5AJD: Not1 C-terminal domain
Not1 C-terminal domain in complex with Not4. Determined by X-ray diffraction at 3.62 Å resolution. Released 29 Apr 2015.
- Method
- X-ray diffraction
- Resolution
- 3.62 Å
- Organism
- SACCHAROMYCES CEREVISIAE
- Chains
- 12
- Atoms
- 24,547
- Mol. weight
- 433.47 kDa
- Released
- 29 Apr 2015
Explore 5AJD in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
5AJD contains 197 α-helices and 18 β-strands across 12 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: 30 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 1569-1583 | 15 | |
| α-helix | 1592-1600 | 9 | |
| β-strand | 1608 | 1 | 1 |
| α-helix | 1609-1627 | 19 | |
| α-helix | 1640-1652 | 13 | |
| β-strand | 1654 | 1 | 2 |
| α-helix | 1660-1680 | 21 | |
| α-helix | 1690-1706 | 17 | |
| α-helix | 1720-1739 | 20 | |
| α-helix | 1750-1757 | 8 | |
| α-helix | 1763-1767 | 5 | |
| α-helix | 1770-1772 | 3 | |
| α-helix | 1775-1789 | 15 | |
| α-helix | 1803-1819 | 17 | |
| α-helix | 1822-1826 | 5 | |
| α-helix | 1828-1833 | 6 | |
| α-helix | 1841-1848 | 8 | |
| α-helix | 1866-1868 | 3 | |
| α-helix | 1875-1877 | 3 | |
| α-helix | 1887-1889 | 3 | |
| α-helix | 1890-1898 | 9 | |
| α-helix | 1902-1913 | 12 | |
| α-helix | 1914-1918 | 5 | |
| α-helix | 1932-1951 | 20 | |
| α-helix | 1964-1975 | 12 | |
| α-helix | 1978-1991 | 14 | |
| α-helix | 1997-2011 | 15 | |
| α-helix | 2020-2031 | 12 | |
| α-helix | 2037 | 1 | |
| α-helix | 2039-2041 | 3 | |
| α-helix | 2042-2054 | 13 | |
| α-helix | 2072-2077 | 6 | |
Chain B: 1 helix, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 426-438 | 13 | |
| β-strand | 444 | 1 | 1 |
| β-strand | 447 | 1 | 2 |
Chain C: 30 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 1569-1583 | 15 | |
| α-helix | 1592-1600 | 9 | |
| β-strand | 1608 | 1 | 3 |
| α-helix | 1609-1627 | 19 | |
| α-helix | 1640-1652 | 13 | |
| β-strand | 1654 | 1 | 4 |
| α-helix | 1660-1680 | 21 | |
| α-helix | 1690-1706 | 17 | |
| α-helix | 1719-1739 | 21 | |
| α-helix | 1747-1749 | 3 | |
| α-helix | 1750-1757 | 8 | |
| α-helix | 1763-1767 | 5 | |
| α-helix | 1775-1789 | 15 | |
| α-helix | 1802-1819 | 18 | |
| α-helix | 1822-1826 | 5 | |
| α-helix | 1828-1834 | 7 | |
| α-helix | 1841-1847 | 7 | |
| α-helix | 1866-1868 | 3 | |
| α-helix | 1871-1873 | 3 | |
| α-helix | 1887-1889 | 3 | |
| α-helix | 1890-1898 | 9 | |
| α-helix | 1902-1913 | 12 | |
| α-helix | 1914-1918 | 5 | |
| α-helix | 1932-1951 | 20 | |
| α-helix | 1964-1975 | 12 | |
| α-helix | 1978-1990 | 13 | |
| α-helix | 1997-2010 | 14 | |
| α-helix | 2020-2034 | 15 | |
| α-helix | 2037 | 1 | |
| α-helix | 2040-2041 | 2 | |
| α-helix | 2042-2054 | 13 | |
| α-helix | 2073-2077 | 5 | |
Chain D: 2 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 427-438 | 12 | |
| β-strand | 444 | 1 | 3 |
| β-strand | 447 | 1 | 4 |
| α-helix | 461-462 | 2 | |
Chain E: 32 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 1570-1585 | 16 | |
| α-helix | 1592-1602 | 11 | |
| α-helix | 1604-1606 | 3 | |
| β-strand | 1608 | 1 | 5 |
| α-helix | 1609-1628 | 20 | |
| α-helix | 1638-1652 | 15 | |
| α-helix | 1660-1681 | 22 | |
| α-helix | 1690-1706 | 17 | |
| α-helix | 1719-1738 | 20 | |
| α-helix | 1739-1741 | 3 | |
| α-helix | 1750-1757 | 8 | |
| α-helix | 1762-1768 | 7 | |
| α-helix | 1770-1772 | 3 | |
| α-helix | 1775-1789 | 15 | |
| α-helix | 1803-1819 | 17 | |
| α-helix | 1822-1826 | 5 | |
| α-helix | 1828-1834 | 7 | |
| α-helix | 1841-1847 | 7 | |
| α-helix | 1871-1873 | 3 | |
| α-helix | 1875-1877 | 3 | |
| α-helix | 1887-1890 | 4 | |
| α-helix | 1892-1898 | 7 | |
| α-helix | 1905-1913 | 9 | |
| α-helix | 1914-1918 | 5 | |
| α-helix | 1932-1952 | 21 | |
| α-helix | 1964-1975 | 12 | |
| α-helix | 1978-1989 | 12 | |
| α-helix | 1997-2010 | 14 | |
| α-helix | 2022-2034 | 13 | |
| α-helix | 2039 | 1 | |
| α-helix | 2042-2053 | 12 | |
| α-helix | 2059-2061 | 3 | |
| α-helix | 2073-2077 | 5 | |
Chain F: 1 helix, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 428-439 | 12 | |
| β-strand | 444 | 1 | 5 |
Chain G: 30 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 1569-1586 | 18 | |
| α-helix | 1592-1602 | 11 | |
| β-strand | 1608 | 1 | 6 |
| α-helix | 1609-1627 | 19 | |
| α-helix | 1638-1653 | 16 | |
| β-strand | 1654-1655 | 2 | 7 |
| α-helix | 1660-1680 | 21 | |
| α-helix | 1690-1711 | 22 | |
| α-helix | 1717-1739 | 23 | |
| α-helix | 1747-1749 | 3 | |
| α-helix | 1750-1757 | 8 | |
| α-helix | 1762-1767 | 6 | |
| α-helix | 1770-1772 | 3 | |
| α-helix | 1775-1789 | 15 | |
| α-helix | 1803-1819 | 17 | |
| α-helix | 1822-1826 | 5 | |
| α-helix | 1828-1834 | 7 | |
| α-helix | 1841-1847 | 7 | |
| α-helix | 1871-1873 | 3 | |
| α-helix | 1875-1877 | 3 | |
| α-helix | 1887-1889 | 3 | |
| α-helix | 1890-1898 | 9 | |
| α-helix | 1904-1913 | 10 | |
| α-helix | 1914-1918 | 5 | |
| α-helix | 1932-1948 | 17 | |
| α-helix | 1964-1974 | 11 | |
| α-helix | 1978-1990 | 13 | |
| α-helix | 1997-2010 | 14 | |
| α-helix | 2022-2031 | 10 | |
| α-helix | 2040-2041 | 2 | |
| α-helix | 2042-2052 | 11 | |
| α-helix | 2071-2074 | 4 | |
Chain H: 2 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 426-438 | 13 | |
| β-strand | 444 | 1 | 6 |
| β-strand | 446-447 | 2 | 7 |
| α-helix | 457-459 | 3 | |
4 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| CDC39P | A, C, E, G, I, K | protein | 556 | SACCHAROMYCES CEREVISIAE | P25655 (AlphaFold model) |
| General negative regulator of transcription subunit 4 | B, D, F, H, J, L | protein | 65 | SACCHAROMYCES CEREVISIAE | P34909 (AlphaFold model) |
Sequence of entity 1 (A, C, E, G, I, K), FASTA
>5AJD_1 CDC39P (chains A, C, E, G, I, K)
RSMEDENVKKFIKEFEDTKIMPVRKGTKTTRTEKFYLVFTEWVKLLQRVENNDVITTVFI
KQLVEKGVISDTDNLLTFVKSSLELSVSSFKESDPTDEVFIAIDALGSLIIKLLILQDFK
DDTRRDYINAIFSVIVLVFAKDHSQEGTTFNERPYFRLFSNILYEWATIRTHNFVRISDS
STRQELIEFDSVFYNTFSGYLHALQPFAFPGFSFAWVTLLSHRMLLPIMLRLPNKIGWEK
LMLLIIDLFKFLDQYTSKHAVSDAVSVVYKGTLRIILGISNDMPSFLIENHYELMNNLPP
TYFQLKNVILSAIPKNMTVPNPYDVDLNMEDIPACKELPEVFFDPVIDLHSLKKPVDNYL
RIPSNSLLRTILSAIYKDTYDIKKGVGYDFLSVDSKLIRAIVLHVGIEAGIEYKRTSSNA
VFNTKSSYYTLLFNLIQNGSIEMKYQIILSIVEQLRYPNIHTYWFSFVLMNMFKSDEWND
QKLEVQEIILRNFLKRIIVNKPHTWGVSVFFTQLINNNDINLLDLPFVQSVPEIKLILQQ
LVKYSKKYTTSEQDDQ
Sequence of entity 2 (B, D, F, H, J, L), FASTA
>5AJD_2 GENERAL NEGATIVE REGULATOR OF TRANSCRIPTION SUBUNIT 4 (chains B, D, F, H, J, L)
GPDSMDPYDALGNAVDFLDARLHSLSNYQKRPISIKSNIIDEETYKKYPSLFSWDKIEAS
KKSDN
Primary citation
Architecture of the Ubiquitylation Module of the Yeast Ccr4-not Complex. Bhaskar, V., Basquin, J., Conti, E. Structure (2015) 23:921. DOI 10.1016/J.STR.2015.03.011 · 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
- 4CV5 3.81 Å, yeast NOT1 CN9BD-CAF40 complex
Browse structure collections
About this viewer
MolViewer shows 5AJD directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.