Structure of PDB 7zw0 Chain LG Binding Site BS01

Receptor Information

>7zw0 Chain LG (length=361) Species: 580240 (Saccharomyces cerevisiae W303)

SRPQVTVHSLTGEATANALPLPAVFSAPIRPDIVHTVFTSVNKNKRQAYA
VSEKAGHQTSAESWGTGRAVARIPRVGGGGTGRSGQGAFGNMCRGGRMFA
PTKTWRKWNVKVNHNEKRYATASAIAATAVASLVLARGHRVEKIPEIPLV
VSTDLESIQKTKEAVAALKAVGAHSDLLKVLKSKKLRAGKGKYRNRRWTQ
RRGPLVVYAEDNGIVKALRNVPGVETANVASLNLLQLAPGAHLGRFVIWT
EAAFTKLDQVWGSETVASSKVGYTLPSHIISTSDVTRIINSSEIQSAIRP
AGQATQKRTHVLKKNPLKNKQVLLRLNPYAKVFAAEKLGSKKAEKTGTKP
AAVFTETLKHD

Ligand information

>7zw0 Chain LA (length=3217)

uugaccucaaaucagguaggaguacccgcugaacuuaagcauaucaauaa
gcggaggaaaagaaaccaaccgggauugccuuaguaacggcgagugaagc
ggcaaaagcucaaauuugaaaucugguaccuucggugcccgaguuguaau
uuggagagggcaacuuuggggccguuccuugucuauguuccuuggaacag
gacgucauagagggugagaaucccguguggcgaggagugcgguucuuugu
aaagugccuucgaagagucgaguuguuugggaaugcagcucuaagugggu
gguaaauuccaucuaaagcuaaauauuggcgagagaccgauagcgaacaa
guacagugauggaaagaugaaaagaacuuugaaaagagagugaaaaagua
cgugaaauuguugaaagggaagggcauuugaucagacaugguguuuugua
uuucacuggccagcaucaguuuugguggcaggauaaauccauaggaaugu
agcuugccucgguaaguauuauagccugugggaauacugccagcugggac
ugaggacugcgacguaagucaaggaugcuggcauaaugguuauaugccgc
ccgucuugaaacacggaccaaggagucuaacgucuaugcgaguguuuggg
uguaaaacccauacgcguaaugaaagugaacguagguuggggccucgcaa
gaggugcacaaucgaccgauccugaugucuucggauggauuugaguaaga
gcauagcuguugggacccgaaagauggugaacuaugccugaauaggguga
agccagaggaaacucugguggaggcucguagcgguucugacgugcaaauc
gaucgucgaauuuggguauaggggcgaaagacuaaucgaaccaucuagua
gcugguuccugccgaaguuucccucaggauagcagaagcucguaucaguu
uuaugagguaaagcgaaugauuagagguuccggggucgaaaugaccuuga
ccuauucucaaacuuuaaauauguaagaaguccuuguuacuuaauugaac
guggacauuugaaugaagagcuuuuagugggccauuuuugguaagcagaa
cuggcgaugcgggaugaaccgaacguagaguuaaggugccggaauacacg
cucaucagacaccacaaaagguguuaguucaucuagacagccggacggug
gccauggaagucggaauccgcuaaggaguguguaacaacucaccggccga
augaacuagcccugaaaauggauggcgcucaagcguguuaccuauacucu
accgucaggguugauaugaugcccugacgaguaggcaggcguggagguca
gugacgaagccuagaccguaaggucgggucgaacggccucuagugcagau
cuuggugguaguagcaaauauucaaaugagaacuuugaagacugaagugg
ggaaagguuccacgucaacagcaguuggacguggguuagucgauccuaag
agauggggaagcuccguuucaaaggccugauuuuaugcaggccaccaucg
aaagggaauccgguuaagauuccggaaccuggauauggauucuucacggu
aacguaacugaauguggagacgucggcgcgagcccugggaggaguuaucu
uuucuucuuaacagcuuaucaccccggaauugguuuauccggagaugggg
ucuuauggcuggaagaggccagcaccuuugcuggcuccggugcgcuugug
acggcccgugaaaauccacaggaaggaauaguuuucaugccaggucguac
ugauaaccgcagcaggucuccaaggugaacagccucuaguugauagaaua
auguagauaagggaagucggcaaaauagauccguaacuucgggauaagga
uuggcucuaagggucggguacgaucaacuuagaacugguacggacaaggg
gaaucugacugucuaauuaaaacauagcauugcgauggucagaaagugau
guugacgcaaugugauuucugcccagugcucugaaugucaaagugaagaa
auucaaccaagcgcggguaaacggcgggaguaacuaugacucucuuaagg
uagccaaaugccucgucaucuaauuagugacgcgcaugaauggauuaacg
agauucccacugucccuaucuacuaucuagcgaaaccacagccaagggaa
cgggcuuggcagaaucagcggggaaagaagacccuguugagcuugacucu
aguuugacauugugaagagacauagaggguguagaauaagugggagcuuc
ggcgccagugaaauaccacuaccuuuauaguuucuuuacuuauucaauga
agcggagcuggaauuccacguucuagcauucaaggucccauucggggcug
auccggguugaagacauugucagguggggaguuuggcuggggcggcacau
cuguuaaacgauaacgcagauguccuaaggggggcucauggagaacagaa
aucuccaguagaacaaaaggguaaaagcccccuugauuuugauuuucagu
gugaauacaaaccaugaaaguguggccuaucgauccuuuagucccucgga
auuugaggcuagaggugccagaaaaguuaccacagggauaacuggcuugu
ggcagucaagcguucauagcgacauugcuuuuugauucuucgaugucggc
ucuuccuaucauaccgaagcagaauucgguaagcguuggauuguucaccc
acuaauagggaacgugagcuggguuuagaccgucgugagacagguuaguu
uuacccuacugaugaauguuaccgcaauaguaauugaacuuaguacgaga
ggaacaguucauucggauaauugguuuuugcggcugucugaucaggcauu
gccgcgaagcuaccauccgcuggauuauggcugaacgccucuaagucaga
auccaugcuagaacgcggugauuucuuugcuccacacaauauagauggau
acgaauaaggcguccuuguggcgucgcugaaccauagcaggcuagcaacg
gugcacuuggcggaaaggccuugggugcuugcuggcgaauugcaauguca
uuuugcguggggauaaaucauuuguauacgacuuagauguacaacggggu
auuguaagcaguagaguagccuuguuguuacgaucugcugagauuaagcc
uuuguugucugauuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7zw0 Sensing of individual stalled 80S ribosomes by Fap1 for nonfunctional rRNA turnover.
• Resolution: 2.4 Å
• Binding residue (original residue number in PDB): R31 I34 H36 T40 K44 N45 K46 R47 Q48 Y50 V52 S53 E54 A56 H58 Q59 T60 S61 T67 G68 A70 V71 A72 R73 P75 R76 G80 G81 T82 R84 Q87 G88 N92 M93 R95 G96 R98 M99 F100 A101 K104 W106 R107 K108 K112 V113 N114 H115 N116 E117 K118 R119 R138 R141 K161 T162 K180 K183 S184 K186 L187 R188 A189 G190 K191 Y194 R195 N196 R197 W199 R202 R203 Y209 V216 K217 R220 N221 T227 A231 S232 N234 P240 G241 H243 K271 V272 N291 R300 A302 G303 A305 Q307 K308 R309 V312 L313 K315 N320 Q322 R326 N328 A331 K332 F334 A335 G340 S341 K342 K343 A344 K346 T347 T349 P351 L359 K360
• Binding residue (residue number reindexed from 1): R30 I33 H35 T39 K43 N44 K45 R46 Q47 Y49 V51 S52 E53 A55 H57 Q58 T59 S60 T66 G67 A69 V70 A71 R72 P74 R75 G79 G80 T81 R83 Q86 G87 N91 M92 R94 G95 R97 M98 F99 A100 K103 W105 R106 K107 K111 V112 N113 H114 N115 E116 K117 R118 R137 R140 K160 T161 K179 K182 S183 K185 L186 R187 A188 G189 K190 Y193 R194 N195 R196 W198 R201 R202 Y208 V215 K216 R219 N220 T226 A230 S231 N233 P239 G240 H242 K270 V271 N290 R299 A301 G302 A304 Q306 K307 R308 V311 L312 K314 N319 Q321 R325 N327 A330 K331 F333 A334 G339 S340 K341 K342 A343 K345 T346 T348 P350 L358 K359

Gene Ontology

Molecular Function

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

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• GO:0005634 nucleus
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:7zw0, PDBe:7zw0, PDBj:7zw0
• PDBsum: 7zw0
• PubMed: 36113412
• UniProt: P10664|RL4A_YEAST Large ribosomal subunit protein uL4A (Gene Name=RPL4A)