Structure of PDB 6m62 Chain R Binding Site BS01

Receptor Information

>6m62 Chain R (length=156) Species: 559292 (Saccharomyces cerevisiae S288C)

ANLRTQKRLAASVVGVGKRKVWLDPNETSEIAQANSRNAIRKLVKNGTIV
KKAVTVHSKSRTRAHAQSKREGRHSGYGKRKGTREARLPSQVVWIRRLRV
LRRLLAKYRDAGKIDKHLYHVLYKESKGNAFKHKRALVEHIIQAKADAQR
EKALNE

Ligand information

>6m62 Chain 1 (length=2972)

guuugaccucaaaucagguaggaguacccgcugaacuuaagcauaucaau
aagcggaggaaaagaaaccaaccgggauugccuuaguaacggcgagugaa
gcggcaaaagcucaaauuugaaaucugguaccuucggugcccgaguugua
auuuggagagggcaacuuuggggccguuccuugucuauguuccuuggaac
aggacgucauagagggugagaaucccguguggcgaggagugcgguucuuu
guaaagugccuucgaagagucgaguuguuugggaaugcagcucuaagugg
gugguaaauuccaucuaaagcuaaauauuggcgagagaccgauagcgaac
aaguacagugauggaaagaugaaaagaacuuugaaaagagagugaaaaag
uacgugaaauuguugaaagggaagggcauuugaucagacaggccagcauc
aguuuugguggcaggauaaauccauaggaauguagcuugccucgguaagu
auuauagccugugggaauacugccagcugggacugaggacugcgacguaa
gucaaggaugcuggcauaaugguuauaugccgcccgucuugaaacacgga
ccaaggagucuaacgucuaugcgaguguuuggguguaaaacccauacgcg
uaaugaaagugaacguagguuggggccucgcaagaggugcacaaucgacc
gauccugaugucuucggauggauuugaguaagagcauagcuguugggacc
cgaaagauggugaacuaugccugaauagggugaagccagaggaaacucug
guggaggcucguagcgguucugacgugcaaaucgaucgucgaauuugggu
auaggggcgaaagacuaaucgaaccaucuaguagcugguuccugccgaag
uuucccucaggauagcagaagcucguaucaguuuuaugagguaaagcgaa
aacuuuaaauauguaagaaguccuuguuugaacguggacauuugaaugaa
gagcuuuuagugggccauuuuugguaagcagaacuggcgaugcgggauga
accgaacguagaguuaaggugccggaauacacgcucaucagacaccacaa
aagguguuaguucaucuagacagccggacgguggccauggaagucggaau
ccgcuaaggaguguguaacaacucaccggccgaaugaacuagcccugaaa
auggauggcgcucaagcguguuaccuauacucuaccgucaggguugauau
gaugcccugacgaguaggcaggcguggaggucagugacgaagccuagacc
guaaggucgggucgaacggccucuagugcagaucuuggugguaguagcaa
auauucaaaugagaacuuugaagacugaaguggggaaagguuccacguca
acagcaguuggacguggguuagucgauccuaagagauggggaagcuccgu
uucaaaggccugauuuuaugcaggccaccaucgaaagggaauccgguuaa
gauuccggaaccuggauauggauucuucacgguaacguaacugaaugugg
agacgucggcgcgagcccugggaggaguuaucuuuucuucuuaacagcuu
aucaccccggaauugguuuauccggagauggggucuuauggcuggaagag
gccagcaccuuugcuggcuccggugcgcuugugacggcccgugaaaaucc
acaggaaggaauaguuuucaugccaggucguacugauaaccgcagcaggu
cuccaaggugaacagccucuaguugauagaauaauguagauaagggaagu
cggcaaaauagauccguaacuucgggauaaggauuggcucuaagggucgg
acgaucaacuuagaacugguacggacaaggggaaucugacugucuaauua
aaacauagcauugcgauggucagaaagugauguugacgcaaugugauuuc
ugcuggauuaacgagauucccacugucccuaucuacuaucuagcgaaacc
acagccaagggggcuuggcagaaucagcggggaaagaagacccuguugag
cuugacucuaguuugacauugugaagagacauaguuucuuuacuuauuca
augaagcggagcuggaauucauuuuccacguucuagcauucaagguccca
uucggggcugauccggguugaagacauugucagguggggaguuugggggc
ggcacaucuguuaaacgauaacgcagauguccuaaggggggcucauggag
aacagaaaucuccaguagaacaaaaggguaaaagcccccuugauuuugau
uuucagugugaauacaaaccaugaaaguguggccuaucgauccuuuaguc
ccucggaauuugaggcuagaggugccagaaaaguuaccacagggauaacu
ggcuuguggcagucaagcguucauagcgacauugcuuuuugauucuucga
ugucggcucuuccuaucauaccgaagcagaauucgguaagcguuggauug
uucacccacuaauagggagugagcuggguuuagaccgucgugagacaggu
uaguuuuacccuacugaugaauguuaccgcaauaguaauugaacuuagua
cgagaggaacaguucauucggauaauugguuuuugcggcugucugaucag
gcauugccgcgaagcuaccauccgcuggauuauggcugaacgccucuaag
ucagaauccaugcuagaacgcggugauuucuuugcuccacacaauauaga
uggauacgaauaaggcguccuuguggcgucgcugaaccauagcaggcuag
caacggugcacuuggcggaaaggccuugggugcuugcuggcgaauugcaa
ugucauuuugcguggggauaaaucauuuguauacgacuuagauguacaac
gggguauuguaagcaguagaguagccuuguuguuacgaucugcugagauu
aagccuuuguugucugauuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6m62 Coupling of 5S RNP rotation with maturation of functional centers during large ribosomal subunit assembly.
• Resolution: 3.2 Å
• Binding residue (original residue number in PDB): A2 L4 R5 T6 K8 R9 G18 K19 R20 K21 W23 L24 P26 S37 R38 R42 K46 T56 V57 H58 S59 K60 S61 R62 R64 K70 R71 R74 H75 G77 Y78 G79 K80 R81 K82 G83 T84 R85 A87 R88 L89 Q92 W95 I96 R100 R103 R104 R110 K117 H118 Y120 H121 Y124 K125 K128 G129 N130 H134 R136
• Binding residue (residue number reindexed from 1): A1 L3 R4 T5 K7 R8 G17 K18 R19 K20 W22 L23 P25 S36 R37 R41 K45 T55 V56 H57 S58 K59 S60 R61 R63 K69 R70 R73 H74 G76 Y77 G78 K79 R80 K81 G82 T83 R84 A86 R87 L88 Q91 W94 I95 R99 R102 R103 R109 K116 H117 Y119 H120 Y123 K124 K127 G128 N129 H133 R135

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:6m62, PDBe:6m62, PDBj:6m62
• PDBsum: 6m62
• PubMed: 32719344
• UniProt: P0CX82|RL19A_YEAST Large ribosomal subunit protein eL19A (Gene Name=RPL19A)