SAXSdb — 5fu7

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

CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 1

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	CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 2 × 1 （Q9NZN8） CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 3 × 1 （O75175） NANOS, ISOFORM B × 1 （A0A0B4KGY5）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 2 × 1 （Q9NZN8） CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 3 × 1 （O75175） NANOS, ISOFORM B × 1 （A0A0B4KGY5）	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	1
Chains and sequence ranges	Author chain A； PDBConstruct 7–535； UniProt 1833–2361 Author chain E； PDBConstruct 7–535； UniProt 1833–2361

CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 2

HOMO SAPIENS

UniProt Q9NZN8

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 1 × 1 （A5YKK6） CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 3 × 1 （O75175） NANOS, ISOFORM B × 1 （A0A0B4KGY5）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 1 × 1 （A5YKK6） CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 3 × 1 （O75175） NANOS, ISOFORM B × 1 （A0A0B4KGY5）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CNOT2_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 7–197； UniProt 350–540 Author chain F； PDBConstruct 7–197； UniProt 350–540

CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 3

HOMO SAPIENS

UniProt O75175

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 1 × 1 （A5YKK6） CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 2 × 1 （Q9NZN8） NANOS, ISOFORM B × 1 （A0A0B4KGY5）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 1 × 1 （A5YKK6） CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 2 × 1 （Q9NZN8） NANOS, ISOFORM B × 1 （A0A0B4KGY5）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CNOT3_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 7–148； UniProt 607–748 Author chain G； PDBConstruct 7–148； UniProt 607–748

NANOS, ISOFORM B

DROSOPHILA MELANOGASTER

UniProt A0A0B4KGY5

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 1 × 1 （A5YKK6） CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 2 × 1 （Q9NZN8） CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 3 × 1 （O75175）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 1 × 1 （A5YKK6） CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 2 × 1 （Q9NZN8） CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 3 × 1 （O75175）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A0B4KGY5_DROME
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 7–54； UniProt 116–163 Author chain H； PDBConstruct 7–54； UniProt 116–163

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	5fu7
Deposition date deposition_date	2016-01-21
Structure title title	drosophila nanos NBR peptide bound to the NOT module of the human CCR4-NOT complex
Keywords keywords	GENE REGULATION, DEADENYLATION, MRNA DECAY, CCR4-NOT, TRANSCRIPTION, TRANSLATIONAL REPRESSION; 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.

5fu7__assembly_1__model_1

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

Download this curve (.dat)

5fu7__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5fu7__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	33.51 Å
Rg (electron density)	32.73 Å
Total Rg	33.23 Å
Atom count	7313
Residues	891
Excluded volume	130560 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5fu7__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5fu7__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 (4)

Entity 1 Entity 1 polymer

Description description	CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 1
Molecular weight formula_weight	61620.1 kDa
Mutation mutation	YES
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,E
Atom count atom_count	14548

GPHMLEHSGISQASEYDDPPGLREKAEYLLREWVNLYHSAAAGRDSTKAFSAFVGQMHQQGILKTDDLITRFFRLCTEMCVEISYRAQAEQQHNPAANPTMIRAKCYHNLDAFVRLIALLVKHSGEATNTVTKINLLNKVLGIVVGVLLQDHDVRQSEFQQLPYHRIFIMLLLELNAPEHVLETINFQTLTAFCNTFHILRPTKAPGFVYAWLELISHRIFIARMLAHTPQQKGWPMYAQLLIDLFKYLAPFLRNVELTKPMQILYKGTLRVLLVLLHDFPEFLCDYHYGFCDVIPPNCIQLRNLILSAFPRNMRLPDPFTPNLKVDMLSEINIAPRILTNFTGVMPPQFKKDLDSYLKTRSPVTFLSDLRSNLQVSNEPGNRYNLQLINALVLYVGTQAIAHIHNKGSTPSMSTITHSAHMDIFQNLAVDLDTEGRYLFLNAIANQLRYPNSHTHYFSCTMLYLFAEANTEAIQEQITRVLLERLIVNRPHPWGLLITFIELIKNPAFKFWNHEFVEEEPEIEKLFQSVAQCCM

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 2 Entity 2 polymer

Description description	CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 2
Molecular weight formula_weight	22945.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

GPHMLEMVTDQFGMIGLLTFIRAAETDPGMVHLALGSDLTTLGLNLNSPENLYPKFASPWASSPCRPQDIDFHVPSEYLTNIHIRDKLAAIKLGRYGEDLLFYLYYMNGGDVLQLLAAVELFNRDWRYHKEERVWITRAPGMEPTMKTNTYERGTYYFFDCLNWRKVAKEFHLEYDKLEERPHLPSTFNYNPAQQAF

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 3
Molecular weight formula_weight	18267.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

GPHMLELTKEQLYQQAMEEAAWHHMPHPSDSERIRQYLPRNPCPTPPYHHQMPPPHSDTVEFYQRLSTETLFFIFYYLEGTKAQYLAAKALKKQSWRFHTKYMMWFQRHEEPKTITDEFEQGTYIYFDYEKWGQRKKEGFTFEYRYLE

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 polymer

Description description	NANOS, ISOFORM B
Molecular weight formula_weight	5745.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

GPHMLESHQQTDEIARSLKIFAQVTTGAAENAAGSMQDVMQEFATNGYASDDLG

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

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	5fu7B00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	1020 — CCR4-NOT complex subunit 2/3/5, C-terminal domain

Domain ID domain_id	5fu7C00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	1020 — CCR4-NOT complex subunit 2/3/5, C-terminal domain

Domain ID domain_id	5fu7F00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	1020 — CCR4-NOT complex subunit 2/3/5, C-terminal domain

Domain ID domain_id	5fu7G00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	1020 — CCR4-NOT complex subunit 2/3/5, C-terminal domain

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Unit-cell length a length_a	75.950 Å
Unit-cell length b length_b	135.670 Å
Unit-cell length c length_c	104.970 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	107.98 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	3.100 Å
Low-resolution limit resolution_low	48.580 Å
R factor r_factor	0.1680
R_work r_work	0.1649
R_free r_free	0.2267

drosophila nanos NBR peptide bound to the NOT module of the human CCR4-NOT complex

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

CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 1

State in the Current Structure

Other States of the Same Protein in the Database

CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 2

State in the Current Structure

Other States of the Same Protein in the Database

CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 3

State in the Current Structure

Other States of the Same Protein in the Database

NANOS, ISOFORM B

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

5fu7__assembly_1__model_1

5fu7__assembly_1__model_1 | I(q)

5fu7__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 (4)

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

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

drosophila nanos NBR peptide bound to the NOT module of the human CCR4-NOT complex

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

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

CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 2

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 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

NANOS, ISOFORM B

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

5fu7__assembly_1__model_1

5fu7__assembly_1__model_1 | I(q)

5fu7__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 (4)

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

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)