Structure of PDB 8i9z Chain LC Binding Site BS01

Receptor Information

>8i9z Chain LC (length=362) Species: 759272 (Thermochaetoides thermophila DSM 1495)

RPTVTVFGADGKPTGATEVLPKVFSAPIRPDIVKHVHTGMAKNKRQPYAV
SEKAGHQTSAESWGTGRAVARIPRVSGGGTHRAGQGAFGNMCRSGRMFAP
TKIWRKWHVKINQGQKRFATASALAASAVAPLLMARGHQVSTVPEVPLVV
DSAAVAGDAVAKTAAAYKLLKAIGAGPDVEKVKKSKKLRAGKGKMRGRRH
RQRRGPLIVYSPEHDGKELVKGFRNIPGVETCPVDALNLLQLAPGGHLGR
FIVWTSAAIKQLDAVYESKKGFFLPANIVSQADLSRLINSTEIQSVLRAP
KGEARTKRACVQKKNPLRNKQIMLRLNPYASTFAKEKLGEVKAEEGKPPK
VPASFKELLHEA

Ligand information

>8i9z Chain C1 (length=2787)

uugaccucggaucagguaggaggacccgcugaacuuaagcauaucaauaa
gcggaggaaaagaaaccaacagggauugcccuaguaacggcgagugaagc
ggcaacagcucaaauuugaaagcuggcuucggcccgcguuguaauuugga
gaggaugcuuugggcgaggcuccuucugaguucccuggaacgggacgcca
cagagggugagagccccguauaguuggaagccaagccuguguaaagcucc
uucgacgagucgaguaguuugggaaugcugcucaaaaugggagguaaauu
ucuucuaaagcuaaauaccggccagagaccgauagcgcacaaguagagug
aucgaaagaugaaaagcacuuugaaaagaggguuaaauagcacgugaaau
uguugaaagggaagcgcuugugaccagacuugcgcccggcggaucauccg
guguucucaccggugcacuccgccgggcucaggccagcaucgguucuggc
ggggggauaaaggcccagggaauguggcuccuccgggaguguuauagccc
uggguguaauacccucgccgggaccgaggaccgcgcucugcaaggaugcu
ggcguaauggucaccagcgacccgucuugaaacacggaccaaggagucaa
gguuuugcgcgaguguuuggguguaaaacccgcacgcguaaggugagagc
uucggcgcaucaucgaccgauccugauguauucggauggauuugaguagg
agcguuaagccuuggacccgaaagauggugaacuaugcuuggauagggug
aagccagaggaaacucugguggaggcucgcugacgugcaagaucgucaaa
ucugagcaugggggcgaaagacuaaccaucuaguagcugguuaccgccga
aguuucccucaggauagcagugucgaccuucaguuuuaugagguaaagcg
aaugaacuuuaaauauguaagaagcccuuguuacuuaacugaacgugggc
auucgaauguaucgacacuagugggccauuuuugguaagcagaacuggcg
augcgggaugaaccgaacgcgggguuaaggugccggaguggacgcucauc
agacaccacaaaaggcguuaguacaucuugacagcaggacgguggccaug
gaagucggaauccgcuaaggacuguguaacaacucaccugccgaauguac
uagcccugaaaauggauggcgcucaagcgucccacccauaccccgcccuc
aggguagaaacgaugcccugaggaguaggcggccguggaggucagugacg
aagccuagggcgugagcccgggucgaacggccucuagugcagaucuuggu
gguaguagcaaauacuucaaugagaacuugaaggaccgaaguggggaaag
guuccaugugaacagcgguuggacauggguuagucgauccuaagccauag
ggaaguuccguuucaaaggggcacucgugccccguguggcgaaagggaag
ccgguuaauauuccggcaccuggauguggguuuugcgcggcaacgcaacu
gaacgcggagacgacggcgggggccccgggcagaguucucuuuucuucuu
aacggucuaucacccuggaaacaguuugucuggagauaggguuuaauggc
cggaagagcccgacacuucugucggguccggugcgcucucgacgucccuu
gaaaauccgcgggagggaauaauucucacgccaggucguacucauaaccg
cagcagguccccaaggugaacagccucugguugauagaacaauguagaua
agggaagucggcuccguaacuucgggaaaagggcucuaaggguugggcac
guugggcuuugggcggacgcccugggagcagagggccucuagccgggcaa
ccggccggcggcccucagcacccgggguugaagcccuuagcccggcgugc
gguuaacaaccaacuuagaacugguacggacacacugucccuaucuacua
ucuagcgaaaccacagccaagggaacgggcuuggcaaaaucagcggggaa
agaagacccuguugagcuugacucuaguuugacauugugaaaagacauag
gagguguagaauaggugggagcuucggcgccagugaaauaccacuacucc
uauuguuuuuuuacuuauucaaugugaagacauugucagguggggaguuc
cuuuagucccucgaaauuugaggcuagaggagaaaaguuaccacagggau
aacuggcuuguggcggccaagcguucauagcgacgucgcugaugucggcu
cuuccuaucauaccgaagcagaauucgguaagcguuggauuguucaccca
cuaauagggagugagcuggaccgucgugagacagguuagucccuacugau
gaacucgucgcaaugguaauucagcuuaguacgagaggaaccgcugauuc
agauaauugguuuuugcgguuguccgaccgggcagugccgcgaagcuacc
aucugcuggauaauggcugaacgccucuaagucagaauccaugccagaac
gcgacgauacuacccgcacguuguagacguauaagaauaggcuccggccu
cguauccuagcaggcgauuccuccgccggccucgaaguggccgucgguaa
uucgcguauugcaauuuagacacgcgcgggaucaaauccuuugcagacga
cuuagaugugcgaaaggguccuguaagcaguagaguagccuuguuguuac
gaucugcugaggguaagcccuccuucgccuagauuuc

........................<<<<<<.....<......>......>
>>>>.>.........<<....>>..<<<<<......<<.....>>.....
>>>>>..<<<..<<.......<<.<<<....>>>.>>.......>>....
<<<<<.<<<<<<<<<..<<<<<<..<<....<<<<......>>>>.((..
....<<<.....))>>>....>>..>>>.>>>..>>>>....>>>>>>>>
.>>........<<<<<<<........>>>>>>>.....<<<<<<......
>>>>>>..>>>..................................<<...
.>>...............<<<<....>>>>....................
..............<<<<.<<<<<<.<...<<.<<<<<<<<<.....<<<
<<<....>>>>>>......>>>>>>>>>.>>.<<<<<<<.<<<<<<<<<<
<<<<<.......<<<<<<<<......<<<<<....>>>>>.......>>>
>>>>>......>>>>>>>>>>>>>>>........<<...>>.....>>>>
>>>....>>>>>>>.>>>>..<<<<.<....>.>>>><<<<<<....<<<
<<<<<.<<<<..<<<...<<<<.....>>>>...>>>....<<<<<..<<
....>>...>>>>>.<<<<<<<<....<....>....>>>.>>>.>>...
.>>>>.>>>>>>>>..<<.<..<<<<<<<.....<<<<<<<<<..<<<<.
..<<<<<<<....>>>>>>>...>.>>>..<<<<<........>>>>>..
>>>>>>>>>..<<.<....>.>>.>>>>>>>.....>.>>...<<<<<..
..<.<<<....>>>.><<<<<<<<<<....<<.<<<<<<<.....<<<..
......>>.>.....>>>>>...<<<<.<<<<.<......>>>>>.>>>>
.....>>>>..>>>>>>>>.>>..<<<<.<<<<<.....>>>>>.>>>>.
...<<<......>>>...<<<<<<<...<<<(((.....<<<<<<.....
.<..........<<<.<<<<<<<<<<.....<.<<<<<.<<<...<<...
......>>...>>>.........<<......>>...>>>>>.>.>>>>>>
>>>>>>>..........))).>....>>>>>>.>>>...>>>>>>><<<<
<<<<<.........>>>>>>>>>....>>>>>.<.<<<<<<<<.<<....
..<<<<.<<<<....>>>>>>>>...>>>>>>>>>>..>.....>>>>>>
<<.....<<.....<<<<<<.......>>>>>><<<<.....<<<<<.<<
...<<<<<<...<<.....>>.>>>>>>....((<<<<<<...<<<...<
<<....>>>........<<<<<......>>>>>....>>>....>>...<
<<<<........>>>>>))<<<<.<<<<.<<<....<<<....>>>....
...<<<<<<...<<<<.<<<<<<<<<<<<<.<<<<...((..>>>>.><.
..<<<<<....<<<<<<....<<<.....>>>....>>>>>>.....>>>
>>....><<<<<<<<....>>>>>>>>>>>>.>.>>>>>>>.>>>>....
.....>>>>>>.........>>>...>>>>>>>>>>>>..>>.....<<.
.....>>>>>>>.<<<<.....>>>>..>>>>..<<<<.....<<<<<<<
.<<.......<.<<<<<<.<.<<.................<<<<<.<<<<
<..<.<<<..<<<<....<<<<<<<<.<<.<<<<<<<.<<.<<<<<....
>>>>>.>>.>>>>>>>.>>.>>>>>>>>....>>>>..>>>>...>>>>>
......>>>>>......>>...>.>>>>>>....>...>>.>>>>>>>..
>>>>>>....>>....<<<<<........>>>>>....<<<<<..<<<..
......<<<<<<.<<<<<<.<<<<<.<<<<<<<<..<<<<<<<<<<<<<<
<<<..........<<<<<......................>>>>>.>>>>
>>>.>>>>>>>>>>...<<<<...>>>>.....>>>>>>>>..>>>>>..
<<<<<<..<<<<<<...>>>>>>>>>>>>.....>>>>>.>.>>>>>>..
.((........<<<<<<...<<.......>>...>>>>>>((....<<<<
.<<<<<..<.<<<<<<<......>>>>>>>...>.<<<.<...))>.>>>
.....>>>>>)).>>>>.<<<<<<<....>>>.>>>>....>>>.>>>>>
....<<<<<<<..<<<<.<.<<<<<.................>>>>>.><
<<<<...<<<<....<<<<<<<<<<))..>>>>>..>>>>>...>>>>..
>>>>>.<<<<...<<<<<...........>>>>>...>>>>.>>>>....
>>>>>>>.....<<<<<.<<.<<<......<<.......<<<....>>>.
...>>........<<<<.....<<<.<<<<<.......>>>>>.>>>...
.>>>>..............>>>>>.>>>>>...<<<<<<<..........
...>>....<<<<<<<<<.<<<....<<<<.<..<<<<<......>>>>>
..>>>>>...>>>....>>>>..>>>>>...>>>>>.

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8i9z Mechanism of 5S RNP recruitment and helicase-surveilled rRNA maturation during pre-60S biogenesis.
• Resolution: 2.7 Å
• Binding residue (original residue number in PDB): R32 T41 M43 A44 K45 N46 K47 R48 Q49 Y51 V53 S54 A57 H59 Q60 T61 S62 R70 A71 V72 R74 P76 G82 T83 R85 Q88 N93 M94 C95 R96 S97 R99 M100 F101 A102 P103 W107 R108 K113 I114 N115 Q116 Q118 K119 R120 F121 R139 T166 K190 L191 R192 A193 G194 K195 K197 M198 R199 R201 R204 R206 R207 Y213 V223 K224 R227 N228 T234 C235 A239 N241 P247 G248 H250 K272 K273 F276 S288 I291 N292 T294 Q297 P303 K304 G305 E306 A307 R308 T309 K310 R311 A312 V314 Q315 K317 R321 N322 K323 Q324 R328 G342 E343 V344 K345 A346 K350 P351 V354 L362
• Binding residue (residue number reindexed from 1): R29 T38 M40 A41 K42 N43 K44 R45 Q46 Y48 V50 S51 A54 H56 Q57 T58 S59 R67 A68 V69 R71 P73 G79 T80 R82 Q85 N90 M91 C92 R93 S94 R96 M97 F98 A99 P100 W104 R105 K110 I111 N112 Q113 Q115 K116 R117 F118 R136 T163 K187 L188 R189 A190 G191 K192 K194 M195 R196 R198 R201 R203 R204 Y210 V220 K221 R224 N225 T231 C232 A236 N238 P244 G245 H247 K269 K270 F273 S285 I288 N289 T291 Q294 P300 K301 G302 E303 A304 R305 T306 K307 R308 A309 V311 Q312 K314 R318 N319 K320 Q321 R325 G339 E340 V341 K342 A343 K347 P348 V351 L359

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8i9z, PDBe:8i9z, PDBj:8i9z
• PDBsum: 8i9z
• PubMed: 37129998
• UniProt: G0SFC3