4by6

Yeast Not1-Not2-Not5 complex

Method: X-RAY DIFFRACTION

▼

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

GENERAL NEGATIVE REGULATOR OF TRANSCRIPTION SUBUNIT 1

SACCHAROMYCES CEREVISIAE

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	GENERAL NEGATIVE REGULATOR OF TRANSCRIPTION SUBUNIT 2 × 1 （P06100） GENERAL NEGATIVE REGULATOR OF TRANSCRIPTION SUBUNIT 5 × 1 （Q12514） CALCIUM ION × 1 ACETATE ION × 1 GLYCEROL × 1 DI(HYDROXYETHYL)ETHER × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	GENERAL NEGATIVE REGULATOR OF TRANSCRIPTION SUBUNIT 2 × 1 （P06100） GENERAL NEGATIVE REGULATOR OF TRANSCRIPTION SUBUNIT 5 × 1 （Q12514） CALCIUM ION × 1 ACETATE ION × 1 GLYCEROL × 1 DI(HYDROXYETHYL)ETHER × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	N1P976_YEASX
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–553； UniProt 1542–2094 Author chain D； PDBConstruct 1–553； UniProt 1542–2094

GENERAL NEGATIVE REGULATOR OF TRANSCRIPTION SUBUNIT 2

SACCHAROMYCES CEREVISIAE

UniProt P06100

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	GENERAL NEGATIVE REGULATOR OF TRANSCRIPTION SUBUNIT 1 × 1 （N1P976） GENERAL NEGATIVE REGULATOR OF TRANSCRIPTION SUBUNIT 5 × 1 （Q12514） CALCIUM ION × 1 ACETATE ION × 1 GLYCEROL × 1 DI(HYDROXYETHYL)ETHER × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	GENERAL NEGATIVE REGULATOR OF TRANSCRIPTION SUBUNIT 1 × 1 （N1P976） GENERAL NEGATIVE REGULATOR OF TRANSCRIPTION SUBUNIT 5 × 1 （Q12514） CALCIUM ION × 1 ACETATE ION × 1 GLYCEROL × 1 DI(HYDROXYETHYL)ETHER × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NOT2_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–191； UniProt 1–191 Author chain E； PDBConstruct 1–191； UniProt 1–191

GENERAL NEGATIVE REGULATOR OF TRANSCRIPTION SUBUNIT 5

SACCHAROMYCES CEREVISIAE

UniProt Q12514

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	GENERAL NEGATIVE REGULATOR OF TRANSCRIPTION SUBUNIT 1 × 1 （N1P976） GENERAL NEGATIVE REGULATOR OF TRANSCRIPTION SUBUNIT 2 × 1 （P06100） CALCIUM ION × 1 ACETATE ION × 1 GLYCEROL × 1 DI(HYDROXYETHYL)ETHER × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	GENERAL NEGATIVE REGULATOR OF TRANSCRIPTION SUBUNIT 1 × 1 （N1P976） GENERAL NEGATIVE REGULATOR OF TRANSCRIPTION SUBUNIT 2 × 1 （P06100） CALCIUM ION × 1 ACETATE ION × 1 GLYCEROL × 1 DI(HYDROXYETHYL)ETHER × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NOT5_YEAST
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–262； UniProt 299–560 Author chain F； PDBConstruct 1–262； UniProt 299–560

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	4by6
Deposition date deposition_date	2013-07-18
Structure title title	Yeast Not1-Not2-Not5 complex
Keywords keywords	TRANSCRIPTION, CTERMINAL COMPONENTS OF THE CCR4_NOT COMPLEX; TRANSCRIPTION
Experimental Method method	X-RAY DIFFRACTION

▼

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.

4by6__assembly_1__model_1

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

Download this curve (.dat)

4by6__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4by6__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	33.30 Å
Rg (electron density)	32.61 Å
Total Rg	33.26 Å
Atom count	7012
Residues	848
Excluded volume	126350 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4by6__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4by6__assembly_2__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Description description	GENERAL NEGATIVE REGULATOR OF TRANSCRIPTION SUBUNIT 1
Molecular weight formula_weight	64436.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,D
Atom count atom_count	14028

EDENVKKFIKEFEDTKIMPVRKGTKTTRTEKFYLVFTEWVKLLQRVENNDVITTVFIKQLVEKGVISDTDNLLTFVKSSLELSVSSFKESDPTDEVFIAIDALGSLIIKLLILQDFKDDTRRDYINAIFSVIVLVFAKDHSQEGTTFNERPYFRLFSNILYEWATIRTHNFVRISDSSTRQELIEFDSVFYNTFSGYLHALQPFAFPGFSFAWVTLLSHRMLLPIMLRLPNKIGWEKLMLLIIDLFKFLDQYTSKHAVSDAVSVVYKGTLRIILGISNDMPSFLIENHYELMNNLPPTYFQLKNVILSAIPKNMTVPNPYDVDLNMEDIPACKELPEVFFDPVIDLHSLKKPVDNYLRIPSNSLLRTILSAIYKDTYDIKKGVGYDFLSVDSKLIRAIVLHVGIEAGIEYKRTSSNAVFNTKSSYYTLLFNLIQNGSIEMKYQIILSIVEQLRYPNIHTYWFSFVLMNMFKSDEWNDQKLEVQEIILRNFLKRIIVNKPHTWGVSVFFTQLINNNDINLLDLPFVQSVPEIKLILQQLVKYSKKYTTSEQDDQ

Source Source

Source organism organism	SACCHAROMYCES CEREVISIAE
Common name common_name	;BAKER'S YEAST ;
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 2
Molecular weight formula_weight	22387.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MEKFGLKALVPLLKLEDKELSSTYDHSMTLGADLSSMLYSLGIPRDSQDHRVLDTFQSPWAETSRSEVEPRFFTPESFTNIPGVLQSTVTPPCFNSIQNDQQRVALFQDETLFFLFYKHPGTVIQELTYLELRKRNWRYHKTLKAWLTKDPMMEPIVSADGLSERGSYVFFDPQRWEKCQRDFLLFYNAIM

Source Source

Source organism organism	SACCHAROMYCES CEREVISIAE
Common name common_name	;BAKER'S YEAST ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	ESCHERICHIA COLI

Entity 3 Entity 3 polymer

Description description	GENERAL NEGATIVE REGULATOR OF TRANSCRIPTION SUBUNIT 5
Molecular weight formula_weight	31208.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

FDNSTLGTPTTHVSMKKKESENDSEQQLNFPPDRTDEIRKTIQHDVETNAAFQNPLFNDELKYWLDSKRYLMQPLQEMSPKMVSQLESSLLNCPDSLDADSPCLYTKPLSLPHPTSIFFPNEPIRFVYPYDVPLNLTNNENDTDNKFGKDSKAKSKKDDDIYSRTSLARIFMKFDLDTLFFIFYHYQGSYEQFLAARELFKNRNWLFNKVDRCWYYKEIEKLPPGMGKSEEESWRYFDYKKSWLARRCGNDFVYNEEDFEKL

Source Source

Source organism organism	SACCHAROMYCES CEREVISIAE
Common name common_name	;BAKER'S YEAST ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	ESCHERICHIA COLI

Entity 4 Entity 4 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	5

▼

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id	4by6A01
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	4by6A02
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	4by6B00
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	4by6C00
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	4by6D01
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	4by6D02
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	4by6E00
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	4by6F00
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

▶

Unit-cell length a length_a	110.452 Å
Unit-cell length b length_b	109.174 Å
Unit-cell length c length_c	133.622 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	94.70 °
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	2.797 Å
Low-resolution limit resolution_low	48.904 Å
R factor r_factor	0.1834
R_work r_work	0.1812
R_free r_free	0.2258

Yeast Not1-Not2-Not5 complex

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

GENERAL NEGATIVE REGULATOR OF TRANSCRIPTION SUBUNIT 1

State in the Current Structure

Other States of the Same Protein in the Database

GENERAL NEGATIVE REGULATOR OF TRANSCRIPTION SUBUNIT 2

State in the Current Structure

Other States of the Same Protein in the Database

GENERAL NEGATIVE REGULATOR OF TRANSCRIPTION SUBUNIT 5

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

4by6__assembly_1__model_1

4by6__assembly_1__model_1 | I(q)

4by6__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (8)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)

Yeast Not1-Not2-Not5 complex

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

GENERAL NEGATIVE REGULATOR OF TRANSCRIPTION 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

GENERAL NEGATIVE REGULATOR OF TRANSCRIPTION 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

GENERAL NEGATIVE REGULATOR OF TRANSCRIPTION SUBUNIT 5

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

4by6__assembly_1__model_1

4by6__assembly_1__model_1 | I(q)

4by6__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (8)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)