SAXSdb — 7ciz

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

Histone H3.3

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Histone H4 × 1 （P62805） DNA replication licensing factor MCM2 × 1 （P49736） DnaJ homolog subfamily C member 9 × 1 （Q8WXX5） SULFATE ION × 2 water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Histone H4 × 1 （P62805） DNA replication licensing factor MCM2 × 1 （P49736） DnaJ homolog subfamily C member 9 × 1 （Q8WXX5） water × 4	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 4	Histone H4 × 1 （P62805） DNA replication licensing factor MCM2 × 1 （P49736） DnaJ homolog subfamily C member 9 × 1 （Q8WXX5） water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H33_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–79； UniProt 58–136 Author chain E； PDBConstruct 1–79； UniProt 58–136 Author chain I； PDBConstruct 1–79； UniProt 58–136

Histone H4

Homo sapiens

UniProt P62805

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Histone H3.3 × 1 （P84243） DNA replication licensing factor MCM2 × 1 （P49736） DnaJ homolog subfamily C member 9 × 1 （Q8WXX5） SULFATE ION × 2 water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Histone H3.3 × 1 （P84243） DNA replication licensing factor MCM2 × 1 （P49736） DnaJ homolog subfamily C member 9 × 1 （Q8WXX5） water × 4	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 4	Histone H3.3 × 1 （P84243） DNA replication licensing factor MCM2 × 1 （P49736） DnaJ homolog subfamily C member 9 × 1 （Q8WXX5） water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H4_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–102； UniProt 2–103 Author chain F； PDBConstruct 1–102； UniProt 2–103 Author chain J； PDBConstruct 1–102； UniProt 2–103

DNA replication licensing factor MCM2

Homo sapiens

UniProt P49736

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Histone H3.3 × 1 （P84243） Histone H4 × 1 （P62805） DnaJ homolog subfamily C member 9 × 1 （Q8WXX5） SULFATE ION × 2 water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Histone H3.3 × 1 （P84243） Histone H4 × 1 （P62805） DnaJ homolog subfamily C member 9 × 1 （Q8WXX5） water × 4	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 4	Histone H3.3 × 1 （P84243） Histone H4 × 1 （P62805） DnaJ homolog subfamily C member 9 × 1 （Q8WXX5） water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MCM2_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–70； UniProt 61–130 Author chain G； PDBConstruct 1–70； UniProt 61–130 Author chain K； PDBConstruct 1–70； UniProt 61–130

DnaJ homolog subfamily C member 9

Homo sapiens

UniProt Q8WXX5

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Histone H3.3 × 1 （P84243） Histone H4 × 1 （P62805） DNA replication licensing factor MCM2 × 1 （P49736） SULFATE ION × 2 water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Histone H3.3 × 1 （P84243） Histone H4 × 1 （P62805） DNA replication licensing factor MCM2 × 1 （P49736） water × 4	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 4	Histone H3.3 × 1 （P84243） Histone H4 × 1 （P62805） DNA replication licensing factor MCM2 × 1 （P49736） water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DNJC9_HUMAN
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 6–75； UniProt 180–249 Author chain H； PDBConstruct 6–75； UniProt 180–249 Author chain L； PDBConstruct 6–75； UniProt 180–249

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	7ciz
Deposition date deposition_date	2020-07-08
Structure title title	Crystal structure of DNAJC9 HBD helix2 in complex with H3.3-H4 dimer and MCM2 HBD
Keywords keywords	Histone chaperone, 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.

7ciz__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

7ciz__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7ciz__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	20.17 Å
Rg (electron density)	19.00 Å
Total Rg	19.97 Å
Atom count	1997
Residues	254
Excluded volume	35378 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7ciz__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`7ciz__assembly_2__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`7ciz__assembly_3__model_1`	tetrameric （4）	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 (6)

Entity 1 Entity 1 polymer

Description description	Histone H3.3
Molecular weight formula_weight	9026.5 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,E,I
Atom count atom_count	6707

STELLIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA

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-Gold(DE3)pLysS AG' ;

Entity 2 Entity 2 polymer

Description description	Histone H4
Molecular weight formula_weight	11263.2 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,F,J

SGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

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-Gold(DE3)pLysS AG' ;

Entity 3 Entity 3 polymer

Description description	DNA replication licensing factor MCM2
Molecular weight formula_weight	7860.4 kDa
EC 编号 ec_number	3.6.4.12
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,G,K

GPLEEEEDGEELIGDGMERDYRAIPELDAYEAEGLALDDEDVEELTASQREAAERAMRQRDREAGRGLGR

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-Gold(DE3)pLysS AG' ;

Entity 4 Entity 4 polymer

Description description	DnaJ homolog subfamily C member 9
Molecular weight formula_weight	8448.6 kDa
Mutation mutation	C243S
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,H,L

GPLGSKESKQKMNARKRRAQEEAKEAEMSRKELGLDEGVDSLKAAIQSRQKDRQKEMDNFLAQMEAKYSKSSKGG

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-Gold(DE3)pLysS AG' ;

Entity 5 Entity 5 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	741

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d7ciza_
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.22.1.1 — Nucleosome core histones

Domain ID domain_id	d7cizb_
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.22.1.1 — Nucleosome core histones

Domain ID domain_id	d7cize_
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.22.1.1 — Nucleosome core histones

Domain ID domain_id	d7cizf_
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.22.1.1 — Nucleosome core histones

Domain ID domain_id	d7cizi_
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.22.1.1 — Nucleosome core histones

Domain ID domain_id	d7cizj_
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.22.1.1 — Nucleosome core histones

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Unit-cell length a length_a	47.638 Å
Unit-cell length b length_b	176.816 Å
Unit-cell length c length_c	202.925 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	24

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	36.884 Å
R factor r_factor	0.1727
R_work r_work	0.1706
R_free r_free	0.2138

Crystal structure of DNAJC9 HBD helix2 in complex with H3.3-H4 dimer and MCM2 HBD

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

Histone H3.3

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 H4

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

DNA replication licensing factor MCM2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

DnaJ homolog subfamily C member 9

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

7ciz__assembly_3__model_1

7ciz__assembly_3__model_1 | I(q)

7ciz__assembly_3__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (6 domains)

7. Citations (1)