SAXSdb — 9fl8

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

Protein bag of marbles

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	CCR4-NOT transcription complex subunit 9 × 2 （Q92600） CCR4-NOT transcription complex subunit 1 × 2 （A5YKK6） 1,4-BUTANEDIOL × 6 water × 5	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	1
Chains and sequence ranges	Author chain F； PDBConstruct 2–18； UniProt 17–33 Author chain G； PDBConstruct 2–18； UniProt 17–33

CCR4-NOT transcription complex subunit 9

Homo sapiens

UniProt Q92600

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Protein bag of marbles × 2 （P22745） CCR4-NOT transcription complex subunit 1 × 2 （A5YKK6） 1,4-BUTANEDIOL × 6 water × 5	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	2
Chains and sequence ranges	Author chain B； PDBConstruct 7–273； UniProt 19–285 Author chain C； PDBConstruct 7–273； UniProt 19–285

CCR4-NOT transcription complex subunit 1

Homo sapiens

UniProt A5YKK6

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Protein bag of marbles × 2 （P22745） CCR4-NOT transcription complex subunit 9 × 2 （Q92600） 1,4-BUTANEDIOL × 6 water × 5	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CNOT1_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain A； PDBConstruct 7–244； UniProt 1351–1588 Author chain D； PDBConstruct 7–244； UniProt 1351–1588

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	9fl8
Deposition date deposition_date	2024-06-04
Last revision last_revision	2025-01-29
Structure title title	Stapled peptide bound to NOT9-NOT1 complex
Keywords keywords	protein-peptide interaction, inhibitor, CCR4-NOT, RNA BINDING PROTEIN; RNA BINDING PROTEIN
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.

9fl8__assembly_1__model_1

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

Download this curve (.dat)

9fl8__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9fl8__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	32.34 Å
Rg (electron density)	31.27 Å
Total Rg	31.98 Å
Atom count	8395
Residues	1040
Excluded volume	150900 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9fl8__assembly_1__model_1`	hexameric （6）	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 (5)

Entity 1 Entity 1 polymer

Description description	Protein bag of marbles
Molecular weight formula_weight	2063.5 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G,F
Atom count atom_count	8498

XLDLNFKLLEEHLALLVEX

Entity 2 Entity 2 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	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,C

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

Entity 3 Entity 3 polymer

Description description	CCR4-NOT transcription complex subunit 1
Molecular weight formula_weight	27617.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

GPHMLEVPPQPQYSYHDINVYSLAGLAPHITLNPTIPLFQAHPQLKQCVRQAIERAVQELVHPVVDRSIKIAMTTCEQIVRKDFALDSEESRMRIAAHHMMRNLTAGMAMITCREPLLMSISTNLKNSFASALRTASPQQREMMDQAAAQLAQDNCELACCFIQKTAVEKAGPEMDKRLATEFELRKHARQEGRRYCDPVVLTYQAERMPEQIRLKVGGVDPKQLAVYEEFARNVPGFLPTNDL

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

Entity 4 Entity 4 non-polymer

Description description	1,4-BUTANEDIOL
Molecular weight formula_weight	90.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	46

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Unit-cell length a length_a	106.562 Å
Unit-cell length b length_b	106.562 Å
Unit-cell length c length_c	262.572 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	2.640 Å
Low-resolution limit resolution_low	46.140 Å
R factor r_factor	0.2052
R_work r_work	0.2028
R_free r_free	0.2495

Stapled peptide bound to NOT9-NOT1 complex

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

Protein bag of marbles

State in the Current Structure

Other States of the Same Protein in the Database

CCR4-NOT transcription complex subunit 9

State in the Current Structure

Other States of the Same Protein in the Database

CCR4-NOT transcription complex subunit 1

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

9fl8__assembly_1__model_1

9fl8__assembly_1__model_1 | I(q)

9fl8__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Citations (1)

Stapled peptide bound to NOT9-NOT1 complex

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

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

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

CCR4-NOT transcription complex subunit 1

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

9fl8__assembly_1__model_1

9fl8__assembly_1__model_1 | I(q)

9fl8__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Citations (1)