Structure of PDB 7old Chain LR Binding Site BS01

Receptor Information

>7old Chain LR (length=184) Species: 759272 (Thermochaetoides thermophila DSM 1495)

VNLRTQKRLAASVLGCGEGKVWLDPNEVSEISNANSRQSIRKLVADGLII
KKPVTMHSRSRARELNLARRIGRHRGFGKRKGTADARMPQQVLWMRRQRV
LRRLLVKYRASGKIDKHLYHELYHLAKGNTFKHKRALVEHIHRAKAEKAR
ERQIKEEMDAKRARTKAARERKQERQAAKRNALL

Ligand information

>7old Chain 1 (length=3192)

guugaccucggaucagguaggaggacccgcugaacuuaagcauaucaaua
agcggaggaaaagaaaccaacagggauugcccuaguaacggcgagugaag
cggcaacagcucaaauuugaaagcuggcuucggcccgcguuguaauuugg
agaggaugcuuugggcgaggcuccuucugaguucccuggaacgggacgcc
acagagggugagagccccguauaguuggaagccaagccuguguaaagcuc
cuucgacgagucgaguaguuugggaaugcugcucaaaaugggagguaaau
uucuucuaaagcuaaauaccggccagagaccgauagcgcacaaguagagu
gaucgaaagaugaaaagcacuuugaaaagaggguuaaauagcacgugaaa
uuguugaaagggaagcgcuugugaccagacuugcgcccggcggaucaucc
gguguucucaccggugcacuccgccgggcucaggccagcaucgguucugg
cggggggauaaaggcccagggaauguggcuccuccgggaguguuauagcc
cuggguguaauacccucgccgggaccgaggaccgcgcucugcaaggaugc
uggcguaauggucaccagcgacccgucuugaaacacggaccaaggaguca
agguuuugcgcgaguguuuggguguaaaacccgcacgcguaaugaaagug
aacguaggugagagcuucggcgcaucaucgaccgauccugauguauucgg
auggauuugaguaggagcguuaagccuuggacccgaaagauggugaacua
ugcuuggauagggugaagccagaggaaacucugguggaggcucgcagcgg
uucugacgugcaaaucgaucgucaaaucugagcaugggggcgaaagacua
aucgaaccaucuaguagcugguuaccgccgaaguuucccucaggauagca
gugucgaccuucaguuuuaugagguaaagcgaaugauuagggacucgggg
gcgauuuuuagccuucauccauucucaaacuuuaaauauguaagaagccc
uuguuacuuaacugaacgugggcauucgaauguaucgacacuagugggcc
auuuuugguaagcagaacuggcgaugcgggaugaaccgaacgcgggguua
aggugccggaguggacgcucaucagacaccacaaaaggcguuaguacauc
uugacagcaggacgguggccauggaagucggaauccgcuaaggacugugu
aacaacucaccugccgaauguacuagcccugaaaauggauggcgcucaag
cgucccacccauaccccgcccucaggguagaaacgaugcccugaggagua
ggcggccguggaggucagugacgaagccuagggcgugagcccgggucgaa
cggccucuagugcagaucuuggugguaguagcaaauacuucaaugagaac
uugaaggaccgaaguggggaaagguuccaugugaacagcgguuggacaug
gguuagucgauccuaagccauagggaaguuccguuucaaaggggcacucg
ugccccguguggcgaaagggaagccgguuaauauuccggcaccuggaugu
ggguuuugcgcggcaacgcaacugaacgcggagacgacggcgggggcccc
gggcagaguucucuuuucuucuuaacggucuaucacccuggaaacaguuu
gucuggagauaggguuuaauggccggaagagcccgacacuucugucgggu
ccggugcgcucucgacgucccuugaaaauccgcgggagggaauaauucuc
acgccaggucguacucauaaccgcagcagguccccaaggugaacagccuc
ugguugauagaacaauguagauaagggaagucggcaaaauagauccguaa
cuucgggaaaaggauuggcucuaaggguugggcacguuggcggcgugcgg
uuaacaaccaacuuagaacugguacggacagggggaaucugacugucuaa
uuaaaacauagcauugcgauggccagaaagugguguugacgcaaugugau
uucugcccagugcucugaaugucaaagugaagaaauucaaccaagcgcgg
guaaacggcgggaguaacuaugacucucuuaagguagccaaaugccucgu
caucuaauuagugacgcgcaugaauggauuaacgagauucccacuguccc
uaucuacuaucuagcgaaaccacagccaagggaacgggcuuggcaaaauc
agcggggaaagaagacccuguugagcuugacucuaguuugacauugugaa
aagacauaggagcuccuauuguuuuuuuacuuauucaaugaagcggggcu
ggacuugcguccaacuucuggaguuaagguccuucgcgggccgacccggg
uugaagacauugucagguggggaguuuggcuggggcggcacaucuguuaa
accauaacgcagguguccuaaggggggcucauggagaacagaaaucucca
guagaacaaaaggguaaaaguccccuugauuuugauuuucagugugaaua
caaaccaugaaaguguggccuaucgauccuuuagucccucgaaauuugag
gcuagaggugccagaaaaguuaccacagggauaacuggcuuguggcggcc
aagcguucauagcgacgucgcuuuuugauccuucgaugucggcucuuccu
aucauaccgaagcagaauucgguaagcguuggauuguucacccacuaaua
gggaacgugagcuggguuuagaccgucgugagacagguuaguuuuacccu
acugaugaacucgucgcaaugguaauucagcuuaguacgagaggaaccgc
ugauucagauaauugguuuuugcgguuguccgaccgggcagugccgcgaa
gcuaccaucugcuggauaauggcugaacgccucuaagucagaauccaugc
cagaacgcgacgauacuacccgcacguuguagacguauaagaauaggcuc
cggccucguauccuagcaggcgauuccuccgccggccucgaaguggccgu
cgguaauucgcguauugcaauuuagacacgcgcgggaucaaauccuuugc
agacgacuuagaugugcgaaaggguccuguaagcaguagaguagccuugu
uguuacgaucugcugaggguaagcccuccuucgccuagauuu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7old High-resolution structures of a thermophilic eukaryotic 80S ribosome reveal atomistic details of translocation.
• Resolution: 3.0 Å
• Binding residue (original residue number in PDB): N3 R5 T6 K8 G18 E19 K21 L24 P26 S37 R38 R42 T56 H58 S59 R60 S61 R62 R64 N67 R71 R74 H75 R76 G77 F78 G79 R81 K82 G83 T84 R88 W95 R100 R103 R104 R110 H118 Y120 H121 Y124 H125 K135 R136 H143
• Binding residue (residue number reindexed from 1): N2 R4 T5 K7 G17 E18 K20 L23 P25 S36 R37 R41 T55 H57 S58 R59 S60 R61 R63 N66 R70 R73 H74 R75 G76 F77 G78 R80 K81 G82 T83 R87 W94 R99 R102 R103 R109 H117 Y119 H120 Y123 H124 K134 R135 H142

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

External links

• PDB: RCSB:7old, PDBe:7old, PDBj:7old
• PDBsum: 7old
• PubMed: 35079002
• UniProt: G0S9T3