Structure of PDB 6ip8 Chain 20 Binding Site BS01

Receptor Information

>6ip8 Chain 20 (length=143) Species: 9606 (Homo sapiens)

PGVTVKDVNQQEFVRALAAFLKKSGKLKVPEWVDTVKLAKHKELAPYDEN
WFYTRAASTARHLYLRGGAGVGSMTKIYGGRQRNGVMPSHFSRGSKSVAR
RVLQALEGLKMVEKDQDGGRKLTPQGQRDLDRIAGQVAAANKK

Ligand information

>6ip8 Chain 2m (length=1742)

uaccugguugauccugccaguagcauaugcuugucucaaagauuaagcca
ugcaugucuaaguacgcacggccgguacagugaaacugcgaauggcucau
uaaaucaguuaugguuccuuuggucgcucgcuccucucccacuuggauaa
cugugguaauucuagagcuaauacaugccgacgggcgcugacccccuucg
cgggggggaugcgugcauuuaucaguggugacucuagauaaccucgggcc
gaucgcacgccccccguggcggcgacgacccauucgaacgucugcccuau
caacuuucgaugguagucgccgugccuaccauggugaccacgggugacgg
ggaaucaggguucgauuccggagagggagccugagaaacggcuaccacau
ccaaggaaggcagcaggcgcgcaaauuacccacucccgacccggggaggu
agugacgaaaaauaacaauacaggacucuuucgaggcccuguaauuggaa
ugaguccacuuuaaauccuuccgcgaggauccauuggagggcaagucugg
ugccagcagccgcgguaauuccagcuccaauagcguauauuaaaguugcu
gcaguuaaaaagcucguaguuggaucuugggagcgggcguccccgccgcc
ucucggccggggcccgaagcauuuacuuugaaaaaauuagaguguucaaa
gcaggcccgagccgccuggauaccgcagcuaggaauaauggaauaggacc
gcgguucuauuuuguugguuuucggaacugaggccaugauuaagagggac
ggccgggggcauucguauugcgccgcuagaggugaaauucuuggaccggc
gcaagacggaccagagcgaaagcauuugccaagaauguuuucauuaauca
agaacgaaagucggagguucgaagacgaucagauaccgucguaguuccga
ccauaaacgaugccgacuggcgaugcggcggcguuauucccaugacccgc
cgggcagcuuccgggaaaccaaagucuuuggguuccggggggaguauggu
ugcaaagcugaaacuuaaaggaauugacggaagggcaccaccaggagugg
agccugcggcuuaauuugacucaacacgggaaaccucacccggcccggac
acggacaggauugacagauugauagcucuuucucgauuccguggguggug
gugcauggccguucuuaguugguggagcgauuugucugguuaauuccgau
aacgaacgagacucuggcaugcuaacuaguuacgcgacccccgagcgguc
ggcgucccccaacuucuuagagggacaaguggcguucagccacccgagau
ugagcaauaacaggucugugaugcccuuagauguccggggcugcacgcgc
gcuacacugacuggcucagcgugugccuacccuacgccggcaggcgcggg
uaacccguugaaccccauucgugauggggaucggggauugcaauuauucc
ccaugaacgaggaauucccaguaagugcgggucauaagcuugcguugauu
aagucccugcccuuuguacacaccgcccgucgcuacuaccgauuggaugg
uuuagugaggcccucggaucggccccgccggggucggcccacggcccugg
cggagcgcugagaagacggucgaacuugacuaucuagaggaaguaaaagu
cguaacaagguuuccguaggugaaccugcggaaggaucauua

...<<<<....((((.>>>><<<.<<<<<<...<.<<..<......<<<.
<<<..<<....<<....<<..........>>...>>.>>......<<...
.....<<<.<....<<....<<.....................<<.....
<<..<<.....>>..>>......>>.........<<<<...<<<<<....
..>>>>>...>>>>....<<<<<.............>>>>>.........
..<<<<.<<<<......>>>>>>>>.....>>...>>..>.>>>.<<<..
..<<<....<<<<<<<.........>>>>>>>>>>......>>>...<<<
.<<<<....>>>>....>>>.>>.<<.<<<..........>>>.>>.<.<
<....>>.>...>>>>>>.........<<<....<<<.....>>>..>>>
..>...>>.>.....<<...<<<<............>>.>>....>>...
...<<..<...........>..>>.........<<<<<((......<<<<
.....<<..))>>.......>>>>.>>>>>..>>>>>>.>>>........
.<.<((.....<.<<...<<<..<..........................
......................<<<<<<.<.......<<...<.......
>.<<<<.......>>>>...>>......>.>>>..>>>.......<<...
.<.<<<<................>>.>>.>...>>....>.....<<<<<
<..<...<<<<..<<..<<<<<<<<...<<<......>>>......>>>>
>>>.>.>>.......<<....>>...>>>>..>..>>>.>>>...>>>..
.>>.>....<<<<<<....<...<<<<.........>>>>...>.>>>>>
>..........<<<.<<.<<<..<.<<<<<<.<<<........>>>>>>>
>>.>..>>>...<<..))>>...>>.....>>>.>.>.<<<......<<<
<....>>>>....>>>..))))..<<<<<.<<<<<<<..<<..<<<<<..
<<<.<<<<........<<........>>..........<<<<<......<
<<<<........<<..<<........>>..>>......>>>>>...<<.<
<<...<.<<<<<<....<<<.<<<<<....>>>...<<<......>>>..
.>>.>>>....<<<...<...<<<<..<<<...........<........
>..........>>>..>>>>..>.....<<<<<.....>>>>>.......
.>>>....>>>.>>>.....>.>>>>>.......>>>>>......>>>>.
>>>.....<<.<<<................<<<.<<<<....>>>>.>>>
..............>>>.>>......<.....<<<<<..........>>>
>>.....>.....>>>>>.....<<<<<<<<.......>>>>>>>>....
..>>...>>>>>>>>>>.>>.......<<.<..<<<<.<<....<<<<<<
<<.<<<..<<<<.<<...<<<<<.<..<<...................>>
..>...>>>>>...>>.>>>>..>>>.>>>>>>>>...>>.>>>>...>.
>>..........<<<<<<<<....>>>>>>>>..........

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6ip8 HCV IRES Captures an Actively Translating 80S Ribosome.
• Resolution: 3.9 Å
• Binding residue (original residue number in PDB): P2 G3 V15 W33 K38 L39 K41 K43 E44 L45 Y48 S59 R62 R67 G68 G71 G73 G80 G81 R82 R84 G86 V87 M88 P89 H91 F92 S96 S98 R101 Q105 D118 G119 R121 P125 Q128 D132 R133
• Binding residue (residue number reindexed from 1): P1 G2 V14 W32 K37 L38 K40 K42 E43 L44 Y47 S58 R61 R66 G67 G70 G72 G79 G80 R81 R83 G85 V86 M87 P88 H90 F91 S95 S97 R100 Q104 D117 G118 R120 P124 Q127 D131 R132

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0017134 fibroblast growth factor binding
• GO:0019901 protein kinase binding
• GO:0042802 identical protein binding

Biological Process

• GO:0000028 ribosomal small subunit assembly
• GO:0000462 maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
• GO:0002181 cytoplasmic translation
• GO:0002548 monocyte chemotaxis
• GO:0006364 rRNA processing
• GO:0006412 translation
• GO:0007000 nucleolus organization
• GO:0030218 erythrocyte differentiation
• GO:0030490 maturation of SSU-rRNA
• GO:0031640 killing of cells of another organism
• GO:0042274 ribosomal small subunit biogenesis
• GO:0050829 defense response to Gram-negative bacterium
• GO:0060265 positive regulation of respiratory burst involved in inflammatory response
• GO:0060266 negative regulation of respiratory burst involved in inflammatory response
• GO:0061844 antimicrobial humoral immune response mediated by antimicrobial peptide

Cellular Component

• GO:0005634 nucleus
• GO:0005654 nucleoplasm
• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0005925 focal adhesion
• GO:0014069 postsynaptic density
• GO:0016020 membrane
• GO:0022626 cytosolic ribosome
• GO:0022627 cytosolic small ribosomal subunit
• GO:0032040 small-subunit processome
• GO:0070062 extracellular exosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6ip8, PDBe:6ip8, PDBj:6ip8
• PDBsum: 6ip8
• PubMed: 31080011
• UniProt: P39019|RS19_HUMAN Small ribosomal subunit protein eS19 (Gene Name=RPS19)