Structure of PDB 6lqt Chain SM Binding Site BS01

Receptor Information

>6lqt Chain SM (length=137) Species: 559292 (Saccharomyces cerevisiae S288C)

TVQSERAFQKQPHIFNNPKVKTSKRTKRWYKNAGLGFKTPKTAIEGSYID
KKCPFTGLVSIRGKILTGTVVSTKMHRTIVIRRAYLHYIPKYNRYEKRHK
NVPVHVSPAFRVQVGDIVTVGQCRPISKTVRFNVVKV

Ligand information

>6lqt Chain SA (length=1155)

aagauaguuaucugguugauccugccaguagucauaugcuugucucaaag
ccaugcaugucuaaguauaagcaauuuauacagugaaacugcgaaucagu
uaucguuuauuugauagcaugguauaacugugguaauucuagagcuaaua
caugcuaaucucgacccuuuggaagagauguauuuauuagagucuucgga
cucuuugaugauucauaauaacuuuucgaaucgcauggccuugugcuggc
gaugguucauucaaauuucugcccuaucaacuuucgaugguaggauagug
gccuaccaugguuucaacggggcaggcgcgcaaauuacccaauccuaauu
cagggagguagugacaauaaauaacgauacagggcccauucgggucuugu
aauuggaaugaguacaauguaaauaccuuaacgaggaacaauuggagggc
aagucuggugccagcagccgcgguaauuccagcuccaauagcguauauug
cucguaguugaacuuugggcccgguuggccgguccggauuuccaacgggg
ccuuuccuuuuuacuuugaaaaaauuagaguguucaaagcaggcguauug
cucgaauauauuagcauggaauaauagaauagguugguucuauuucuagg
accugauuaauagggacggucgggggcaucaguauucaauugucagaggu
gaaauucuuggauuuauugaagacuaacuacugcgaaagcauuugccaag
gacguuuucauuaaucaagaacguagggaucgggugguguuuuuuuaaug
acccacucggcaccuugggggaguauggucgcaaggcugaaacuuaaagg
aauugacggaagggcaccaccaggaguggagccugcggcgcgcgcuacac
ugacggagccagcgaguaacuccgucgugcugacgaggaauuccuaguaa
gcgcaagucaucagcuugcguugauuacgucccugcccuuuguacacacc
gcccgucgcuaguaccgauugaauggcuuagugaggccucaggaucugcu
uagagaagggggcaacuccaucucagagcggagaauuuggacaaacuugg
ucauuuagaggaacuaaaaggguuuccguaggugaaccugcggaaggauc
auuaa

..............................<..<<<<<<...<......<
<<.<<<..<<....<<....<<..........>>...>>.>>....<<<.
.<<..<<....<<<.......<<....<<.<<<.....>>>.>>.....>
>......<<<<<..<<....>>..>>>>><...<<<<<<..<<<<..>>>
>....<<......>>>>>>>>.....>...<<<<..<<<.....>>>.>>
>>....>>>...>>>>..>>>..<<....<<.....<<<<<<<<......
.>>>>>>>>.>>......>>.>>>>>>.........<<<....<<<....
.>>>..>>>.........>.....<<<<<<<..<<<<....>>>>..>>>
>.>>>......<<..<...........>..>>.........<<<<<<...
....<<<....>>>..................>>>>>>..>>>>>>.>.<
.<<...<<<.<<.....<<<<<.<<<<<..<.<...>.>..>>>>>.>>>
>>........<<<<<.<<............<.......>...<<.....>
>.............>>.>>..>>>..........<..<...<..>..>..
>.....>>....<<<<<<.<<...<<<<..<<..<<<<<<.<...<<<..
....>>>......>.>>>>>>..>>.......<<....>>...>>>>..>
.>>>>.>>>...>>>...>>.>..<<<..<<<<<<<<.<<<........>
>>>>>>>>>>..>>>.....................<<.........>>.
....<<<<<<<<<<<<..<<.<<<<<<..<<<.<<<<.>>>>.>>>....
.<<<<<<<...........>>>>>>>.............>>>>>>....<
<<<<<<<.......>>>>>>>>......>>...>>>>>>>..........
..>>>>>..<<<<.<<....<.<<<<.<..<<..<.<<......<<...<
<......<<<<....>>>>......>>...>>......>>.>..>>..>.
>>>>>....>>.>>>>.......<<<<<<<<<....>>>>>>>>>.....
.....

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6lqt Cryo-EM structure of 90 S small ribosomal subunit precursors in transition states.
• Resolution: 4.9 Å
• Binding residue (original residue number in PDB): E10 Q14 P17 H18 I19 F20 W34 N37 A38 G39 L40 K56 K57 L63 S65 I66 R67 K69 S77 K79 M80 H81 R82 T83 Y90 H92 Y93 K102 R103 H104 N106 H110 Q127 R129 P130 I131 S132 K133 T134 R136 F137
• Binding residue (residue number reindexed from 1): E5 Q9 P12 H13 I14 F15 W29 N32 A33 G34 L35 K51 K52 L58 S60 I61 R62 K64 S72 K74 M75 H76 R77 T78 Y85 H87 Y88 K97 R98 H99 N101 H105 Q122 R124 P125 I126 S127 K128 T129 R131 F132

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA 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:0006412 translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0022627 cytosolic small ribosomal subunit
• GO:0030686 90S preribosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6lqt, PDBe:6lqt, PDBj:6lqt
• PDBsum: 6lqt
• PubMed: 32943522
• UniProt: P0CX47|RS11A_YEAST Small ribosomal subunit protein uS17A (Gene Name=RPS11A)