Structure of PDB 6n8j Chain F Binding Site BS01

Receptor Information

>6n8j Chain F (length=222) Species: 559292 (Saccharomyces cerevisiae S288C)

AEQVAAERAARKAANKEKRAIILERNAAYQKEYETAERNIIQAKRDAKAA
GSYYVEAQHKLVFVVRIKGINKIPPKPRKVLQLLRLTRINSGTFVKVTKA
TLELLKLIEPYVAYGYPSYSTIRQLVYKRGFGKINKQRVPLSDNAIIEAN
LGKYGILSIDDLIHEIITVGPHFKQANNFLWPFKLSNPSGGWGVPRKFKH
FIQGGSFGNREEFINKLVKSMN

Ligand information

>6n8j Chain 1 (length=3047)

uugaccucaaaucagguaggaguacccgcugaacuuaagcauaucaauaa
gcggaggaaaagaaaccaaccgggauugccuuaguaacggcgagugaagc
ggcaaaagcucaaauuugaaaucugguaccuucggugcccgaguuguaau
uuggagagggcaacuuuggggccguuccuugucuauguuccuuggaacag
gacgucauagagggugagaaucccguguggcgaggagugcgguucuuugu
aaagugccuucgaagagucgaguuguuugggaaugcagcucuaagugggu
gguaaauuccaucuaaagcuaaauauuggcgagagaccgauagcgaacaa
guacagugauggaaagaugaaaagaacuuugaaaagagagugaaaaagua
cgugaaauuguugaaagggaagggcauuugaucagacaggccagcaucag
uuuugguggcaggauaaauccauaggaauguagcuugccucgguaaguau
uauagccugugggaauacugccagcugggacugaggacugcgacguaagu
caaggaugcuggcauaaugguuauaugccgcccgucuugaaacacggacc
aaggagucuaacgucuaugcgaguguuuggguguaaaacccauacgcgua
augaaagugaacguagguuggggccucgcaagaggugcacaaucgaccga
uccugaugucuucggauggauuugaguaagagcauagcuguugggacccg
aaagauggugaacuaugccugaauagggugaagccagaggaaacucuggu
ggaggcucguagcgguucugacgugcaaaucgaucgucgaauuuggguau
aggggcgaaagacuaaucgaaccaucuaguagcugguuccugccgaaguu
ucccucaggauagcagaagcucguaucaguuuuaugagguaaagcgaauc
uuuaaauauguaagaaguccuuguuacuuaauugaacguggacauuugaa
ugaagagcuuuuagugggccauuuuugguaagcagaacuggcgaugcggg
augaaccgaacguagaguuaaggugccggaauacacgcucaucagacacc
acaaaagguguuaguucaucuagacagccggacgguggccauggaagucg
gaauccgcuaaggaguguguaacaacucaccggccgaaugaacuagcccu
gaaaauggauggcgcucaagcguguuaccuauacucuaccgucaggguug
auaugaugcccugacgaguaggcaggcguggaggucagugacgaagccua
gaccguaaggucgggucgaacggccucuagugcagaucuuggugguagua
gcaaauauucaaaugagaacuuugaagacugaaguggggaaagguuccac
gucaacagcaguuggacguggguuagucgauccuaagagauggggaagcu
ccguuucaaaggccugauuuuaugcaggccaccaucgaaagggaauccgg
uuaagauuccggaaccuggauauggauucuucacgguaacguaacugaau
guggagacgucggcgcgagcccugggaggaguuaucuuuucuucuuaaca
gcuuaucaccccggaauugguuuauccggagauggggucuuauggcugga
agaggccagcaccuuugcuggcuccggugcgcuugugacggcccgugaaa
auccacaggaaggaauaguuuucaugccaggucguacugauaaccgcagc
aggucuccaaggugaacagccucuaguugauagaauaauguagauaaggg
aagucggcaaaauagauccguaacuucgggauaaggauuggcucuaaggg
ucggguacgaucaacuuagaacugguacggacaaggggaaucugacuguc
uaauuaaaacauagcauugcgauggucagaaagugauguugacgcaaugu
gauuucugcccagugcucugaaugucaaagugaagaaauucaaccaagcg
cggguaaacggcaauggauuaacgagauucccacugucccuaucuacuau
cuagcgaaaccacagccaagggaacgggcuuggcagaaucagcggggaaa
gaagacccuguugagcuugacucuaguuugacauugugaagagacauaga
ggguaccuuuauaguuucuuuacuuauucaaugaagcggagcuggaauuc
auuuuccacguucuagcauucaaggucccauucggggcugauccggguug
aagacauugucagguggggaguuuggacaucuguuaaacgauaacgcaga
uguccuaaggggggcucauggagaacagaaaucuccaguagaacaaaagg
guaaaagcccccuugauuuugauuuucagugugaauacaaaccaugaaag
uguggccuaucgauccuuuagucccucggaauuugaggcuagaggugcca
gaaaaguuaccacagggauaacuggcuuguggcagucaagcguucauagc
gacauugcuuuuugauucuucgaugucggcucuuccuaucauaccgaagc
agaauucgguaagcguuggauuguucacccacuaauagggaacgugagcu
ggguuuagaccgucgugagacagguuaguuuuacccuacugaugaauguu
accgcaauaguaauugaacuuaguacgagaggaacaguucauucggauaa
uugguuuuugcggcugucugaucaggcauugccgcgaagcuaccauccgc
uggauuauggcugaacgccucuaagucagaauccaugcuagaacgcggug
auuucuuugcuccacacaauauagauggauacgaauaaggcguccuugug
gcgucgcugaaccauagcaggcuagcaacggugcacuuggcggaaaggcc
uugggugcuugcuggcgaauugcaaugucauuuugcguggggauaaauca
uuuguauacgacuuagauguacaacgggguauuguaagcaguagaguagc
cuuguuguuacgaucugcugagauuaagccuuuguugucugauuugu

........................<<<<<<.....<......>......>
>>>>.>.........<<....>>..<<<<<......<<.....>>.....
>>>>>..[[[...........<<.<<<<<<...>>>>>>.>>........
.....<<<<<<.<<<<<<<<<<<<<<<<<<<<<<....<<<<......>>
>>.(.......<<<......)>>>..>.>>>>>>>>..>>>>>>>>....
>>>>>>>>>>>........<<<<<<<........>>>>>>>.....((((
(..<<<<<<)))))..]]]...............................
...<<....>>...............<<<<....>>>>............
......................<<<<<.<<<<<......<<<<<<<.<<<
<<<<<<<<<<<<.....<<<<<<<<<......<<<<<<<..>>>>>>>..
.....>>>>>>>.>.>.>>>>>.>>>>>>>>>>........<<<....>>
>.....>>>>>>>.....>>>>>.>>>>>..<<<<........>>>><<<
<<<...<<<<<<<.<<<<<<..<<<...<<<<.....>>>>...>>>...
<<....>>.......<<<<<..<<<<<....>>>>>...>>>>>.<<<<<
<<<...<......>...>>>.>>>.>>....>>>>>>.>>>>>>>.<<.<
..<<<<<<<.....<<<<<<<<<..<<<....<<<<<<<....>>>>>>>
.....>>>...<<<<.<<.<<........>>>>>>>>....>>>>>>>>>
...<<.......>>......>>>>>>...>..>.>>..<<<<<<....<.
<<<....>>>.><<<<<<<<<<...<<<.<<<<<<<.....<<<......
>>>.....>>>>>...<<<<.<<<<.<......>>>>>.>>>>.....>>
>>>.>>>>>>>>.>>..<<<<.<<<<<.....>>>>>.>>>>....<<<.
.....>>>...<<<<<<<..<<<<(((.....<<<<<<......<.....
.....<<<.<<<<<<<<<<.......<<<<<.<<....<<.........>
>....>>.........<<......>>...>>>>>...>>>>>>>>>>>>>
..........))).>....>>>>>>.>>>>..>>>>>>><<<<<<<<<..
.......>>>>>>>>>....>>>>>><<<<<<<<<..<<......<<<<.
<<<<....>>>>>>>>...>>.>>>>>>>.>>.....>>>>>><<.....
<<.....<<<<<<.......>>>>>><<<<.....<<<<<.<<...<<<<
<<...<<.....>>.>>>>>>....((<<<<<<...<<....<<<....>
>>........<<<<<<........>>>>>>....>>....>>...<<<<<
........>>>>>))<<<<.<<<<<<<.....<<<....>>>.......<
<<<<<...<<<<.<<<<<<<<<<<<<<<<<<..{{{..>>>>>>....<<
<<<....<<<<<<....<<<.....>>>....>>>>>>.....>>>>>..
...<<<<<<<<....>>>>>>>>>>>>.>.>>>>>>>.>>>>........
.>>>>>>..........>>>..>>>>>>>>>>>>..>>.....<<.....
.>>>>>>>.<<<<.....>>>>..>>>>..<<<<.....<<<<<<<.<<.
........<.....<<<<<.....<..>......>>>>><<.<<<<<<<<
<<<....>>>>>..>>>>>>.>>............<<<<<<<<<..<<<.
........>>>..<<<<<<<....<<<<.....>>>>......>>>>>>>
...<<...<<..<<<<<<.<..<<<....<<<<<....>>>>.>...>>>
>>>>>..>>>>.....>>....>>.>>>>>>>..>..>>.>>>>>>>..>
>>>>>....>>....<<<<<........>>>>>....[[[[[..{{{...
.....[[[[[.{{[[[[..<<<<<.<<<<<<<<..<<<<<<<<<<.<<<.
<.....>.>>>..>>>>>>>>>>...<<<<<.....<<<<..<<<<<...
...>>>>>...............<<<<<<....>>>>>>..>>>>..>>>
>>.....>>>>>>>>..>>>>>......<<<<<<...........>>>>>
>..<<...<<<<<<<...<<<<<<.......>>>>>>.....<<...(((
>>....>>>>>>>...<<<.<<<<<.......>>>>.>>>>.<<<....>
>>.>>))).......((((((..((((.>>>>>>))))))))))......
....]]]]..}}]]]]]..............<<<<<...<<.......>>
...>>>>>...................<<<.<.<<<<..<.<<<<<<<..
....>>>>>>>...>.<<<.........>>>.....>>>>...>...>>>
.......<<<<<<<....>>>.>>>>........}}}.]]]]]....<<<
<<<<<..<<<<.<.<<<<<<...............>>>>>>.><<<<<..
.<<<<....<<<<<<<<<<}}}.>>>>>..>>>>>...>>>>..>>>>>.
<<<<...<<<<<...........>>>>>...>>>>.>>>>....>>>>>>
>>.......<<<<<<.<<<.<.....<<...........<<<<<.....>
>>>>.......>>.......<<<<<<...<<<<<.<..<<<......>>>
..>.>>>>>.>>>>>>..............>.>>>.>>>>>>..<<<<<.
<.............>.....<<<<<<<<<.<<<....<<<<....<<.<.
........>>>...>>>>...>>>....>>>>.>>>>>..>>>>>..

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6n8j Tightly-orchestrated rearrangements govern catalytic center assembly of the ribosome.
• Resolution: 3.5 Å
• Binding residue (original residue number in PDB): R30 R33 K34 N37 R41 R67 K70 G91 I92 N93 K94 P97 K98 K101 L105 R110 I111 A122 E125 L126 S142 R145 R151 K158 Q159 R160 K196 N200 K206 S208 N209 P210 S211 W214 R218 K219
• Binding residue (residue number reindexed from 1): R8 R11 K12 N15 R19 R45 K48 G69 I70 N71 K72 P75 K76 K79 L83 R88 I89 A100 E103 L104 S120 R123 R129 K136 Q137 R138 K174 N178 K184 S186 N187 P188 S189 W192 R196 K197

Gene Ontology

Molecular Function

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

Biological Process

• GO:0000463 maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
• GO:0000470 maturation of LSU-rRNA
• GO:0002181 cytoplasmic translation
• GO:0042273 ribosomal large subunit biogenesis

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6n8j, PDBe:6n8j, PDBj:6n8j
• PDBsum: 6n8j
• PubMed: 30814529
• UniProt: P05737|RL7A_YEAST Large ribosomal subunit protein uL30A (Gene Name=RPL7A)