4B8C: Nuclease module of the yeast Ccr4-Not complex
nuclease module of the yeast Ccr4-Not complex. Determined by X-ray diffraction at 3.41 Å resolution. Released 21 Nov 2012.
- Method
- X-ray diffraction
- Resolution
- 3.41 Å
- Organisms
- SACCHAROMYCES CEREVISIAE, SACCHAROMYCES CEREVISIAE S288C
- Chains
- 12
- Atoms
- 24,298
- Mol. weight
- 579.03 kDa
- Released
- 21 Nov 2012
Explore 4B8C in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
4B8C contains 190 α-helices and 99 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.
Chains A and C: 17 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 155-158 | 4 | |
| β-strand | 160-163 | 4 | 1 |
| α-helix | 168-178 | 11 | |
| β-strand | 184-190 | 7 | 1 |
| β-strand | 197-199 | 3 | 2 |
| α-helix | 205-219 | 15 | |
| β-strand | 224-230 | 7 | 1 |
| β-strand | 243-247 | 5 | 1 |
| β-strand | 248 | 1 | 3 |
| α-helix | 252-254 | 3 | |
| α-helix | 259-268 | 10 | |
| α-helix | 272-277 | 6 | |
| α-helix | 279 | 1 | |
| β-strand | 280 | 1 | 3 |
| α-helix | 281 | 1 | |
| α-helix | 282-291 | 10 | |
| β-strand | 301-304 | 4 | 1 |
| α-helix | 308-319 | 12 | |
| α-helix | 322-324 | 3 | |
| α-helix | 327-337 | 11 | |
| β-strand | 341-343 | 3 | 1 |
| α-helix | 344-352 | 9 | |
| α-helix | 373-380 | 8 | |
| α-helix | 386-389 | 4 | |
| α-helix | 391-408 | 18 | |
| β-strand | 412 | 1 | 4 |
| β-strand | 418 | 1 | 4 |
| α-helix | 419-422 | 4 | |
Chains B, G, H and I: 19 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 761 | 1 | 5 |
| β-strand | 767 | 1 | 6 |
| α-helix | 770-772 | 3 | |
| α-helix | 776-778 | 3 | |
| α-helix | 783-794 | 12 | |
| α-helix | 801-811 | 11 | |
| α-helix | 814-816 | 3 | |
| α-helix | 817-823 | 7 | |
| α-helix | 824-829 | 6 | |
| α-helix | 833-835 | 3 | |
| α-helix | 836-846 | 11 | |
| α-helix | 849-868 | 20 | |
| β-strand | 869 | 1 | 5 |
| α-helix | 872-874 | 3 | |
| α-helix | 877-890 | 14 | |
| α-helix | 892-894 | 3 | |
| α-helix | 897-899 | 3 | |
| β-strand | 903 | 1 | 6 |
| α-helix | 905-915 | 11 | |
| α-helix | 918-929 | 12 | |
| α-helix | 932-934 | 3 | |
| α-helix | 943-958 | 16 | |
| α-helix | 963-975 | 13 | |
Chain D: 14 helices, 13 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 143-146 | 3 | |
| α-helix | 155-169 | 15 | |
| α-helix | 176-186 | 11 | |
| α-helix | 245-258 | 14 | |
| β-strand | 338-340 | 3 | 2 |
| α-helix | 351-355 | 5 | |
| β-strand | 363 | 1 | 2 |
| α-helix | 374-379 | 6 | |
| β-strand | 384-386 | 3 | 2 |
| α-helix | 399-402 | 4 | |
| β-strand | 407-409 | 3 | 2 |
| β-strand | 431-432 | 2 | 2 |
| α-helix | 441-460 | 20 | |
| α-helix | 515-517 | 3 | |
| α-helix | 528-531 | 4 | |
| α-helix | 533-546 | 14 | |
| β-strand | 552-554 | 3 | 11 |
| α-helix | 559-561 | 3 | |
| α-helix | 562-566 | 5 | |
| β-strand | 577-578 | 2 | 11 |
| β-strand | 600-602 | 3 | 11 |
| β-strand | 770 | 1 | 12 |
| β-strand | 777 | 1 | 12 |
| α-helix | 800-803 | 4 | |
| β-strand | 811 | 1 | 13 |
| β-strand | 814 | 1 | 13 |
| β-strand | 818 | 1 | 12 |
Chain E: 18 helices, 12 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 155-158 | 4 | |
| β-strand | 160-163 | 4 | 14 |
| α-helix | 168-181 | 14 | |
| β-strand | 184-190 | 7 | 14 |
| α-helix | 196 | 1 | |
| β-strand | 197-199 | 3 | 15 |
| α-helix | 205-219 | 15 | |
| β-strand | 224-230 | 7 | 14 |
| β-strand | 243-247 | 5 | 14 |
| β-strand | 248 | 1 | 16 |
| α-helix | 252-254 | 3 | |
| β-strand | 258 | 1 | 17 |
| α-helix | 259-268 | 10 | |
| α-helix | 272-277 | 6 | |
| α-helix | 279 | 1 | |
| β-strand | 280 | 1 | 16 |
| α-helix | 281 | 1 | |
| α-helix | 282-291 | 10 | |
| β-strand | 301-304 | 4 | 14 |
| α-helix | 308-319 | 12 | |
| α-helix | 322-324 | 3 | |
| α-helix | 327-337 | 11 | |
| β-strand | 341-343 | 3 | 14 |
| α-helix | 344-352 | 9 | |
| α-helix | 373-380 | 8 | |
| α-helix | 386-389 | 4 | |
| α-helix | 391-408 | 18 | |
| β-strand | 412 | 1 | 18 |
| β-strand | 418 | 1 | 18 |
| α-helix | 419-422 | 4 | |
Chain F: 18 helices, 10 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 155-158 | 4 | |
| β-strand | 160-163 | 4 | 19 |
| α-helix | 168-181 | 14 | |
| β-strand | 184-190 | 7 | 19 |
| α-helix | 195-198 | 4 | |
| α-helix | 205-219 | 15 | |
| β-strand | 224-230 | 7 | 19 |
| β-strand | 243-247 | 5 | 19 |
| β-strand | 248 | 1 | 20 |
| α-helix | 252-254 | 3 | |
| α-helix | 259-268 | 10 | |
| α-helix | 272-277 | 6 | |
| α-helix | 279 | 1 | |
| β-strand | 280 | 1 | 20 |
| α-helix | 281 | 1 | |
| α-helix | 282-291 | 10 | |
| β-strand | 301-304 | 4 | 19 |
| α-helix | 308-319 | 12 | |
| α-helix | 322-324 | 3 | |
| α-helix | 327-337 | 11 | |
| β-strand | 341-343 | 3 | 19 |
| α-helix | 344-352 | 9 | |
| α-helix | 373-380 | 8 | |
| α-helix | 386-389 | 4 | |
| α-helix | 391-408 | 18 | |
| β-strand | 412 | 1 | 21 |
| β-strand | 418 | 1 | 21 |
| α-helix | 419-422 | 4 | |
Chain J: 8 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 143-147 | 4 | |
| α-helix | 155-169 | 15 | |
| α-helix | 176-186 | 11 | |
| α-helix | 245-258 | 14 | |
| β-strand | 340 | 1 | 28 |
| α-helix | 351-355 | 5 | |
| β-strand | 363 | 1 | 28 |
| α-helix | 374-379 | 6 | |
| β-strand | 384-386 | 3 | 28 |
| α-helix | 400-402 | 3 | |
| β-strand | 407-409 | 3 | 28 |
| β-strand | 430-432 | 3 | 28 |
| α-helix | 441-461 | 21 | |
Chain K: 14 helices, 15 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 143-146 | 3 | |
| α-helix | 155-169 | 15 | |
| α-helix | 176-186 | 11 | |
| α-helix | 245-258 | 14 | |
| β-strand | 338-340 | 3 | 8 |
| α-helix | 351-355 | 5 | |
| β-strand | 363 | 1 | 8 |
| α-helix | 374-379 | 6 | |
| β-strand | 384-386 | 3 | 8 |
| α-helix | 399-402 | 4 | |
| β-strand | 407-409 | 3 | 8 |
| β-strand | 431-432 | 2 | 8 |
| α-helix | 441-460 | 20 | |
| α-helix | 515-518 | 4 | |
| α-helix | 528-531 | 4 | |
| α-helix | 533-546 | 14 | |
| β-strand | 552-554 | 3 | 29 |
| β-strand | 558 | 1 | 30 |
| α-helix | 559-561 | 3 | |
| α-helix | 562-566 | 5 | |
| β-strand | 577-578 | 2 | 29 |
| β-strand | 597 | 1 | 30 |
| β-strand | 600-602 | 3 | 29 |
| β-strand | 770 | 1 | 31 |
| β-strand | 777 | 1 | 31 |
| α-helix | 800-803 | 4 | |
| β-strand | 811 | 1 | 32 |
| β-strand | 814 | 1 | 32 |
| β-strand | 818 | 1 | 31 |
Chain L: 8 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 143-147 | 4 | |
| α-helix | 155-169 | 15 | |
| α-helix | 176-186 | 11 | |
| α-helix | 245-258 | 14 | |
| β-strand | 338-340 | 3 | 15 |
| β-strand | 346 | 1 | 17 |
| α-helix | 351-355 | 5 | |
| β-strand | 363 | 1 | 15 |
| α-helix | 374-379 | 6 | |
| β-strand | 384-386 | 3 | 15 |
| α-helix | 400-402 | 3 | |
| β-strand | 407-409 | 3 | 15 |
| β-strand | 430-432 | 3 | 15 |
| α-helix | 441-461 | 21 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Poly(a) ribonuclease POP2 | A, C, E, F | protein | 288 | SACCHAROMYCES CEREVISIAE | P39008 (AlphaFold model) |
| General negative regulator of transcription subunit 1 | B, G, H, I | protein | 249 | SACCHAROMYCES CEREVISIAE S288C | P25655 (AlphaFold model) |
| Glucose-repressible alcohol dehydrogenase transcriptional effector | D, J, K, L | protein | 727 | SACCHAROMYCES CEREVISIAE S288C | P31384 (AlphaFold model) |
Sequence of entity 1 (A, C, E, F), FASTA
>4B8C_1 POLY(A) RIBONUCLEASE POP2 (chains A, C, E, F)
SMPPIFLPPPNYLFVRDVWKSNLYSEFAVIRQLVSQYNHVSISTEFVGTLARPIGTFRSK
VDYHYQTMRANVDFLNPIQLGLSLSDANGNKPDNGPSTWQFNFEFDPKKEIMSTESLELL
RKSGINFEKHENLGIDVFEFSQLLMDSGLMMDDSVTWITYHAAYDLGFLINILMNDSMPN
NKEDFEWWVHQYMPNFYDLNLVYKIIQEFKNPQLQQSSQQQQQQQYSLTTLADELGLPRF
SIFTTTGGQSLLMLLSFCQLSKLSMHKFPNGTDFAKYQGVIYGIDGDQ
Sequence of entity 2 (B, G, H, I), FASTA
>4B8C_2 GENERAL NEGATIVE REGULATOR OF TRANSCRIPTION SUBUNIT 1 (chains B, G, H, I)
RSMSRPVQEMIPLKFFAVDEVSCQINQEGAPKDVVEKVLFVLNNVTLANLNNKVDELKKS
LTPNYFSWFSTYLVTQRAKTEPNYHDLYSKVIVAMGSGLLHQFMVNVTLRQLFVLLSTKD
EQAIDKKHLKNLASWLGCITLALNKPIKHKNIAFREMLIEAYKENRLEIVVPFVTKILQR
ASESKIFKPPNPWTVGILKLLIELNEKANWKLSLTFEVEVLLKSFNLTTKSLKPSNFINT
PEVIETLSG
Sequence of entity 3 (D, J, K, L), FASTA
>4B8C_3 GLUCOSE-REPRESSIBLE ALCOHOL DEHYDROGENASE TRANSCRIPTIONAL EFFECTOR (chains D, J, K, L)
MNASTAAVNSIGMVPTVGTPVNINVNASNPLLHPHLDDPSLLNNPIWKLQLHLAAVSAQS
LGQPNIYARQNAMKKYLATQQAQQAQQQAQQQAQQQVPGPFGPGPQAAPPALQPTDFQQS
HIAEASKSLVDCTKQALMEMADTLTDSKTAKKQQPTGDSTPSGTATNSAVSTPLTPKIEL
FANGKDEANQALLQHKKLSQYSIDEDDDIENRMVMPKDSKYDDQLWHALDLSNLQIFNIS
ANIFKYDFLTRLYLNGNSLTELPAEIKNLSNLRVLDLSHNRLTSLPAELGSCFQLKYFYF
FDNMVTTLPWEFGNLCNLQFLGVEGNPLEKQFLKILTEKSVTGLIFYLRDNRPEIPLPHE
RRFIEINTDGEPQREYDSLQQSTEHLATDLAKRTFTVLSYNTLCQHYATPKMYRYTPSWA
LSWDYRRNKLKEQILSYDSDLLCLQEVESKTFEEYWVPLLDKHGYTGIFHAKARAKTMHS
KDSKKVDGCCIFFKRDQFKLITKDAMDFSGAWMKHKKFQRTEDYLNRAMNKDNVALFLKL
QHIPSGDTIWAVTTHLHWDPKFNDVKTFQVGVLLDHLETLLKEETSHNFRQDIKKFPVLI
CGDFNSYINSAVYELINTGRVQIHQEGNGRDFGYMSEKNFSHNLALKSSYNCIGELPFTN
FTPSFTDVIDYIWFSTHALRVRGLLGEVDPEYVSKFIGFPNDKFPSDHIPLLARFEFMKT
NTGSKKV
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 P39008 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 1UOC 2.3 Å, X-ray structure of the RNase domain of the yeast Pop2 protein
- 4B8A 2.4 Å, Structure of yeast NOT1 MIF4G domain co-crystallized with CAF1
Browse structure collections
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