4B8A: PDB entry 4B8A

Structure of yeast NOT1 MIF4G domain co-crystallized with CAF1. Determined by X-ray diffraction at 2.4 Å resolution. Released 21 Nov 2012.

Method: X-ray diffraction
Resolution: 2.4 Å
Organism: SACCHAROMYCES CEREVISIAE S288C
Chains: 2
Atoms: 4,027
Mol. weight: 61.68 kDa
Released: 21 Nov 2012

Explore 4B8A in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4B8A contains 36 α-helices and 14 β-strands across 2 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: 19 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	771	1	1
β-strand	777	1	2
α-helix	787-788	2
α-helix	790-792	3
α-helix	793-805	13
α-helix	811-819	9
α-helix	824-826	3
α-helix	827-834	8
α-helix	835-839	5
α-helix	843-845	3
α-helix	846-855	10
α-helix	859-878	20
β-strand	879	1	1
α-helix	882-884	3
α-helix	887-900	14
α-helix	902-904	3
α-helix	907-909	3
β-strand	913	1	2
α-helix	915-924	10
α-helix	928-940	13
α-helix	941-944	4
α-helix	953-968	16
α-helix	973-985	13

Chain B: 17 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	11-13	3
β-strand	17-19	3	3
α-helix	21-23	3
α-helix	24-34	11
β-strand	40-47	8	3
α-helix	63-75	13
β-strand	78-86	9	3
β-strand	99-103	5	3
β-strand	104	1	4
α-helix	128-134	7
α-helix	135	1
β-strand	136	1	4
α-helix	137	1
α-helix	138-146	9
β-strand	157-160	4	3
α-helix	164-175	12
α-helix	178-180	3
α-helix	183-193	11
β-strand	197-199	3	3
α-helix	200-208	9
α-helix	209-211	3
α-helix	229-235	7
α-helix	242-245	4
α-helix	247-265	19
β-strand	268	1	5
β-strand	274	1	5
α-helix	275-278	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
General negative regulator of transcription subunit 1	A	protein	249	SACCHAROMYCES CEREVISIAE S288C	P25655 (AlphaFold model)
Poly(a) ribonuclease POP2	B	protein	286	SACCHAROMYCES CEREVISIAE S288C	P39008 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4B8A_1 GENERAL NEGATIVE REGULATOR OF TRANSCRIPTION SUBUNIT 1 (chains A)
RSMSRPVQEMIPLKFFAVDEVSCQINQEGAPKDVVEKVLFVLNNVTLANLNNKVDELKKS
LTPNYFSWFSTYLVTQRAKTEPNYHDLYSKVIVAMGSGLLHQFMVNVTLRQLFVLLSTKD
EQAIDKKHLKNLASWLGCITLALNKPIKHKNIAFREMLIEAYKENRLEIVVPFVTKILQR
ASESKIFKPPNPWTVGILKLLIELNEKANWKLSLTFEVEVLLKSFNLTTKSLKPSNFINT
PEVIETLSG

Sequence of entity 2 (B), FASTA

>4B8A_2 POLY(A) RIBONUCLEASE POP2 (chains B)
RSMFLPPPNYLFVRDVWKSNLYSEFAVIRQLVSQYNHVSISTEFVGTLARPIGTFRSKVD
YHYQTMRANVDFLNPIQLGLSLSDANGNKPDNGPSTWQFNFEFDPKKEIMSTESLELLRK
SGINFEKHENLGIDVFEFSQLLMDSGLMMDDSVTWITYHAAYDLGFLINILMNDSMPNNK
EDFEWWVHQYMPNFYDLNLVYKIIQEFKNPQLQQSSQQQQQQQYSLTTLADELGLPRFSI
FTTTGGQSLLMLLSFCQLSKLSMHKFPNGTDFAKYQGVIYGIDGDQ

Primary citation

Architecture of the Nuclease Module of the Yeast Ccr4-not Complex: The not1-Caf1-Ccr4 Interaction. Basquin, J., Roudko, V.V., Rode, M. et al. Mol Cell (2012) 48:207. DOI 10.1016/J.MOLCEL.2012.08.014 · 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
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
4CV5 3.81 Å, yeast NOT1 CN9BD-CAF40 complex

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