Structure of PDB 4v95 Chain AS Binding Site BS01

Receptor Information

>4v95 Chain AS (length=81) Species: 300852 (Thermus thermophilus HB8)

SLKKGVFVDDHLLEKVLELNAKGEKRLIKTWSRRSTIVPEMVGHTIAVYN
GKQHVPVYITENMVGHKLGEFAPTRTYRGHG

Ligand information

>4v95 Chain AA (length=1466)

uuggagaguuugauccuggcucagggugaacgcuggcggcgugccuaaga
caugcaagucgugcgggccgcggccguggucagcggcggacgggugagua
acgcgugggugaccuacccggaagagggggacaacccggggaaacucggg
cuaaucccccauguggacccgccccuugggguguguccaaagggcuuugc
ccgcuuccggaugggcccgcgucccaucagcuaguuggugggguaauggc
ccaccaaggcgacgacggguagccggucugagaggauggccggccacagg
ggcacugagacacgggccccacuccuacgggaggcagcaguuaggaaucu
uccgcaaugggcgcaagccugacggagcgacgccgcuuggaggaagaagc
ccuucgggguguaaacuccugaacccgggacgaaacccccgacgagggga
cugacgguaccgggguaauagcgccggccaacuccgugccagcagccgcg
guaauacggagggcgcgagcguuacccggauucacugggcguaaagggcg
uguaggcggccuggggcgucccaugugaaagaccacggcucaaccguggg
ggagcgugggauacgcucaggcuagacggugggagagggugguggaauuc
ccggaguagcggugaaaugcgcagauaccgggaggaacgccgauggcgaa
ggcagccaccugguccacccgugacgcugaggcgcgaaagcguggggagc
aaaccggauuagauacccggguaguccacgcccuaaacgaugcgcgcuag
gucucugggucuccugggggccgaagcuaacgcguuaagcgcgccgccug
gggaguacggccgcaaggcugaaacucaaaggaauugacgggggcccgca
caagcgguggagcaugugguuuaauucgaagcaacgcgaagaaccuuacc
aggccuugacaugcccgggugaaagccugggcacaggugcugcauggccg
ucgucagcucgugccgugagguguuggguuaagucccgcaacgagcgcaa
cccccgccguuaguugccagcgguucggccgggcacucuaacgggacugc
ccgcgaaagcgggaggaaggaggggacgacgucuggucagcauggcccuu
acggccugggcgacacacgugcuacaaugcccacuacaaagcgaugccac
ccggcaacggggagcuaaucgcaaaaaggugggcccaguucggauugggg
ucugcaacccgaccccaugaagccggaaucgcuaguaaucgcggaucagc
caugccgcggugaauacguucccgggccuuguacacaccgcccgucacgc
caugggagcgggcucuacccgaagucgccgggagccuacgggcaggcgcc
gaggguagggcccgugacuggggcgaagucguaacaagguagcuguaccg
gaaggugcggcuggau

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4v95 Structural basis for the rescue of stalled ribosomes: structure of YaeJ bound to the ribosome.
• Resolution: 3.2 Å
• Binding residue (original residue number in PDB): S4 K6 F10 H14 W34 R36 R37 Y52 N53 G54 K55 G72 E73 T77 R78 T79 Y80 H83
• Binding residue (residue number reindexed from 1): S1 K3 F7 H11 W31 R33 R34 Y49 N50 G51 K52 G69 E70 T74 R75 T76 Y77 H80

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding

Biological Process

• GO:0000028 ribosomal small subunit assembly
• GO:0006412 translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005840 ribosome
• GO:0015935 small ribosomal subunit
• GO:0022627 cytosolic small ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:4v95, PDBe:4v95, PDBj:4v95
• PDBsum: 4v95
• PubMed: 22422986
• UniProt: Q5SHP2|RS19_THET8 Small ribosomal subunit protein uS19 (Gene Name=rpsS)