Structure of PDB 8g6j Chain Lf Binding Site BS01

Receptor Information

>8g6j Chain Lf (length=109) Species: 9606 (Homo sapiens)

SGRLWSKAIFAGYKRGLRNQREHTALLKIEGVYARDETEFYLGKRCAYVY
KAKNNTVTPGGKPNKTRVIWGKVTRAHGNSGMVRAKFRSNLPAKAIGHRI
RVMLYPSRI

Ligand information

>8g6j Chain L5 (length=3687)

cgcgaccucagaucagacguggcgacccgcugaauuuaagcauauuaguc
agcggaggagaagaaacuaaccaggauucccucaguaacggcgagugaac
agggaagagcccagcgccgaauccccgccccgcggcggggcgcgggacau
guggcguacggaagacccgcuccccggcgccgcucguggggggcccaagu
ccuucugaucgaggcccagcccguggacggugugaggccgguagcggccc
ccggcgcgccgggcccgggucuucccggagucggguugcuugggaaugca
gcccaaagcgggugguaaacuccaucuaaggcuaaauaccggcacgagac
cgauagucaacaaguaccguaagggaaaguugaaaagaacuuugaagaga
gaguucaagagggcgugaaaccguuaagagguaaacgggugggguccgcg
caguccgcccggaggauucaacccggcggcggguccggccgugucggcgc
ggcggaucuuucccgcgggggaccgucccccgaccggcgaccggccgccg
ccgggcgcauuuccaccgcggcggugcgccgcgaccggcuccgggacggc
ugggaaggcccggcggggaagguggcucgggggcccccgaguguuacagc
ccccccggcagcagcacucgccgaaucccggggccgagggagcgagaccc
gucgccgcgcucuccccccugggggggccgggccaccccucccacggcgc
gaccgcucggggcggacuguccccagugcgccccgggcgggucgcgccgu
cgggcccggggggccacgcgcgcgucccccgaagagggggacggcggagc
gagcgcacggggucggcggcgacgucggcuacccacccgacccgucuuga
aacacggaccaaggagucuaacacgugcgcgagucgggggcucgcacgaa
agccgccguggcgcaaugaaggugaaggccggcgcgcucgccggccgagg
ugggaucccgaggccucuccaguccgccgagggcgcaccaccggcccguc
ucgcccgccgcgccggggagguggagcacgagcgcacguguuaggacccg
aaagauggugaacuaugccugggcagggcgaagccagaggaaacucuggu
ggagguccguagcgguccugacgugcaaaucggucguccgaccuggguau
aggggcgaaagacuaaucgaaccaucuaguagcugguucccuccgaaguu
ucccucaggauagcuggcgcucucgcagacccgaacgcaguuuuauccgg
uaaagcgaaugauuagaggucuuggggccgaaacgaucucaaccuauucu
caaacuuuaaauggguaagaagcccggcucgcuggcguggagccgggcgu
ggaaugcgagugccuagugggccacuuuugguaagcagaacuggcgcugc
gggaugaaccgaacgccggguuaaggcgcccgaugccgacgcucaucaga
ccccagaaaagguguugguugauauagacagcaggacgguggccauggaa
gucggaauccgcuaaggaguguguaacaacucaccugccgaaucaacuag
cccugaaaauggauggcgcuggagcgucgggcccauacccggccgucgcc
ggcagucgagaguggacgggagcggcgggccggagccccgcggacgcuac
gccgcgacgaguaggagggccgcugcggugagccuugaagccuagggcgc
gggcccggguggagccgccgcaggugcagaucuuggugguaguagcaaau
auucaaacgagaacuuugaaggccgaaguggagaaggguuccaugugaac
agcaguugaacaugggucagucgguccugagagaugggcgagcgccguuc
cgaagggacgggcgauggccuccguugcccucggccgaucgaaagggagu
cggguucagauccccgaauccggagcggagaugggcgccgcgaggcgucc
agugcgguaacgcgaccgaucccggagaagccggcgggagccccggggag
aguucucuuuucuuugugaagggcagggcgcccuggaauggguucgcccc
gagagaggggcccgugccuuggaaagcgucgcgguuccggcggcguccgg
ugagcucucgcuggcccuugaaaauccgggggagaggguguaaaucucgc
gccgggccguacccauauccgcagcaggucuccaaggugaacagccucug
gcauguuggaacaauguagguaagggaagucggcaagccggauccguaac
uucgggauaaggauuggcucuaagggcugggucggucgcggccggcgccu
agcagccgacuuagaacuggugcggaccaggggaauccgacuguuuaauu
aaaacaaagcaucgcgaaggcccgcggcggguguugacgcgaugugauuu
cugcccagugcucugaaugucaaagugaagaaauucaaugaagcgcgggu
aaacggcgggaguaacuaugacucucuuaagguagccaaaugccucguca
ucuaauuagugacgcgcaugaauggaugaacgagauucccacugucccua
ccuacuauccagcgaaaccacagccaagggaacgggcuuggcggaaucag
cggggaaagaagacccuguugagcuugacucuagucuggcacggugaaga
gacaugagagguguagaauaagugggaggcccgggccgccggugaaauac
cacuacucugaucguuuuuucacugacccggugaggcgggggggcgagcc
ccgaggggcucucgcuucuggcgccaagcgcccggccgcgcgccggccgg
gcgcgacccgcuccggggacagugccagguggggaguuugacuggggcgg
uacaccugucaaacgguaacgcagguguccuaaggcgagcucagggagga
cagaaaccucccguggagcagaagggcaaaagcucgcuugaucuugauuu
ucaguacgaauacagaccgugaaagcggggccucacgauccuucugaccu
uuuggguuuuaagcaggaggugucagaaaaguuaccacagggauaacugg
cuuguggcggccaagcguucauagcgacgucgcuuuuugauccuucgaug
ucggcucuuccuaucauugugaagcagaauucaccaagcguuggauuguu
cacccacuaauagggaacgugagcuggguuuagaccgucgugagacaggu
uaguuuuacccuacugaugauguguuguugccaugguaauccugcucagu
acgagaggaaccgcagguucagacauuugguguaugugcuuggcugagga
gccaauggggcgaagcuaccaucugugggauuaugacugaacgccucuaa
gucagaaucccgcccaggcggaacgauacggcagcgccgcggagccucgg
uuggccucggauagccggucccccgccgggguccggugcggagugcccuu
cguccugggaaacggggcgcggccggagaggcggccgcccccucgcccgu
cacgcaccgcacguucguggggaaccuggcgcuaaaccauucguagacga
ccugcuucugggucgggguuucguacguagcagagcagcucccucgcugc
gaucuauugaaagucagcccucgacacaaggguuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8g6j mRNA decoding in human is kinetically and structurally distinct from bacteria.
• Resolution: 2.8 Å
• Binding residue (original residue number in PDB): S2 G3 R4 W6 K8 K15 R16 G17 L18 R19 N20 Q21 R22 E23 H24 K29 Y34 R36 G44 Y51 K52 A53 K54 N55 N56 T57 V58 P60 T67 R68 V69 W71 K73 T75 R76 H78 G79 N80 S81 R85 R89 S90 N91 P93 A94 R100 R102
• Binding residue (residue number reindexed from 1): S1 G2 R3 W5 K7 K14 R15 G16 L17 R18 N19 Q20 R21 E22 H23 K28 Y33 R35 G43 Y50 K51 A52 K53 N54 N55 T56 V57 P59 T66 R67 V68 W70 K72 T74 R75 H77 G78 N79 S80 R84 R88 S89 N90 P92 A93 R99 R101

Gene Ontology

Molecular Function

• GO:0000049 tRNA binding
• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006364 rRNA processing
• GO:0006412 translation
• GO:0042273 ribosomal large subunit biogenesis

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0016020 membrane
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:0070062 extracellular exosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8g6j, PDBe:8g6j, PDBj:8g6j
• PDBsum: 8g6j
• PubMed: 37020024
• UniProt: P18077|RL35A_HUMAN Large ribosomal subunit protein eL33 (Gene Name=RPL35A)