4BY6: Yeast Not1-Not2-Not5 complex
Yeast Not1-Not2-Not5 complex. Determined by X-ray diffraction at 2.8 Å resolution. Released 16 Oct 2013.
- Method
- X-ray diffraction
- Resolution
- 2.8 Å
- Organism
- SACCHAROMYCES CEREVISIAE
- Chains
- 6
- Atoms
- 14,028
- Mol. weight
- 236.66 kDa
- Ligands
- CA
- Released
- 16 Oct 2013
Explore 4BY6 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
4BY6 contains 106 α-helices and 34 β-strands across 6 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: 33 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 1568-1583 | 16 | |
| α-helix | 1591-1601 | 11 | |
| α-helix | 1609-1628 | 20 | |
| α-helix | 1638-1652 | 15 | |
| α-helix | 1661-1681 | 21 | |
| α-helix | 1690-1711 | 22 | |
| α-helix | 1717-1740 | 24 | |
| α-helix | 1747-1749 | 3 | |
| α-helix | 1750-1757 | 8 | |
| α-helix | 1763-1766 | 4 | |
| α-helix | 1770-1772 | 3 | |
| α-helix | 1775-1791 | 17 | |
| α-helix | 1801-1819 | 19 | |
| α-helix | 1821-1826 | 6 | |
| α-helix | 1828-1834 | 7 | |
| α-helix | 1840-1847 | 8 | |
| α-helix | 1856-1858 | 3 | |
| α-helix | 1866-1868 | 3 | |
| α-helix | 1870-1873 | 4 | |
| α-helix | 1875-1877 | 3 | |
| α-helix | 1882-1889 | 8 | |
| α-helix | 1890-1898 | 9 | |
| α-helix | 1902-1916 | 15 | |
| β-strand | 1917-1921 | 5 | 1 |
| β-strand | 1926-1930 | 5 | 1 |
| α-helix | 1932-1952 | 21 | |
| α-helix | 1964-1974 | 11 | |
| α-helix | 1978-1990 | 13 | |
| α-helix | 1997-2011 | 15 | |
| α-helix | 2019-2034 | 16 | |
| α-helix | 2039 | 1 | |
| α-helix | 2042-2052 | 11 | |
| α-helix | 2059-2061 | 3 | |
| α-helix | 2063-2066 | 4 | |
| α-helix | 2069-2077 | 9 | |
Chain B: 8 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 35-40 | 6 | |
| α-helix | 53-55 | 3 | |
| α-helix | 76-78 | 3 | |
| α-helix | 84-86 | 3 | |
| β-strand | 94 | 1 | 2 |
| α-helix | 101-104 | 4 | |
| α-helix | 109-118 | 10 | |
| β-strand | 122 | 1 | 3 |
| α-helix | 123-134 | 12 | |
| β-strand | 138-140 | 3 | 4 |
| β-strand | 145-149 | 5 | 4 |
| β-strand | 156-157 | 2 | 4 |
| β-strand | 163-172 | 10 | 4 |
| β-strand | 177-186 | 10 | 4 |
| α-helix | 187-189 | 3 | |
| β-strand | 190 | 1 | 4 |
Chain C: 13 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 353-355 | 3 | |
| α-helix | 356-364 | 9 | |
| α-helix | 367-370 | 4 | |
| α-helix | 378-389 | 12 | |
| α-helix | 394-397 | 4 | |
| α-helix | 399-400 | 2 | |
| β-strand | 408 | 1 | 2 |
| β-strand | 410 | 1 | 3 |
| α-helix | 464-469 | 6 | |
| α-helix | 474-483 | 10 | |
| α-helix | 488-495 | 8 | |
| α-helix | 496-500 | 5 | |
| α-helix | 501 | 1 | |
| β-strand | 504-505 | 2 | 5 |
| β-strand | 506 | 1 | 6 |
| β-strand | 512-515 | 4 | 5 |
| β-strand | 532-535 | 4 | 5 |
| β-strand | 543-545 | 3 | 5 |
| α-helix | 546-547 | 2 | |
| α-helix | 554-556 | 3 | |
| β-strand | 557 | 1 | 6 |
Chain D: 31 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 1568-1583 | 16 | |
| α-helix | 1591-1602 | 12 | |
| α-helix | 1609-1628 | 20 | |
| α-helix | 1638-1652 | 15 | |
| α-helix | 1661-1681 | 21 | |
| α-helix | 1689-1711 | 23 | |
| α-helix | 1717-1740 | 24 | |
| α-helix | 1747-1749 | 3 | |
| α-helix | 1750-1757 | 8 | |
| α-helix | 1763-1766 | 4 | |
| α-helix | 1770-1772 | 3 | |
| α-helix | 1775-1791 | 17 | |
| α-helix | 1801-1819 | 19 | |
| α-helix | 1821-1826 | 6 | |
| α-helix | 1828-1834 | 7 | |
| α-helix | 1840-1847 | 8 | |
| α-helix | 1866-1868 | 3 | |
| α-helix | 1870-1873 | 4 | |
| α-helix | 1875-1877 | 3 | |
| α-helix | 1882-1889 | 8 | |
| α-helix | 1890-1898 | 9 | |
| α-helix | 1902-1916 | 15 | |
| β-strand | 1917-1921 | 5 | 7 |
| β-strand | 1926-1930 | 5 | 7 |
| α-helix | 1932-1952 | 21 | |
| α-helix | 1964-1974 | 11 | |
| α-helix | 1978-1990 | 13 | |
| α-helix | 1997-2011 | 15 | |
| α-helix | 2019-2034 | 16 | |
| α-helix | 2039 | 1 | |
| α-helix | 2042-2052 | 11 | |
| α-helix | 2063-2066 | 4 | |
| α-helix | 2069-2077 | 9 | |
Chain E: 8 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 35-40 | 6 | |
| α-helix | 53-55 | 3 | |
| α-helix | 76-78 | 3 | |
| α-helix | 84-86 | 3 | |
| α-helix | 101-104 | 4 | |
| α-helix | 109-118 | 10 | |
| β-strand | 122 | 1 | 8 |
| α-helix | 123-134 | 12 | |
| β-strand | 138-140 | 3 | 9 |
| β-strand | 145-149 | 5 | 9 |
| β-strand | 156-157 | 2 | 9 |
| β-strand | 163-172 | 10 | 9 |
| β-strand | 177-186 | 10 | 9 |
| α-helix | 187-189 | 3 | |
| β-strand | 190 | 1 | 9 |
Chain F: 13 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 353-355 | 3 | |
| α-helix | 356-364 | 9 | |
| α-helix | 367-370 | 4 | |
| α-helix | 378-389 | 12 | |
| α-helix | 394-397 | 4 | |
| α-helix | 399-400 | 2 | |
| β-strand | 410 | 1 | 8 |
| α-helix | 464-469 | 6 | |
| α-helix | 474-483 | 10 | |
| α-helix | 488-495 | 8 | |
| α-helix | 496-500 | 5 | |
| α-helix | 501 | 1 | |
| β-strand | 504-505 | 2 | 10 |
| β-strand | 506 | 1 | 11 |
| β-strand | 512-515 | 4 | 10 |
| β-strand | 532-536 | 5 | 10 |
| β-strand | 542-545 | 4 | 10 |
| α-helix | 546-547 | 2 | |
| α-helix | 554-556 | 3 | |
| β-strand | 557 | 1 | 11 |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| General negative regulator of transcription subunit 1 | A, D | protein | 553 | SACCHAROMYCES CEREVISIAE | P25655 (AlphaFold model) |
| General negative regulator of transcription subunit 2 | B, E | protein | 191 | SACCHAROMYCES CEREVISIAE | P06100 (AlphaFold model) |
| General negative regulator of transcription subunit 5 | C, F | protein | 262 | SACCHAROMYCES CEREVISIAE | Q12514 (AlphaFold model) |
Sequence of entity 1 (A, D), FASTA
>4BY6_1 GENERAL NEGATIVE REGULATOR OF TRANSCRIPTION SUBUNIT 1 (chains A, D)
EDENVKKFIKEFEDTKIMPVRKGTKTTRTEKFYLVFTEWVKLLQRVENNDVITTVFIKQL
VEKGVISDTDNLLTFVKSSLELSVSSFKESDPTDEVFIAIDALGSLIIKLLILQDFKDDT
RRDYINAIFSVIVLVFAKDHSQEGTTFNERPYFRLFSNILYEWATIRTHNFVRISDSSTR
QELIEFDSVFYNTFSGYLHALQPFAFPGFSFAWVTLLSHRMLLPIMLRLPNKIGWEKLML
LIIDLFKFLDQYTSKHAVSDAVSVVYKGTLRIILGISNDMPSFLIENHYELMNNLPPTYF
QLKNVILSAIPKNMTVPNPYDVDLNMEDIPACKELPEVFFDPVIDLHSLKKPVDNYLRIP
SNSLLRTILSAIYKDTYDIKKGVGYDFLSVDSKLIRAIVLHVGIEAGIEYKRTSSNAVFN
TKSSYYTLLFNLIQNGSIEMKYQIILSIVEQLRYPNIHTYWFSFVLMNMFKSDEWNDQKL
EVQEIILRNFLKRIIVNKPHTWGVSVFFTQLINNNDINLLDLPFVQSVPEIKLILQQLVK
YSKKYTTSEQDDQ
Sequence of entity 2 (B, E), FASTA
>4BY6_2 GENERAL NEGATIVE REGULATOR OF TRANSCRIPTION SUBUNIT 2 (chains B, E)
MEKFGLKALVPLLKLEDKELSSTYDHSMTLGADLSSMLYSLGIPRDSQDHRVLDTFQSPW
AETSRSEVEPRFFTPESFTNIPGVLQSTVTPPCFNSIQNDQQRVALFQDETLFFLFYKHP
GTVIQELTYLELRKRNWRYHKTLKAWLTKDPMMEPIVSADGLSERGSYVFFDPQRWEKCQ
RDFLLFYNAIM
Sequence of entity 3 (C, F), FASTA
>4BY6_3 GENERAL NEGATIVE REGULATOR OF TRANSCRIPTION SUBUNIT 5 (chains C, F)
FDNSTLGTPTTHVSMKKKESENDSEQQLNFPPDRTDEIRKTIQHDVETNAAFQNPLFNDE
LKYWLDSKRYLMQPLQEMSPKMVSQLESSLLNCPDSLDADSPCLYTKPLSLPHPTSIFFP
NEPIRFVYPYDVPLNLTNNENDTDNKFGKDSKAKSKKDDDIYSRTSLARIFMKFDLDTLF
FIFYHYQGSYEQFLAARELFKNRNWLFNKVDRCWYYKEIEKLPPGMGKSEEESWRYFDYK
KSWLARRCGNDFVYNEEDFEKL
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| CA | Calcium ion | Ca | 2 |
Water and common crystallization additives (PEG, GOL, ACT) are not listed.
Primary citation
Structure and RNA-Binding Properties of the not1-not2-not5 Module of the Yeast Ccr4-not Complex. Bhaskar, V., Roudko, V., Basquin, J. et al. Nat Struct Mol Biol (2013) 20:1281. DOI 10.1038/NSMB.2686 · 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
- 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
Browse structure collections
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