Structure of PDB 8pv2 Chain LA Binding Site BS01

Receptor Information

>8pv2 Chain LA (length=191) Species: 759272 (Thermochaetoides thermophila DSM 1495)

RKAPAKFRPLDYAERHGYIRGIVKEIIHDPGRGAPLARVVFRSPYKYKQI
TETFIANEGMYTGQFIYAGKNAALTVGNILPLSSVPEGTVVSNVEEKPGD
RGALGRTSGNYVTVVGHNPDEGKTRIKLPSGAKKVVPSSSRGMIGIVAGG
GRTDKPLLKASRAKHKFAVKRNRWPKTRGVAMNPVDHPHGG

Ligand information

>8pv2 Chain C1 (length=3056)

uugaccucggaucagguaggaggacccgcugaacuuaagcauaucaauaa
gcggaggaaaagaaaccaacagggauugcccuaguaacggcgagugaagc
ggcaacagcucaaauuugaaagcuggcuucggcccgcguuguaauuugga
gaggaugcuuugggcgaggcuccuucugaguucccuggaacgggacgcca
cagagggugagagccccguauaguuggaagccaagccuguguaaagcucc
uucgacgagucgaguaguuugggaaugcugcucaaaaugggagguaaauu
ucuucuaaagcuaaauaccggccagagaccgauagcgcacaaguagagug
aucgaaagaugaaaagcacuuugaaaagaggguuaaauagcacgugaaau
uguugaaagggaagcgcuugugaccagacuugcgcccggcggaucauccg
guguucucaccggugcacuccgccgggcucaggccagcaucgguucuggc
ggggggauaaaggcccagggaauguggcuccuccgggaguguuauagccc
uggguguaauacccucgccgggaccgaggaccgcgcucugcaaggaugcu
ggcguaauggucaccagcgacccgucuugaaacacggaccaaggagucaa
gguuuugcgcgaguguuuggguguaaaacccgcacgcguaaugaaaguga
acguaggugagagcuucggcgcaucaucgaccgauccugauguauucgga
uggauuugaguaggagcguuaagccuuggacccgaaagauggugaacuau
gcuuggauagggugaagccagaggaaacucugguggaggcucgcagcggu
ucugacgugcaaaucgaucgucaaaucugagcaugggggcgaaagacuaa
ucgaaccaucuaguagcugguuaccgccgaaguuucccucaggauagcag
ugucgaccuucaguuuuaugagguaaagcgaaugaacuuuaaauauguaa
gaagcccuuguuacuuaacugaacgugggcauucgaauguaucgacacua
gugggccauuuuugguaagcagaacuggcgaugcgggaugaaccgaacgc
gggguuaaggugccggaguggacgcucaucagacaccacaaaaggcguua
guacaucuugacagcaggacgguggccauggaagucggaauccgcuaagg
acuguguaacaacucaccugccgaauguacuagcccugaaaauggauggc
gcucaagcgucccacccauaccccgcccucaggguagaaacgaugcccug
aggaguaggcggccguggaggucagugacgaagccuagggcgugagcccg
ggucgaacggccucuagugcagaucuuggugguaguagcaaauacuucaa
ugagaacuugaaggaccgaaguggggaaagguuccaugugaacagcgguu
ggacauggguuagucgauccuaagccauagggaaguuccguuucaaaggg
gcaugccccguguggcgaaagggaagccgguuaauauuccggcaccugga
uguggguuuugcgcggcaacgcaacugaacgcggagacgacggcgggggc
cccgggcagaguucucuuuucuucuuaacggucuaucacccuggaaacag
uuugucuggagauaggguuuaauggccggaagagcccgacacuucugucg
gguccggugcgcucucgacgucccuugaaaauccgcgggagggaauaauu
cucacgccaggucguacucauaaccgcagcagguccccaaggugaacagc
cucugguugauagaacaauguagauaagggaagucggcaaaauagauccg
uaacuucgggaaaaggauuggcucuaaggguugguaacaaccaacuuaga
acugguacggacagggggaaucugacugucuaauuaaaacauagcauugc
gauggccagaaagugguguugacgcaaugugauuucugcccagugcucug
aaugucaaagugaagaaauucaaccaagcgcggguaaacggcgggaguaa
cuaugacucucuguagccaaauggauuaacgagauucccacugucccuau
cuacuaucuagcgaaaccacagccaagggaacgggcuuggcaaaaucagc
ggggaaagaagacccuguugagcuugacucuaguuugacauugugaaaag
auuuuuuuacuuauucaaugaagcggggcuggacuugcguccaacuucug
gaguuaagguccuucgcgggccgacccggguugaagacauugucaggugg
ggaguuuggcuggggcggcacaucugugcagguguccuaaggggggcuca
uggagaacagaaaucuccaguagaacaaaaggguaaaaguccccuugauu
uugauuuucagugugaauacaaaccaugaaaguguggccuaucgauccuu
uagucccucgaaauuugaggcuagaggugccagaaaaguuaccacaggga
uggcuuguggcggccaagcguucauagcgacgucgcuuugauccuucgau
gucggcucuuccuaucauaccgaagcagaauucgguaagcguuggauugu
ucacccacuaauagggaacgugagcuggguuuagaccgucgugagacagg
uuaguuuuacccuacugaugaacucgucgcaaugguaauucagcuuagua
cgagaggaaccgcugauucagauaauugguuuuugcgguuguccgaccgg
gcagugccgcgaagcuaccaucugcuggauaauggcugaacgccucuaag
ucagaauccaugccagaacgcgacgauacuacccgcacguuguagacgua
uaagaauaggcuccggccucguauccuagcaggcgauuccuccgccggcc
ucgaaguggccgucgguaauucgcguauugcaauuuagacacgcgcggga
ucaaauccuuugcagacgacuuagaugugcgaaaggguccuguaagcagu
agaguagccuuguuguuacgaucugcugaggguaagcccuccuucgccua
gauuuc

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8pv2 Structural insights into coordinating 5S RNP rotation with ITS2 pre-RNA processing during ribosome formation.
• Resolution: 2.63 Å
• Binding residue (original residue number in PDB): R23 K24 A25 P26 P31 Y34 R37 H38 G39 Y40 I44 H50 P52 R54 R64 Y67 K68 Y69 K70 G85 F87 Y89 A94 A95 E118 A125 L126 G127 R128 T129 S130 G131 N132 L150 P151 S152 K156 G173 R174 K177 L179 L180 K181 A182 S183 A185 K186 H187 K188 K192 R193 N194 W196 P197 K198 T199 R200 G201 V202 A203 M204 N205 V207 D208 H209 G213
• Binding residue (residue number reindexed from 1): R1 K2 A3 P4 P9 Y12 R15 H16 G17 Y18 I22 H28 P30 R32 R42 Y45 K46 Y47 K48 G63 F65 Y67 A72 A73 E96 A103 L104 G105 R106 T107 S108 G109 N110 L128 P129 S130 K134 G151 R152 K155 L157 L158 K159 A160 S161 A163 K164 H165 K166 K170 R171 N172 W174 P175 K176 T177 R178 G179 V180 A181 M182 N183 V185 D186 H187 G191

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:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8pv2, PDBe:8pv2, PDBj:8pv2
• PDBsum: 8pv2
• PubMed: 37921038
• UniProt: G0S4P8