5ajd

Not1 C-terminal domain in complex with Not4

Method: X-RAY DIFFRACTION

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

CDC39P

SACCHAROMYCES CEREVISIAE

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	GENERAL NEGATIVE REGULATOR OF TRANSCRIPTION SUBUNIT 4 × 1 （P34909）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	GENERAL NEGATIVE REGULATOR OF TRANSCRIPTION SUBUNIT 4 × 1 （P34909）	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	GENERAL NEGATIVE REGULATOR OF TRANSCRIPTION SUBUNIT 4 × 1 （P34909）	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	GENERAL NEGATIVE REGULATOR OF TRANSCRIPTION SUBUNIT 4 × 1 （P34909）	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 2	GENERAL NEGATIVE REGULATOR OF TRANSCRIPTION SUBUNIT 4 × 1 （P34909）	Consistent with protein count
6	Protein heterocomplex	Heteromer	Protein 2	GENERAL NEGATIVE REGULATOR OF TRANSCRIPTION SUBUNIT 4 × 1 （P34909）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	N1P976_YEASC
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–556； UniProt 1542–2094 Author chain C； PDBConstruct 4–556； UniProt 1542–2094 Author chain E； PDBConstruct 4–556； UniProt 1542–2094 Author chain G； PDBConstruct 4–556； UniProt 1542–2094 Author chain I； PDBConstruct 4–556； UniProt 1542–2094 Author chain K； PDBConstruct 4–556； UniProt 1542–2094

GENERAL NEGATIVE REGULATOR OF TRANSCRIPTION SUBUNIT 4

SACCHAROMYCES CEREVISIAE

UniProt P34909

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	CDC39P × 1 （N1P976）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	CDC39P × 1 （N1P976）	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	CDC39P × 1 （N1P976）	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	CDC39P × 1 （N1P976）	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 2	CDC39P × 1 （N1P976）	Consistent with protein count
6	Protein heterocomplex	Heteromer	Protein 2	CDC39P × 1 （N1P976）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NOT4_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 6–65； UniProt 418–477 Author chain D； PDBConstruct 6–65； UniProt 418–477 Author chain F； PDBConstruct 6–65； UniProt 418–477 Author chain H； PDBConstruct 6–65； UniProt 418–477 Author chain J； PDBConstruct 6–65； UniProt 418–477 Author chain L； PDBConstruct 6–65； UniProt 418–477

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	5ajd
Deposition date deposition_date	2015-02-23
Structure title title	Not1 C-terminal domain in complex with Not4
Keywords keywords	TRANSCRIPTION, CCR4-NOT, NOT1, NOT4; TRANSCRIPTION
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.

5ajd__assembly_6__model_1

Assembly 6 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

5ajd__assembly_6__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5ajd__assembly_6__model_1 | P(r) · Pending

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

Rg（Guinier）	29.56 Å
Rg (electron density)	28.62 Å
Total Rg	29.25 Å
Atom count	7771
Residues	535
Excluded volume	72418 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5ajd__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5ajd__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`5ajd__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`5ajd__assembly_4__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`5ajd__assembly_5__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`5ajd__assembly_6__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 (2)

Entity 1 Entity 1 polymer

Description description	CDC39P
Molecular weight formula_weight	64811.6 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E,G,I,K
Atom count atom_count	47509

RSMEDENVKKFIKEFEDTKIMPVRKGTKTTRTEKFYLVFTEWVKLLQRVENNDVITTVFIKQLVEKGVISDTDNLLTFVKSSLELSVSSFKESDPTDEVFIAIDALGSLIIKLLILQDFKDDTRRDYINAIFSVIVLVFAKDHSQEGTTFNERPYFRLFSNILYEWATIRTHNFVRISDSSTRQELIEFDSVFYNTFSGYLHALQPFAFPGFSFAWVTLLSHRMLLPIMLRLPNKIGWEKLMLLIIDLFKFLDQYTSKHAVSDAVSVVYKGTLRIILGISNDMPSFLIENHYELMNNLPPTYFQLKNVILSAIPKNMTVPNPYDVDLNMEDIPACKELPEVFFDPVIDLHSLKKPVDNYLRIPSNSLLRTILSAIYKDTYDIKKGVGYDFLSVDSKLIRAIVLHVGIEAGIEYKRTSSNAVFNTKSSYYTLLFNLIQNGSIEMKYQIILSIVEQLRYPNIHTYWFSFVLMNMFKSDEWNDQKLEVQEIILRNFLKRIIVNKPHTWGVSVFFTQLINNNDINLLDLPFVQSVPEIKLILQQLVKYSKKYTTSEQDDQ

Source Source

Source organism organism	SACCHAROMYCES CEREVISIAE
NCBI taxonomy ID ncbi_taxonomy_id	889517
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 polymer

Description description	GENERAL NEGATIVE REGULATOR OF TRANSCRIPTION SUBUNIT 4
Molecular weight formula_weight	7434.2 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

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

GPDSMDPYDALGNAVDFLDARLHSLSNYQKRPISIKSNIIDEETYKKYPSLFSWDKIEASKKSDN

Source Source

Source organism organism	SACCHAROMYCES CEREVISIAE
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	ESCHERICHIA COLI

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6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

Domain ID domain_id	5ajdA01
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	790 —

Domain ID domain_id	5ajdA02
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	800 —

Domain ID domain_id	5ajdC01
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	790 —

Domain ID domain_id	5ajdC02
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	800 —

Domain ID domain_id	5ajdE01
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	790 —

Domain ID domain_id	5ajdE02
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	800 —

Domain ID domain_id	5ajdG01
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	790 —

Domain ID domain_id	5ajdG02
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	800 —

Domain ID domain_id	5ajdI01
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	790 —

Domain ID domain_id	5ajdI02
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	800 —

Domain ID domain_id	5ajdK01
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	790 —

Domain ID domain_id	5ajdK02
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	800 —

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Unit-cell length a length_a	173.658 Å
Unit-cell length b length_b	173.658 Å
Unit-cell length c length_c	262.612 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	36

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

Resolution resolution	3.620 Å
Low-resolution limit resolution_low	75.655 Å
R factor r_factor	0.2688
R_work r_work	0.2662
R_free r_free	0.3187

Not1 C-terminal domain in complex with Not4

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

CDC39P

State in the Current Structure

Other States of the Same Protein in the Database

GENERAL NEGATIVE REGULATOR OF TRANSCRIPTION SUBUNIT 4

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

5ajd__assembly_6__model_1

5ajd__assembly_6__model_1 | I(q)

5ajd__assembly_6__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

7. Citations (1)

Not1 C-terminal domain in complex with Not4

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

CDC39P

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

GENERAL NEGATIVE REGULATOR OF TRANSCRIPTION SUBUNIT 4

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

5ajd__assembly_6__model_1

5ajd__assembly_6__model_1 | I(q)

5ajd__assembly_6__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

7. Citations (1)