Structure of PDB 6rbd Chain h Binding Site BS01

Receptor Information

>6rbd Chain h (length=181) Species: 559292 (Saccharomyces cerevisiae S288C)

KFESRKIMVPPHRMTPLRNSWTKIYPPLVEHLKLQVRMNLKTKSVELRTN
PKFTTDPGALQKGADFIKAFTLGFDLDDSIALLRLDDLYIETFEVKDVKT
LTGDHLSRAIGRIAGKDGKTKFAIENATRTRIVLADSKIHILGGFTHIRM
ARESVVSLILGSPPGKVYGNLRTVASRLKER

Ligand information

>6rbd Chain 2 (length=1777)

aucugguugauccugccaguagucauaugcuugucucaaagauuaagcca
ugcaugucuaaguauaagcaauuuauacagugaaacugcgaauggcucau
uaaaucaguuaucguuuauuugauaguuccuuuacuacaugguauaacug
ugguaauucuagagcuaauacaugcuuaaaaucucgacccuuuggaagag
auguauuuauuagauaaaaaaucaaugucuucggacucuuugaugauuca
uaauaacuuuucgaaucgcauggccuugugcuggcgaugguucauucaaa
uuucugcccuaucaacuuucgaugguaggauaguggccuaccaugguuuc
aacggguaacggggaauaaggguucgauuccggagagggagccugagaaa
cggcuaccacauccaaggaaggcagcaggcgcgcaaauuacccaauccua
auucagggagguagugacaauaaauaacgauacagggcccauucgggucu
uguaauuggaaugaguacaauguaaauaccuuaacgaggaacaauuggag
ggcaagucuggugccagcagccgcgguaauuccagcuccaauagcguaua
uuaaaguuguugcaguuaaaaagcucguaguugaacuuugggcccgguug
gccggucggauuuccaacggggccuuuccuucuggcuaaccuugaguccu
uguggcucuuggcgaaccaggacuuuuacuuugaaaaaauuagaguguuc
aaagcaggcguauugcucgaauauauuagcauggaauaauagaauaggac
guuugguucuauuuuguugguuucuaggaccaucguaaugauuaauaggg
acggucgggggcaucaguauucaauugucagaggugaaauucuuggauuu
auugaagacuaacuacugcgaaagcauuugccaaggacguuuucauuaau
caagaacgaaaguuaggggaucgaagaugaucagauaccgucguagucuu
aaccauaaacuaugccgacuagggaucgggugguguuuuuuuaaugaccc
acucggcaccuuacgagaaaucaaagucuuuggguucuggggggaguaug
gucgcaaggcugaaacuuaaaggaauugacggaagggcaccaccaggagu
ggagccugcggcuuaauuugacggggaaacucaccagguccagacacaau
aaggauugacagauugagagcucuuucuugauuuugugggugguggugca
uggccguucuuaguugguggagugauuugucugcuuaauugcgauaacga
acgagaccuuaaccuacuaaauaguggugcuagcauuugcugguuaucca
cuucuuagagggacuaucgguuucaagccgauggaaguuugaggcaauaa
caggucugugaugcccuuagacguucugggccgcacgcgcgcuacacuga
cggagccagcgagucuaaccuuggccgagaggucuugguaaucuugugaa
acuccgucgugcuggggauagagcauuguaauuauugcucuucaacgagg
aauuccuaguaagcgcaagucaucagcuugcguugauuacgucccugccc
uuuguacacaccgcccgucgcuaguaccgauugaauggcuuagugaggcc
ucaggaucugcuuagagaagggggcaacuccaucucagagcggagaauuu
ggacaaacuuggucauuuagaggaacuaaaagucguaacaagguuuccgu
aggugaaccugcggaaggaucauuaaa

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6rbd Conformational proofreading of distant 40S ribosomal subunit maturation events by a long-range communication mechanism.
• Resolution: 3.47 Å
• Binding residue (original residue number in PDB): H104 T107 H197 S199 R200 I202 G203 R204 A206 G207 K208 D209 G210 L226 R241 G253 P255 P256 K258 Y260 R264 R269
• Binding residue (residue number reindexed from 1): H12 T15 H105 S107 R108 I110 G111 R112 A114 G115 K116 D117 G118 L134 R149 G161 P163 P164 K166 Y168 R172 R177

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0042134 rRNA primary transcript binding
• GO:0051082 unfolded protein binding

Biological Process

• GO:0000056 ribosomal small subunit export from nucleus
• GO:0000447 endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
• GO:0000472 endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
• GO:0042254 ribosome biogenesis
• GO:0042255 ribosome assembly
• GO:0043248 proteasome assembly

Cellular Component

• GO:0005634 nucleus
• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0030686 90S preribosome

External links

• PDB: RCSB:6rbd, PDBe:6rbd, PDBj:6rbd
• PDBsum: 6rbd
• PubMed: 31227701
• UniProt: Q99216|PNO1_YEAST Pre-rRNA-processing protein PNO1 (Gene Name=PNO1)