Structure of PDB 8cdr Chain GG Binding Site BS01

Receptor Information

>8cdr Chain GG (length=361) Species: 4932 (Saccharomyces cerevisiae)

SRPQVTVHSLTGEATANALPLPAVFSAPIRPDIVHTVFTSVNKNKRQAYA
VSEKAGHQTSAESWGTGRAVARIPRVGGGGTGRSGQGAFGNMCRGGRMFA
PTKTWRKWNVKVNHNEKRYATASAIAATAVASLVLARGHRVEKIPEIPLV
VSTDLESIQKTKEAVAALKAVGAHSDLLKVLKSKKLRAGKGKYRNRRWTQ
RRGPLVVYAEDNGIVKALRNVPGVETANVASLNLLQLAPGAHLGRFVIWT
EAAFTKLDQVWGSETVASSKVGYTLPSHIISTSDVTRIINSSEIQSAIRP
AGQATQKRTHVLKKNPLKNKQVLLRLNPYAKVFAAEKLGSKKAEKTGTKP
AAVFTETLKHD

Ligand information

>8cdr Chain AA (length=3197)

uugaccucaaaucagguaggaguacccgcugaacuuaagcauaucaauaa
gcggaggaaaagaaaccaaccgggauugccuuaguaacggcgagugaagc
ggcaaaagcucaaauuugaaaucugguaccuucggugcccgaguuguaau
uuggagagggcaacuuuggggccguuccuugucuauguuccuuggaacag
gacgucauagagggugagaaucccguguggcgaggagugcgguucuuugu
aaagugccuucgaagagucgaguuguuugggaaugcagcucuaagugggu
gguaaauuccaucuaaagcuaaauauuggcgagagaccgauagcgaacaa
guacagugauggaaagaugaaaagaacuuugaaaagagagugaaaaagua
cgugaaauuguugaaagggaagggcauuugaucagaggccagcaucaguu
uugguggcaggauaaauccauaggaauguagcuugccucgguaaguauua
uagccugugggaauacugccagcugggacugaggacugcgacguaaguca
aggaugcuggcauaaugguuauaugccgcccgucuugaaacacggaccaa
ggagucuaacgucuaugcgaguguuuggguguaaaacccauacgcguaau
gaaagugaacguagguuggggccucgcaagaggugcacaaucgaccgauc
cugaugucuucggauggauuugaguaagagcauagcuguugggacccgaa
agauggugaacuaugccugaauagggugaagccagaggaaacucuggugg
aggcucguagcgguucugacgugcaaaucgaucgucgaauuuggguauag
gggcgaaagacuaaucgaaccaucuaguagcugguuccugccgaaguuuc
ccucaggauagcagaagcucguaucaguuuuaugagguaaagcgaaugau
uagagguuccggggucgaaaugaccuugaccuauucucaaacuuuaaaua
uguaagaaguccuuguuacuuaauugaacguggacauuugaaugaagagc
uuuuagugggccauuuuugguaagcagaacuggcgaugcgggaugaaccg
aacguagaguuaaggugccggaauacacgcucaucagacaccacaaaagg
uguuaguucaucuagacagccggacgguggccauggaagucggaauccgc
uaaggaguguguaacaacucaccggccgaaugaacuagcccugaaaaugg
auggcgcucaagcguguuaccuauacucuaccgucaggguugauaugaug
cccugacgaguaggcaggcguggaggucagugacgaagccuagaccguaa
ggucgggucgaacggccucuagugcagaucuuggugguaguagcaaauau
ucaaaugagaacuuugaagacugaaguggggaaagguuccacgucaacag
caguuggacguggguuagucgauccuaagagauggggaagcuccguuuca
aaggccugauuuuaugcaggccaccaucgaaagggaauccgguuaagauu
ccggaaccuggauauggauucuucacgguaacguaacugaauguggagac
gucggcgcgagcccugggaggaguuaucuuuucuucuuaacagcuuauca
ccccggaauugguuuauccggagauggggucuuauggcuggaagaggcca
gcaccuuugcuggcuccggugcgcuugugacggcccgugaaaauccacag
gaaggaauaguuuucaugccaggucguacugauaaccgcagcaggucucc
aaggugaacagccucuaguugauagaauaauguagauaagggaagucggc
aaaauagauccguaacuucgggauaaggauuggcucuaagggucgacgau
caacuuagaacugguacggacaaggggaaucugacugucuaauuaaaaca
uagcauugcgauggucagaaagugauguugacgcaaugugauuucugccc
agugcucugaaugucaaagugaagaaauucaaccaagcgcggguaaacgg
cgggaguaacuaugacucucuuaagguagccaaaugccucgucaucuaau
uagugacgcgcaugaauggauuaacgagauucccacugucccuaucuacu
aucuagcgaaaccacagccaagggaacgggcuuggcagaaucagcgggga
aagaagacccuguugagcuugacucuaguuugacauugugaagagacaua
gaggguguagaauaagugggagcuucggcgccagugaaauaccacuaccu
uuauaguuucuuuacuuauucaaugaagcggagcuggaauucauuuucca
cguucuagcauucaaggucccauucggggcugauccggguugaagacauu
gucagguggggaguuuggcuggggcggcacaucuguuaaacgauaacgca
gauguccuaaggggggcucauggagaacagaaaucuccaguagaacaaaa
ggguaaaagcccccuugauuuugauuuucagugugaauacaaaccaugaa
aguguggccuaucgauccuuuagucccucggaauuugaggcuagaggugc
cagaaaaguuaccacagggauaacuggcuuguggcagucaagcguucaua
gcgacauugcuuuuugauucuucgaugucggcucuuccuaucauaccgaa
gcagaauucgguaagcguuggauuguucacccacuaauagggaacgugag
cuggguuuagaccgucgugagacagguuaguuuuacccuacugaugaaug
uuaccgcaauaguaauugaacuuaguacgagaggaacaguucauucggau
aauugguuuuugcggcugucugaucaggcauugccgcgaagcuaccaucc
gcuggauuauggcugaacgccucuaagucagaauccaugcuagaacgcgg
ugauuucuuugcuccacacaauauagauggauacgaauaaggcguccuug
uggcgucgcugaaccauagcaggcuagcaacggugcacuuggcggaaagg
ccuugggugcuugcuggcgaauugcaaugucauuuugcguggggauaaau
cauuuguauacgacuuagauguacaacgggguauuguaagcaguagagua
gccuugguuacgaucugcugagauuaagccuuuguugucugauuugu

........................<<<<<<.....<......>......>
>>>>.>.........<<....>>..<<<<<......<<.....>>.....
>>>>>..<<<...<.......<<.<<<<<<...>>>>>>.>>.......>
.....<<<<<<.<<<<<..<<<<<<<<<<<<<<<....<<<<......>>
>>.(.......<<<......)>>>..>.>>>>>>>>>..>>>>>......
>>>>>>>>>>>........<<<<<<<........>>>>>>>.....<<<<
<..((((((>>>>>..>>>...............................
...<<....>>...............<<<<....>>>>............
......................<<<<<.<<<<<....<<<<<<<.<<<<<
<<<<<<<<<<.....<<<<<<<<<......<<<<<<<..>>>>>>>....
...>>>>>>>.>.>.>>>>>.>>>>>>>>>>........<<<....>>>.
....>>>>>>>.....>>>>>.>>>>>..<<<<........>>>><<<<<
<...<<<<<<<.<<<<<<..<<<...<<<<.....>>>>...>>>...<<
....>>.......<<<<<..<<<<<....>>>>>...>>>>>.<<<<<<<
<...<<....>>...>>>.>>>.>>....>>>>>>.>>>>>>>.<<.<..
<<<<<<<.....<<<<<<<<<..<<<....<<<<<<<....>>>>>>>..
...>>>...<<<..<<.<<........>>>>.>>>....>>>>>>>>>..
.<<.......>>......>>>>>>...>..>.>>..<<<<<<....<.<<
<....>>>.><<<<<<<<<<...<<<.<<<<<<<.....<<<....<<<.
.<.<<<<....<<<<<.....>>>>>..>>>>.>..>>>..>.>>.....
>>>>>...<<<<.<<<<.<......>>>>>.>>>>.....>>>>>.>>>>
>>>>.>>..<<<<.<<<<<.....>>>>>.>>>>....<<<......>>>
...<<<<<<<..<<<<(((.....<<<<<<......<..........<<<
.<<<<<<<<<<.......<<<<<.<<<...<<.........>>...>>>.
........<<......>>...>>>>>...>>>>>>>>>>>>>........
..))).>....>>>>>>.>>>>..>>>>>>><<<<<<<<<.........>
>>>>>>>>....>>>>>>..<<<<<<<<.<<......<<<<.<<<<....
>>>>>>>>...>>>>>>>>>>........>>>>>><<.....<<.....<
<<<<<.......>>>>>><<<<.....<<<<<.<<...<<<<<<...<<.
....>>.>>>>>>....((<<<<<<...<<....<<<....>>>......
...<..<...........>..>....>>....>>...<<<<<........
>>>>>))<<<<.<<<<<<<.....<<<....>>>...<...<<<<<<...
<<<<.<<<<<<<.<<<<<<<<<<..[[[..>>>>>><...<<<<<....<
<<<<<....<<<.....>>>....>>>>>>.....>>>>>....><<<<<
<<<....>>>>>>>>>>>>...>>>>>>>.>>>>.........>>>>>>.
..>......>>>..>>>>>>>>>>>>..>>.....<<......>>>>>>>
.<<<<.....>>>>..>>>>..<<<<.....<<<<<<<.<<.........
......<<<<<....<....>.....>>>>><<.<<<<<<<<<<<.>>>>
>..>>>>>>.>>............<<<<<<<<<..<<<.........>>>
..<<<<<<<....<<<<.....>>>>......>>>>>>>...<<..<<<.
.<<<<<<....<<<.....<<<<....>>>>.....>>>.>>>>..>>>>
><<<<<<.......>>>>>>........<...........<<<<<.....
..>>>>>.....>.....>>....>>.>>>>>>>.....>>.>>>>>>>.
.>>>>>>....>>....<<<<<........>>>>>....<<<<<..<<<.
<<......<<<<.<<<<<<..<<<<<.<<<<<<<<..<<<<<<<<<<<<.
<<<<<..........................................>>>
>>>>.>>>>>>>>>>...<<<<<.....<<<<..<<<<<......>>>>>
...............<<<<<<....>>>>>>..>>>>..>>>>>.....>
>>>>>>>..>>>>>...<<<.....>>>..<<<<<<...........>>>
>>>..<<...<<<<<<<...<<<<<<.......>>>>>>.....<<...(
((>>....>>>>>>>...<<<.<<<<<.......>>>>.>>>>.<<<...
.>>>.>>)))......<<<<<<<..<<<<.))))))>>>>>>>>>>>...
......>>>>..>>>>>>.......<<.<...<<<<<<...<<.......
>>...>>>>>>....>.>.>.......<<<<<.<<<<<<..<.<<<<<<<
......>>>>>>>...>.<<<.........>>>.....>>>>>..>...>
>>.>>....<<<<<<<....>>>.>>>>....>>..>>>.>>>>>....<
<<<<<<<..<<<<.<.<<<<<<...............>>>>>>.><<<<<
...<<<<....<<<<<<<<<<]]].>>>>>..>>>>>...>>>>..>>>>
>.<<<<...<<<<<...........>>>>>...>>>>.>>>>....>>>>
>>>>.......<<<<<<.<<<.<<....<<..........<<<<<<....
.>>>>>>......>>.......<<<<<<...<<<<<.<..<<<......>
>>..>.>>>>>.>>>>>>.............>>.>>>.>>>>>>..<<<<
<.<.............>.....<<<<<<<<<.<<<....<<<<.<..<<<
<<....>>>>>..>>>>>...>>>....>>>>.>>>>>..>>>>>..

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8cdr mRNA reading frame maintenance during eukaryotic ribosome translocation
• Resolution: 2.04 Å
• Binding residue (original residue number in PDB): R31 I34 H36 T40 N43 K44 N45 K46 R47 Q48 Y50 V52 S53 E54 A56 G57 H58 Q59 T60 S61 T67 G68 A70 V71 A72 R73 I74 P75 R76 G80 G81 T82 R84 Q87 G88 N92 M93 C94 R95 G96 R98 M99 F100 A101 P102 K104 W106 R107 K108 K112 V113 N114 H115 N116 E117 K118 R119 Y120 R138 G139 R141 K161 T162 K163 K180 L182 K183 S184 K186 L187 R188 A189 G190 K191 K193 Y194 R195 N196 R197 W199 R202 R203 Y209 V216 K217 R220 N221 P223 T227 A228 S232 N234 P240 G241 H243 K271 V272 N291 R300 A302 G303 Q304 A305 Q307 K308 R309 H311 V312 L313 K314 K315 N316 N320 Q322 L325 R326 N328 A331 K332 F334 A335 G340 S341 K342 K343 A344 T347 T349 P351 F355 L359
• Binding residue (residue number reindexed from 1): R30 I33 H35 T39 N42 K43 N44 K45 R46 Q47 Y49 V51 S52 E53 A55 G56 H57 Q58 T59 S60 T66 G67 A69 V70 A71 R72 I73 P74 R75 G79 G80 T81 R83 Q86 G87 N91 M92 C93 R94 G95 R97 M98 F99 A100 P101 K103 W105 R106 K107 K111 V112 N113 H114 N115 E116 K117 R118 Y119 R137 G138 R140 K160 T161 K162 K179 L181 K182 S183 K185 L186 R187 A188 G189 K190 K192 Y193 R194 N195 R196 W198 R201 R202 Y208 V215 K216 R219 N220 P222 T226 A227 S231 N233 P239 G240 H242 K270 V271 N290 R299 A301 G302 Q303 A304 Q306 K307 R308 H310 V311 L312 K313 K314 N315 N319 Q321 L324 R325 N327 A330 K331 F333 A334 G339 S340 K341 K342 A343 T346 T348 P350 F354 L358

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:8cdr, PDBe:8cdr, PDBj:8cdr
• PDBsum: 8cdr
• PubMed: 38030725
• UniProt: P10664|RL4A_YEAST Large ribosomal subunit protein uL4A (Gene Name=RPL4A)