SAXSdb — 4u68

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

Rhino

Drosophila melanogaster

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	H3K9me3 × 2 （P02299） water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	H3K9me3 × 2 （P02299） water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q7JXA8_DROME
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–75； UniProt 20–90 Author chain B； PDBConstruct 5–75； UniProt 20–90 Author chain C； PDBConstruct 5–75； UniProt 20–90

H3K9me3

OrganismNot specified

UniProt P02299

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Rhino × 2 （Q7JXA8） water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Rhino × 2 （Q7JXA8） water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H3_DROME
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain D； PDBConstruct 1–11； UniProt 5–15 Author chain E； PDBConstruct 1–11； UniProt 5–15 Author chain F； PDBConstruct 1–11； UniProt 5–15

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	4u68
Deposition date deposition_date	2014-07-28
Structure title title	Crystal structure of Rhino chromodomain in complex with H3K9me3
Keywords keywords	Rhino, H3K9me3, piRNA, PROTEIN BINDING; PROTEIN BINDING
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.

4u68__assembly_1__model_1

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

Download this curve (.dat)

4u68__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4u68__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	16.94 Å
Rg (electron density)	15.90 Å
Total Rg	16.98 Å
Atom count	1160
Residues	140
Excluded volume	20726 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4u68__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4u68__assembly_2__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 (3)

Entity 1 Entity 1 polymer

Description description	Rhino
Molecular weight formula_weight	8441.6 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	1853

GPGSHVEEYVVEKILGKRFVNGRPQVLVKWSGFPNENNTWEPLENVGNCMKLVSDFESEVFRLHRKAAAKSVGKS

Source Source

Source organism organism	Drosophila melanogaster
Common name common_name	fruit fly
NCBI taxonomy ID ncbi_taxonomy_id	7227
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	H3K9me3
Molecular weight formula_weight	1207.4 kDa
Source method src_method	syn
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,E,F

KQTARKSTGGK

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	175

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6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id	4u68A00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	4u68B00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	4u68C00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	40 —

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Unit-cell length a length_a	50.946 Å
Unit-cell length b length_b	67.679 Å
Unit-cell length c length_c	79.750 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	106.46 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

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

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	25.494 Å
R factor r_factor	0.1862
R_work r_work	0.1844
R_free r_free	0.2062

Crystal structure of Rhino chromodomain in complex with H3K9me3

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

Rhino

State in the Current Structure

Other States of the Same Protein in the Database

H3K9me3

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

4u68__assembly_1__model_1

4u68__assembly_1__model_1 | I(q)

4u68__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

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

7. Citations (1)

Crystal structure of Rhino chromodomain in complex with H3K9me3

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

Rhino

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

H3K9me3

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

4u68__assembly_1__model_1

4u68__assembly_1__model_1 | I(q)

4u68__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

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

7. Citations (1)