGRLHRILRKGNYAQRVGAGAPVYLAAVLEYLAAEVLELAGNAARDNKKTRIAPRHLQLAVRNDEELNKLLAGVTIAQGGVLPNIQAVLLPKK

Source Source

Source organism organism	Caenorhabditis elegans
NCBI taxonomy ID ncbi_taxonomy_id	6239
Host organism host_organism	Escherichia coli K-12

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	116

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6. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d6k09a1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.305 — NAP-like
Superfamily Superfamily superfamily	d.305.1 — NAP-like
Family Family family	d.305.1.0 — automated matches

Domain ID domain_id	d6k09a2
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	d6k09b1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.305 — NAP-like
Superfamily Superfamily superfamily	d.305.1 — NAP-like
Family Family family	d.305.1.0 — automated matches

Domain ID domain_id	d6k09b2
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	d6k09d1
Class class	a — All alpha proteins
Fold Fold fold	a.22 — Histone-fold
Superfamily Superfamily superfamily	a.22.1 — Histone-fold
Family Family family	a.22.1.0 — automated matches

Domain ID domain_id	d6k09d2
Class class	a — All alpha proteins
Fold Fold fold	a.22 — Histone-fold
Superfamily Superfamily superfamily	a.22.1 — Histone-fold
Family Family family	a.22.1.0 — automated matches

CATH v4.4 (1 domains)

Domain ID domain_id	6k09D00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	20 — Histone, subunit A
Homologous superfamily homologous superfamily	10 — Histone, subunit A

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Unit-cell length a length_a	68.795 Å
Unit-cell length b length_b	79.180 Å
Unit-cell length c length_c	172.340 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	8

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

Resolution resolution	2.248 Å
Low-resolution limit resolution_low	49.723 Å
R factor r_factor	0.2157
R_work r_work	0.2141
R_free r_free	0.2485

Crystal structure B of ceNAP1-H2A-H2B complex

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

Nucleosome Assembly Protein

State in the Current Structure

Other States of the Same Protein in the Database

Histone H2B 1,Histone H2A

State in the Current Structure

Other States of the Same Protein in the Database

Histone H2B 1,Histone H2A

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

6k09__assembly_1__model_1

6k09__assembly_1__model_1 | I(q)

6k09__assembly_1__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) 7 domains

SCOP 2.08 (6 domains)

CATH v4.4 (1 domains)

7. Citations (1)

Crystal structure B of ceNAP1-H2A-H2B complex

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

Nucleosome Assembly 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

Histone H2B 1,Histone H2A

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Histone H2B 1,Histone H2A

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

6k09__assembly_1__model_1

6k09__assembly_1__model_1 | I(q)

6k09__assembly_1__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) 7 domains

SCOP 2.08 (6 domains)

CATH v4.4 (1 domains)

7. Citations (1)