Structure of PDB 6lss Chain Y Binding Site BS01

Receptor Information

>6lss Chain Y (length=153) Species: 9606 (Homo sapiens)

VRYSLDPENPTKSCKSRGSNLRVHFKNTRETAQAIKGMHIRKATKYLKDV
TLQKQCVPFRRYNGGVGRCAQAKQWGWTQGRWPKKSAEFLLHMLKNAESN
AELKGLDVDSLVIEHIQVNKAPKMRRRTYRAHGRINPYMSSPCHIEMILT
EKE

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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..>>>>>..<<<<<<<<<<...<<..<<<<........<<<<<<<<....
<<<<......>>>>.....((......<<<.....))>>>...>.>>>>>
>>...>>>>..>>..>>>>>>>>>>.......<<<<<<<........>>>
>>>>.....<<<<<..((((((>>>>>..>>>..................
................<<....>>...............<<<......>>
>..................................<<<<<<<<..<<<.<
<...<<<<<<<<.<<<.....<<<<<<<<<<<..<<<<<<<.......<<
....<<<<.<<<..<........>>>>>>>>>>......>>>>...>>>>
>>>>>>>>>>......>>>.>>>.>>>>>...<<<<<<<.<<<<<<<<<<
<<<<<...<<..<<<.<<.<<<<......<<<<<<<<..>>>>>>>>...
....>>>>.>>>>>........>>>>>>..>>>>>>>>>>>.........
...........<<<<<<.<<<<<<<............>>>>>>>.<<<<<
<.<<<<.<<<<<<<<<<..<<<<<.<<<<<.<.<........>>..>>>>
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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): V2 R3 Y4 L6 K16 R18 S20 R23 H25 F26 K27 R30 Q34 K43 R62 Y63 N64 G65 G66 G68 R69 A71 Q72 K74 W78 Q80 R82 W83 P84 K85 K86 N97 S100 N101 Q118 V119 R127 T129 Y130 R131 A132 H133 G134 N137 P138 Y139 M140 S141
• Binding residue (residue number reindexed from 1): V1 R2 Y3 L5 K15 R17 S19 R22 H24 F25 K26 R29 Q33 K42 R61 Y62 N63 G64 G65 G67 R68 A70 Q71 K73 W77 Q79 R81 W82 P83 K84 K85 N96 S99 N100 Q117 V118 R126 T128 Y129 R130 A131 H132 G133 N136 P137 Y138 M139 S140

Gene Ontology

Molecular Function

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

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• GO:0005634 nucleus
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0015934 large ribosomal subunit
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6lss, PDBe:6lss, PDBj:6lss
• PDBsum: 6lss
• PubMed: 32669547
• UniProt: P18621|RL17_HUMAN Large ribosomal subunit protein uL22 (Gene Name=RPL17)