SAXSdb — 5onb

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

CCR4-NOT transcription complex subunit 9

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Protein bag-of-marbles × 1 （P22745）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Protein bag-of-marbles × 1 （P22745）	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	Protein bag-of-marbles × 1 （P22745）	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	Protein bag-of-marbles × 1 （P22745） GLYCEROL × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CNOT9_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 7–273； UniProt 19–285 Author chain C； PDBConstruct 7–273； UniProt 19–285 Author chain E； PDBConstruct 7–273； UniProt 19–285 Author chain G； PDBConstruct 7–273； UniProt 19–285

Protein bag-of-marbles

OrganismNot specified

UniProt P22745

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	CCR4-NOT transcription complex subunit 9 × 1 （Q92600）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	CCR4-NOT transcription complex subunit 9 × 1 （Q92600）	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	CCR4-NOT transcription complex subunit 9 × 1 （Q92600）	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	CCR4-NOT transcription complex subunit 9 × 1 （Q92600） GLYCEROL × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	BAM_DROME
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–24； UniProt 13–36 Author chain D； PDBConstruct 1–24； UniProt 13–36 Author chain F； PDBConstruct 1–24； UniProt 13–36 Author chain H； PDBConstruct 1–24； UniProt 13–36

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	5onb
Deposition date deposition_date	2017-08-03
Structure title title	Drosophila Bag-of-marbles CBM peptide bound to human CAF40
Keywords keywords	DEADENYLATION, CCR4-NOT, TRANSLATIONAL REPRESSION, TRANSLATION, GENE REGULATION; GENE REGULATION
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.

5onb__assembly_4__model_1

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

Download this curve (.dat)

5onb__assembly_4__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5onb__assembly_4__model_1 | P(r) · Pending

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

Rg（Guinier）	21.57 Å
Rg (electron density)	20.47 Å
Total Rg	21.34 Å
Atom count	2345
Residues	291
Excluded volume	42268 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5onb__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5onb__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`5onb__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`5onb__assembly_4__model_1`	dimeric （2）	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	CCR4-NOT transcription complex subunit 9
Molecular weight formula_weight	31072.2 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E,G
Atom count atom_count	9358

GPHMLEREKIYQWINELSSPETRENALLELSKKRESVPDLAPMLWHSFGTIAALLQEIVNIYPSINPPTLTAHQSNRVCNALALLQCVASHPETRSAFLAAHIPLFLYPFLHTVSKTRPFEYLRLTSLGVIGALVKTDEQEVINFLLTTEIIPLCLRIMESGSELSKTVATFILQKILLDDTGLAYICQTYERFSHVAMILGKMVLQLSKEPSARLLKHVVRCYLRLSDNPRAREALRQCLPDQLKDTTFAQVLKDDTTTKRWLAQLVKNLQE

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 polymer

Description description	Protein bag-of-marbles
Molecular weight formula_weight	2874.1 kDa
Source method src_method	syn
Copy count entity_count	4

Polymer Polymer

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

DDQQLDHNFKQMEEHLALMVEGNE

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	5onbA00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	10 — Leucine-rich Repeat Variant
Homologous superfamily homologous superfamily	10 — Leucine-rich Repeat Variant

Domain ID domain_id	5onbC00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	10 — Leucine-rich Repeat Variant
Homologous superfamily homologous superfamily	10 — Leucine-rich Repeat Variant

Domain ID domain_id	5onbE00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	10 — Leucine-rich Repeat Variant
Homologous superfamily homologous superfamily	10 — Leucine-rich Repeat Variant

Domain ID domain_id	5onbG00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	10 — Leucine-rich Repeat Variant
Homologous superfamily homologous superfamily	10 — Leucine-rich Repeat Variant

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Unit-cell length a length_a	105.570 Å
Unit-cell length b length_b	200.930 Å
Unit-cell length c length_c	59.600 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	16

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	3.000 Å
Low-resolution limit resolution_low	46.730 Å
R factor r_factor	0.2182
R_work r_work	0.2156
R_free r_free	0.2679

Drosophila Bag-of-marbles CBM peptide bound to human CAF40

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

CCR4-NOT transcription complex subunit 9

State in the Current Structure

Other States of the Same Protein in the Database

Protein bag-of-marbles

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

5onb__assembly_4__model_1

5onb__assembly_4__model_1 | I(q)

5onb__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 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Drosophila Bag-of-marbles CBM peptide bound to human CAF40

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

CCR4-NOT transcription complex subunit 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

Protein bag-of-marbles

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

5onb__assembly_4__model_1

5onb__assembly_4__model_1 | I(q)

5onb__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 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)