4CV5: Yeast NOT1 CN9BD-CAF40 complex

yeast NOT1 CN9BD-CAF40 complex. Determined by X-ray diffraction at 3.81 Å resolution. Released 7 May 2014.

Method: X-ray diffraction
Resolution: 3.81 Å
Organism: SACCHAROMYCES CEREVISIAE
Chains: 4
Atoms: 6,172
Mol. weight: 125.33 kDa
Ligands: TBR
Released: 7 May 2014

Explore 4CV5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4CV5 contains 56 α-helices and 0 β-strands across 4 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 7 helices, 0 β-strands

Element	Residues	Length
α-helix	1073-1076	4
α-helix	1081-1083	3
α-helix	1086-1126	41
α-helix	1133-1170	38
α-helix	1186-1216	31
α-helix	1218-1229	12
α-helix	1262-1267	6

Chain B: 20 helices, 0 β-strands

Element	Residues	Length
α-helix	108-116	9
α-helix	122-130	9
α-helix	139-144	6
α-helix	148-157	10
α-helix	161-163	3
α-helix	171-186	16
α-helix	190-198	9
α-helix	202-204	3
α-helix	206-209	4
α-helix	216-232	17
α-helix	238-244	7
α-helix	249-258	10
α-helix	262-277	16
α-helix	281-284	4
α-helix	289-305	17
α-helix	314-326	13
α-helix	330-339	10
α-helix	342-345	4
α-helix	350-353	4
α-helix	357-369	13

Chain C: 9 helices, 0 β-strands

Element	Residues	Length
α-helix	1073-1076	4
α-helix	1081-1083	3
α-helix	1086-1126	41
α-helix	1133-1170	38
α-helix	1186-1216	31
α-helix	1218-1230	13
α-helix	1235-1236	2
α-helix	1244-1246	3
α-helix	1262-1269	8

Chain D: 20 helices, 0 β-strands

Element	Residues	Length
α-helix	108-116	9
α-helix	122-130	9
α-helix	139-144	6
α-helix	148-157	10
α-helix	161-163	3
α-helix	170-188	19
α-helix	190-198	9
α-helix	201-204	4
α-helix	206-209	4
α-helix	216-232	17
α-helix	238-246	9
α-helix	249-258	10
α-helix	262-277	16
α-helix	281-284	4
α-helix	289-304	16
α-helix	315-326	12
α-helix	330-339	10
α-helix	342-345	4
α-helix	350-353	4
α-helix	357-369	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
General negative regulator of transcription subunit 1	A, C	protein	212	SACCHAROMYCES CEREVISIAE	P25655 (AlphaFold model)
Protein CAF40	B, D	protein	320	SACCHAROMYCES CEREVISIAE	P53829 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>4CV5_1 GENERAL NEGATIVE REGULATOR OF TRANSCRIPTION SUBUNIT 1 (chains A, C)
NPFNNLLGSTIFVTHPDLKRVFQMALAKSVREILLEVVEKSSGIAVVTTTKIILKDFATE
VDESKLKTAAIIMVRHLAQSLARATSIEPLKEGIRSTMQSLAPNLMSLSSSPAEELDTAI
NENIGIALVLIEKASMDKSTQDLADQLMQAIAIRRYHKERRADQPFITQNTNPYSLSLPE
PLGLKNTGVTPQQFRVYEEFGKNIPNLDVIPF

Sequence of entity 2 (B, D), FASTA

>4CV5_2 PROTEIN CAF40 (chains B, D)
LMGNTPNNNNSNENGENNGNNGNNGGNDANATRNNPNMVNNRGAVHALDDPNVYHWICQL
TYGPQKEQALLELGRKREQFDDLAVVLWSSFGVMTSLLNEIISVYPMLQPQMLSNNLSNR
VCNALVLLQCVASHPETKHLFLQAHIPLFLFPFLNTTSRQRTFEYLRLTSLGVIGALVKN
DSQDVITFLLRTDIVPLCLRIMESSSELSKTVAIFILQKILLDDVGLQYICATLERFYAV
TNVLKDMVEHLTVSTPPGRLLKHIIRCYLRLSDDLEARRLLKIVLPAKLRDNTFTEVLRD
DVGSKRCLAQLLLTLNEETS

Ligands and cofactors

ID	Name	Formula	Copies
TBR	Hexatantalum dodecabromide	Br12 Ta6	3

Primary citation

Structural and Biochemical Insights to the Role of the Ccr4-not Complex and Ddx6 ATPase in Microrna Repression. Mathys, H., Basquin, J., Ozgur, S. et al. Mol Cell (2014) 54:751. DOI 10.1016/J.MOLCEL.2014.03.036 · PubMed

Other PDB entries of the same protein (UniProt P25655 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4B89 1.5 Å, MIF4G domain of the yeast Not1
4B8A 2.4 Å, Structure of yeast NOT1 MIF4G domain co-crystallized with CAF1
4BY6 2.8 Å, Yeast Not1-Not2-Not5 complex
4B8B 2.8 Å, N-Terminal domain of the yeast Not1
4B8C 3.41 Å, nuclease module of the yeast Ccr4-Not complex
5AJD 3.62 Å, Not1 C-terminal domain in complex with Not4

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