Structure of PDB 6lss Chain F Binding Site BS01

Receptor Information

>6lss Chain F (length=109) Species: 9606 (Homo sapiens)

VQRLTYRRRLSYNTASNKTRLSRTPGNRIVYLYTKKVGKAPKSACGVCPG
RLRGVRAVRPKVLMRLSKTKKHVSRAYGGSMCAKCVRDRIKRAFLIEEQK
IVVKVLKAQ

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 R4 L5 T6 Y7 R8 R10 L11 S12 Y13 N14 T15 S17 K19 R21 R24 T25 P26 G27 N28 R29 I30 Y32 K40 P42 K43 R54 G55 P61 K62 L64 M65 R66 S68 K69 T70 K72 V74 S75 R76 Y78 G80 R88 R90 R93 A94 I97 E98 K101
• Binding residue (residue number reindexed from 1): V1 R3 L4 T5 Y6 R7 R9 L10 S11 Y12 N13 T14 S16 K18 R20 R23 T24 P25 G26 N27 R28 I29 Y31 K39 P41 K42 R53 G54 P60 K61 L63 M64 R65 S67 K68 T69 K71 V73 S74 R75 Y77 G79 R87 R89 R92 A93 I96 E97 K100

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

Cellular Component

• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005783 endoplasmic reticulum
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:0045202 synapse
• GO:0070062 extracellular exosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6lss, PDBe:6lss, PDBj:6lss
• PDBsum: 6lss
• PubMed: 32669547
• UniProt: P49207|RL34_HUMAN Large ribosomal subunit protein eL34 (Gene Name=RPL34)