Structure of PDB 6lss Chain U Binding Site BS01

Receptor Information

>6lss Chain U (length=203) Species: 9606 (Homo sapiens)

GAYKYIQELWRKKQSDVMRFLLRVRCWQYRQLSALHRAPRPTRPDKARRL
GYKAKQGYVIYRIRVRRGGRKRPVPKGATYGKPVHHGVNQLKFARSLQSV
AEERAGRHCGALRVLNSYWVGEDSTYKFFEVILIDPFHKAIRRNPDTQWI
TKPVHKHREMRGLTSAGRKSRGLGKGHKFHHTIGGSRRAAWRRRNTLQLH
RYR

Ligand information

>6lss Chain 2 (length=3474)

cgcgaccucagaucagacguggcgacccgcugaauuuaagcauauuaguc
agcggaggagaagaaacuaaccaggauucccucaguaacggcgagugaac
agggaagagcccagcgccgaauccccgccccgcggcggggcgcgggacau
guggcguacggaagacccgcuccccggcgccgcucguggggggcccaagu
ccuucugaucgaggcccagcccguggacggugugaggccgguagcggccc
ccggcgcgccgggcccgggucuucccggagucggguugcuugggaaugca
gcccaaagcgggugguaaacuccaucuaaggcuaaauaccggcacgagac
cgauagucaacaaguaccguaagggaaaguugaaaagaacuuugaagaga
gaguucaagagggcgugaaaccguuaagagguaaacgggugggguccgcg
caguccgcccggaggauucaacccggcggcggguccggccgugucggcgg
cccggcggaucuuucccgcgcgggggaccgucccccgaccggcgaccggc
cgccgccgggcgcauuuccaccgcggcggugcgccgcgaccggcuccggg
acggcugggaaggcccggcggggaagguggcucgggggcccccgaguguu
acagcccccccggcagcagcacucgccgaaucccggggccgagggagcga
gacccgucgccgcgcucuccccccucccggcgcgccggggggggccgggc
caccccucccacggcgcgaccgcucggggcggacuguccccagugcgccc
cgggcgggucgcgccgucgggcccgggggaggccacgcgcgcgucccccg
aagagggggacggcggagcgagcgcacggggucggcggcgacgucggcua
cccacccgacccgucuugaaacacggaccaaggagucuaacacgugcgcg
agucgggggcucgcacgaaagccgccguggcgcaaugaaggugaaggccg
gcgcgcucgccggccgaggugggaucccgaggccucuccaguccgccgag
ggcgcaccaccggcccgucucgcccgccgcgccggggagguggagcacga
gcgcacguguuaggacccgaaagauggugaacuaugccugggcagggcga
agccagaggaaacucugguggagguccguagcgguccugacgugcaaauc
ggucguccgaccuggguauaggggcgaaagacuaaucgaaccaucuagua
gcugguucccuccgaaguuucccucaggauagcuggcgcucucgcagacc
cgacgcccgccacgcaguuuuauccgguaaaacuuuaaauggguaagaag
cccggcucgcuggcguggagccgggcguggaaugcgagugccuagugggc
cacuuuugguaacagaacuggcgcugcgggaugaaccgaacgccggguua
aggcgcccgaugccgacgcucaucagaccccagaaaagguguugguugau
auagacagcaggacaccugccgaaucaacuagcccugaaaauggauggcg
cuggagcgucgggcccauacccggccgucgccggcagucgagaguggacg
ggagcggcggcccggagccccgcggacgcuacgccgcgacgaguaggagg
gccgcugcggugagccuugaagccuagggcgcgggcccggguggagccgc
cgcaggugcagaucuuggugguaguagcaaauauucaaacgagaacuuug
aaggccgaaguggagaaggguuccaugugaacagcaguugaacauggguc
agucgguccugagagaugggcgagcgccguuccgaagggacgggcgaugg
ccuccguugcccucggccgaucgaaagggagucggguucagauccccgaa
uccggaguggcggagaugggcgccgcgaggcguccagugcgguaacgcga
ccgaucccggagaagccggcgggagccccggggagaguucucuuuucuuu
gugaagggcagggcgcccuggaauggguucgccccgagagaggggcccgu
gccuuggaaagcgucgcgguuccggcggcguccggugagcucucgcuggc
ccuugaaaauccgggggagaggguguaaaucucgcgccgggccguaccca
uauccgcagcaggucuccaaggugaacagccucuggcauguuggaacaau
guagguaagggaagucggcaagccggauccguaacuucgggauaaggauu
ggcucuaagggcugggucggucgcggccggcgccuagcagccgacuuaga
acuggugcggaccaggggaauccgacuguuuaauuaaaacaaagcaucgc
gaaggcccgcggcggguguugacgcgaugugauuucugcccagugcucug
aaugucaaagugaagaaauucaaugaagcgcggguaaacggcaagaugaa
cgagauucccacugucccuaccuacuauccagcgaaaccacagccaaggg
aacgggcuuggcggaaucagcggggaaagaagacccuguugagcuugacu
cuagucuggcacggugaaguuuuuucacugacccggugaggcgggggggc
gagccccgaggggcucucgcuucuggcgccaagcgcccggccgcgcgccg
gccgggcgcgacccgcuccggggacagugccagguggggaguuugacugg
ggcgguacaccugucaaacgguaacgcagguguccuaaggcgagcucagg
gaggacagaaaccucccguggagcagaagggcaaaagcucgcuugaucuu
gauuuucaguacgaauacagaccgugaaagcggggccucacgauccuucu
gaccuuuuggguuuuaagcaggaggugucagaaaaguuaccacagggaua
uuguggcggccaagcguucauagcgacgucgcugaugucggcucuuccua
ucauugugaagcagaauucaccaagcguuggauuguucacccacuaauag
ggaacgugagcuggguuuagaccgucgugagacagguuaguuuuacccua
cugaugauguguuguugccaugguaauccugcucaguacgagaggaaccg
cagguucagacauuugguguaugugcuuggcugaggagccaauggggcga
agcuaccaucugugggauuaugacugaacgccucuaagucagaaucccgc
ccaggcggaacgauacggcagcgccgcggagccucgguuggccucggaua
gccggucccccgccgggguccggugcggagugcccuucguccugggaaac
ggggcgcggccggagaggcggccgcccccucgcccgucacgcaccgcacg
uucguggggaaccuggcgcuaaaccauucguagacgaccugcuucugggu
cgggguuucguacguagcagagcagcucccucgcugcgaucuauugaaag
ucagcccucgacacaaggguuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6lss Structural snapshots of human pre-60S ribosomal particles before and after nuclear export.
• Resolution: 3.23 Å
• Binding residue (original residue number in PDB): G2 Y4 R12 K14 Q15 R24 R31 P40 R44 K47 R49 R50 K54 A55 Q57 R65 R67 R68 G69 G70 R73 P74 K77 Y81 G82 K83 P84 V85 H87 N90 Q91 K93 F94 A95 R96 S97 E104 R105 R108 A112 S125 F138 R144 W150 P154 V155 H156 K157 H158 M161 R162 L164 R169 K170 S171 R172 K176 H178 K179 F180 H181 H182 I184 S187 R189 W192 R193 R194 R195 H201 R202 Y203 R204
• Binding residue (residue number reindexed from 1): G1 Y3 R11 K13 Q14 R23 R30 P39 R43 K46 R48 R49 K53 A54 Q56 R64 R66 R67 G68 G69 R72 P73 K76 Y80 G81 K82 P83 V84 H86 N89 Q90 K92 F93 A94 R95 S96 E103 R104 R107 A111 S124 F137 R143 W149 P153 V154 H155 K156 H157 M160 R161 L163 R168 K169 S170 R171 K175 H177 K178 F179 H180 H181 I183 S186 R188 W191 R192 R193 R194 H200 R201 Y202 R203

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0045296 cadherin binding

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0045471 response to ethanol

Cellular Component

• GO:0005634 nucleus
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:0031672 A band
• GO:0044391 ribosomal subunit
• GO:0045202 synapse
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6lss, PDBe:6lss, PDBj:6lss
• PDBsum: 6lss
• PubMed: 32669547
• UniProt: P61313|RL15_HUMAN Large ribosomal subunit protein eL15 (Gene Name=RPL15)