Structure of PDB 8c01 Chain o Binding Site BS01

Receptor Information

>8c01 Chain o (length=314) Species: 4932 (Saccharomyces cerevisiae)

AHVRALILDATPLITQSYTHYQNYAQSFYTTPTVFQEIKDAQARKNLEIW
QSLGTLKLVHPSENSIAKVSTFAKLTGDYSVLSANDLHILALTYELEIKL
NNGDWRLRKKPGGDWITPENLTEAIIKDSGEDTTGSLGVEAPENQVALAT
GDFAVQNVALQMNLNLMNFMSGLKIKRIRNYMLRCHACFKIFPLPKDGKP
KHFCASCGGQGTLLRCAVSVDSRTGNVTPHLKSNFQWNNRGNRYSVASPL
SKNSQKRYGKKGHVHSKPQENVILREDQKEYEKVIKQEEWTRRHNEKILN
VRIGKGRYVNSSKR

Ligand information

>8c01 Chain 2 (length=1545)

aucugguugauccugccaguagucauaugcuugucucaaagauuaagcca
ugcaugucuaaguauaagcaaauacagugaaacugcgaauggcucauuaa
aucaguuaucguuuauuugauaguuacaugguauaacugugguaauucua
gagcuaauacaugcuuaaaaucucgaagagauguauuuauuagauaaaaa
uugaugauucauaauaacuuuucgaaucgcauggccgcuggcgaugguuc
auucaaauuucugcccuaucaacuuucgaugguaggauaguggccuacca
ugguuucaacggguaacggggaauaaggguucgauuccggagagggagcc
ugagaaacggcuaccacauccaaggaaggcagcaggcgcgcaaauuaccc
aauccuaauucagggagguagugacaauaaauaacgauacagguuguauu
ggaaugaguacaauguaaauaccuuaacgaggaacaauuggagggcaagu
cuggugccagcagccgcgguaauuccagcuccaauagcguauauuaaagu
uguugcaguuaaaaagcucguaguugaacuuugggcccgguuggccaacg
gggccuuuuuuacuuugaaaaaauuagaguguucaaagcaggcgugcucg
aauauauuagcauggaauaauagaauaggacguuugguucuauuuuuuuc
uaggaccaucguaaugauuaauagggacggucgggggcaucaguauucaa
uugucagaggugaaauucuuggauuuauugaagacuaacuacugcgaaag
cauuugccaaggacguuuucauuaaucaagaacgaaaguuaggggaucga
agaugaucagauaccgucguagucuuaaccauaaacuaugccgacuaggg
aucgggugguguuuuuaaugacccacucggcaccuuacgagaaaucaaag
ucuuuggguucuggggggaguauggucgcaaggcugaaacuuaaaggaau
ugacagggcaccaccaggaguggagccugcggcuuaauuuggaaacucac
cagguccacacaauaagauugacagauugagagcucuuucuugauuuugu
ggguggugggccgguugguggagugauuugucugcuuaauugcgauaacg
aacgaccuuaaccacuaauaguggugcuagcauuugcugguuccacuucu
uagagggacuaggaaggaggggucccuuagacguucugggccgcacgcgc
gcuacacugacggagccagcgagucuaaccuuggccgagaggucuuggua
aucuugugaaacuccgucgugcuggggauagagcauuguaauuauugcuc
uucaacgaggaauuccuaguaagcgcaagucaucagcuugcguugauuac
gucccugcccuguaccuaguaccgauugaauggcuuagugaggccucagg
aucugcuuagagucagagcggagaauuuggacaaacuuggucauuuagag
gaacuaagguuuccguaggugaaccugcggaaggaucauuaaaga

..<<<<<.{.((((>>>>><<<<.<<<<<<...<.<...<......<<<.
<<<..<<....<<....<<.......>>...>>.>>......<<......
..<<<..<<..<<....<<<........<<......<<.<<.......>>
.>>......>>........<<<<<...>>>>><.<.<<<<<<......((
...........>>>>>>.>...>...<<<<..<<<.>>>.>>>>....>>
>...>>>>..>>>.<<<....<<<....<<<<<<<<.......>>>>>>>
>>>>......>>>...<<<.<<<<....>>>>....>>>.>>.<<.<<<.
.........>>>.>>.<.<<<..>>>.>...>>>>>>.........<<<.
...<<<.....>>>..>>>..>....>.>.....<<<<<<<<.>>>>>>>
>......<<..<...........>..>>.........<<<<<((....<.
<<<<.....<<..))>>.......>>>>>>>>>>..>>>>>>>>>>....
.....<<<[[.....<.<<...<<<.<<....<<<<<<.<<<<..>>>>.
>>>>>>...<<<<<.<<.......<<...<.......>..<<<..>>>..
..>>......>>.>>..>>>.........<<<..<<<<<<<<.....)).
>>>>>>>>.>>>.....>>....<<<<<<.<<...<<<<..<<..<<<<<
<.<...<<<..(...>>>......>.>>>>>>..>>.......<<....>
>...>>>>...>>>>>.>>>...>>>...>>.>....<<<<<<<...<..
.<<<<..)......>>>>...>>>>>>>>..........<<<.<<.<<<.
.<<<<<<<<.<<<......>>>>>>>>>>>..>>>...<<..]]>>...>
>.....>>>.>>>.<<<......<<<<....>>>>....>>>..)))).}
....<<<<<<..<<.<<<<<<..<<<.<<<<<<................<
<<<<.<..<<<<<.......<<.<<<........>>>.>>......>>>>
>......<<<<<.<<<.<<<<......>>...<<<......>>>...>>.
>>>..<<<<..<<.<<<..<<<<<.<<<<<<<..>>>>>>>.>>>>>...
>>>.>>..........>>>>>>>>>.......>.>>>>>...>>.>>>>.
>>>.....<<<<<<<......<<.....<<..<<<<....>>>>..>>..
..>>.......>>>>>>>......<....<<<<<<..........>>>>>
>....>.....>>>>>>....<<<<<<<<.......>>>>>>>>......
>>...>>>>>>.....<<<<.<<....<<<<<<<<.<<<..<.<<..<..
.<<<<<<<.......>>>>>>>...>..>>.>..>>>.>>>>>>>>...>
>.>>>>....<<<<<<<<<....>>>>>>>>>.............

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8c01 Impact of the yeast S0/uS2-cluster ribosomal protein rpS21/eS21 on rRNA folding and the architecture of small ribosomal subunit precursors.
• Resolution: 2.7 Å
• Binding residue (original residue number in PDB): L333 C335 L350 K351 S352 F354 N357 R359 R362 S364 S370 K371 N372 K375 R376 K379 K380 H382 H384 K398 R445 R450 N453 S455 K456 R457
• Binding residue (residue number reindexed from 1): L214 C216 L231 K232 S233 F235 N238 R240 R243 S245 S251 K252 N253 K256 R257 K260 K261 H263 H265 K279 R302 R307 N310 S312 K313 R314

Enzymatic activity

• Enzyme Commision number: 3.1.-.-

Gene Ontology

Molecular Function

• GO:0004518 nuclease activity
• GO:0004521 RNA endonuclease activity
• GO:0008270 zinc ion binding
• GO:0046872 metal ion binding
• GO:0070181 small ribosomal subunit rRNA binding

Biological Process

• GO:0000462 maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
• GO:0030490 maturation of SSU-rRNA
• GO:0042254 ribosome biogenesis
• GO:0042274 ribosomal small subunit biogenesis
• GO:0043248 proteasome assembly

Cellular Component

• GO:0005634 nucleus
• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005783 endoplasmic reticulum
• GO:0030688 preribosome, small subunit precursor

External links

• PDB: RCSB:8c01, PDBe:8c01, PDBj:8c01
• PDBsum: 8c01
• PubMed: 36996028
• UniProt: Q08444|NOB1_YEAST 20S-pre-rRNA D-site endonuclease NOB1 (Gene Name=NOB1)