Structure of PDB 6yly Chain R Binding Site BS01

Receptor Information

>6yly Chain R (length=154) Species: 4932 (Saccharomyces cerevisiae)

ANLRTQKRLAASVVGVGKRKVWLDPNETSEIAQANSRNAIRKLVKNGTIV
KKAVTVHSKSRTRAHAQSKREGRHSGYGKRKGTREARLPSQVVWIRRLRV
LRRLLAKYRDAGKIDKHLYHVLYKESKGNAFKHKRALVEHIIQAKADAQR
EKAL

Ligand information

>6yly Chain 1 (length=2676)

uugaccucaaaucagguaggaguacccgcugaacuuaagcauaucaauaa
gcggaggaaaagaaaccaaccgggauugccuuaguaacggcgagugaagc
ggcaaaagcucaaauuugaaaucugguaccuucggugcccgaguuguaau
uuggagagggcaacuuuggggccguuccuugucuauguuccuuggaacag
gacgucauagagggugagaaucccguguggcgaggagugcgguucuuugu
aaagugccuucgaagagucgaguuguuugggaaugcagcucuaagugggu
gguaaauuccaucuaaagcuaaauauuggcgagagaccgauagcgaacaa
guacagugauggaaagaugaaaagaacuuugaaaagagagugaaaaagua
cgugaaauuguugaaagggaagggcauuugaucagacaggccagcaucag
uuuugguggcaggauaaauccauaggaauguagcuugccucgguaaguau
uauagccugugggaauacugccagcugggacugaggacugcgacguaagu
caaggaugcuggcauaaugguuauaugccgcccgucucacggaccaagga
gucuaacgucuaugcgaguguuuggguguaaaacccauacgcguaaugaa
agugaacguagguuggggccucgcaagaggugcacaaucgaccgauccug
augucuucggauggauuugaguaagagcauagcuguugggacccgaaaga
uggugaacuaugccugaauagggugaagccagaggaaacucugguggagg
cucguagcgguucugacgugcaaaucgaucgucgaauuuggguauagggg
cgaaagacuaaucgaaccaucuaguagcugguuccugccgaaguuucccu
caggauagcagaagcucguaucaguuuuaugagaauauguaagaaguccg
acauuugaaugaagagcuuuuagugggccauuuuugguaagcagaacugg
cgaugcgggaugaaccgaacguagaguuaaggugccggaauacacgcuca
ucagacaccacaaaagguguuaguucaucuagacagccggacgguggcca
uggaagucggaauccgcuaaggaguguguaacaacucaccggccgaauga
acuagcccugaaaauggauggcgcucaagcguguuaccuauacucuaccg
ucaggguugauaugaugcccugacgaguaggcaggcguggaggucaguga
cgaagccuagaccguaaggucgggucgaacggccucuagugcagaucuug
gugguaguagcaaauauucaaaugagaacuuugaagacugaaguggggaa
agguuccacgucaacagcaguuggacguggguuagucgauccuaagagau
ggggaagcuccguuucaaaggccugacaggccaccaucgaaagggaaucc
gguuaagauuccggaaccuggauauggauucuucacgguaacguaacuga
auguggagacgucggcgcgagcccugggaggaguuaucuuuucuucuuaa
cagcuuaucaccccggaauugguuuauccggagauggggucuuauggcug
gaagaggccagcaccuuugcuggcuccggugcgcuugugacggcccguga
aaauccacaggaaggaauaguuuucaugccaggucguacugauaaccgca
gcaggucuccaaggugaacagccucuaguugauagaauaauguagauaag
ggaagucggcaaaauagauccguaacuucgggauaaggauuggcucuaag
ggucggacgaucaacuuagaacugguacggacaaggggaaucugacuguc
uaauuaaaacauagcauugcgauggucagaaagugauguugacgcaaugu
gauuuauggauuaacgagauucccacugucccuaucuacuaucuagcgaa
accacagccaaggggcuuggcagaaucagcggggacuaguuugacauugu
gaagagacauaguuucuuuacuuauucaaugaagcggagcuggaauucau
uuuccacguucuagcauucaaggucccauucggggcugauccggguugaa
gacauugucaggugguagucccucggaauuugaggcuaaacuggcuugug
gcagucaagcguucauagcgacauugcuuuuugauucuucgaugucggcu
cuuccuaucauaccgaagcagaauucgguaagcguuggauuguucaccca
cuaauagggauacccuacugaugaauguuaccgcaauaguaauugaacuu
aguacgagaggaacaguucauucggauaauugguuuuugcggcugucuga
ucaggcauugccgcgaagcuaccauccgcuggauuauggcugaacgccuc
uaagucagaauccaugcuagaacgcggugauuucuuugcuccacacaaua
uagauggauacgaauaaggcguccuuguggcgucgcugaaccauagcagg
cuagcaacggugcacuuggcggaaaggccuugggugcuugcuggcgaauu
gcaaugucauuuugcguggggauaaaucauuuguauacgacuuagaugua
caacgggguauuguaagcaguagaguagccuuguuguuacgaucugcuga
gauuaagccuuuguugucugauuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6yly Construction of the Central Protuberance and L1 Stalk during 60S Subunit Biogenesis.
• Resolution: 3.8 Å
• Binding residue (original residue number in PDB): L4 R5 K8 R9 G18 K19 R20 K21 W23 L24 S37 R38 R42 K43 K46 V55 T56 V57 H58 S59 K60 S61 R62 R64 R71 R74 H75 G77 Y78 G79 K80 R81 K82 G83 T84 R85 E86 A87 R88 Q92 W95 I96 R97 R100 R103 R104 R110 K114 H118 Y120 H121 Y124 K125 E126 K128 N130 H134 K135 R136 I143
• Binding residue (residue number reindexed from 1): L3 R4 K7 R8 G17 K18 R19 K20 W22 L23 S36 R37 R41 K42 K45 V54 T55 V56 H57 S58 K59 S60 R61 R63 R70 R73 H74 G76 Y77 G78 K79 R80 K81 G82 T83 R84 E85 A86 R87 Q91 W94 I95 R96 R99 R102 R103 R109 K113 H117 Y119 H120 Y123 K124 E125 K127 N129 H133 K134 R135 I142

Gene Ontology

Molecular Function

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

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation

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:6yly, PDBe:6yly, PDBj:6yly
• PDBsum: 6yly
• PubMed: 32668200
• UniProt: P0CX82|RL19A_YEAST Large ribosomal subunit protein eL19A (Gene Name=RPL19A)