Structure of PDB 8i9v Chain Lf Binding Site BS01

Receptor Information

>8i9v Chain Lf (length=108) Species: 759272 (Thermochaetoides thermophila DSM 1495)

PSEAGHRLYVKGRHLSYQRGRRNTHPKTSLIKIEGVDDTAAANFYLGKRV
AYVYRAQKEVRGTKIRVIWGKITRPHGNSGVVRAKFTHPLPARSFGASVR
IMLYPSSI

Ligand information

>8i9v Chain C1 (length=2152)

uugaccucggaucagguaggaggacccgcugaacuuaagcauaucaauaa
gcggaggaaaagaaaccaacagggauugcccuaguaacggcgagugaagc
ggcaacagcucaaauuugaaagcuggcuucggcccgcguuguaauuugga
gaggaugcuuugggcgaggcuccuucugaguucccuggaacgggacgcca
cagagggugagagccccguauaguuggaagccaagccuguguaaagcucc
uucgacgagucgaguaguuugggaaugcugcucaaaaugggagguaaauu
ucuucuaaagcuaaauaccggccagagaccgauagcgcacaaguagagug
aucgaaagaugaaaagcacuuugaaaagaggguuaaauagcacgugaaau
uguugaaagggaagcgcuugugaccagacuugcgcccggcggaucauccg
guguucucaccggugcacuccgccgggcucaggccagcaucgguucuggc
ggggggauaaaggcccagggaauguggcuccuccgggaguguuauagccc
uggguguaauacccucgccgggaccgaggaccgcgcucugcaaggaugcu
ggcguaauggucaccagcgacccgucuugaaacacggaccaaggagucaa
gguuuugcgcgaguguuuggguguaaaacccgcacgcguaaugaaaguga
acguaggugagagcuucggcgcaucaucgaccgauccugauguauucgga
uggauuugaguaggagcguuaagccuuggacccgaaagauggugaacaac
caucuaguagcugguuaccgccgaaguuucccucaggauagcagugucga
ccuucaguuuuaugagguaaagcgaaugaacuuuaaauauguaagaagcc
cuuguuacuuaacugaacgugggcauucgaauguaucgacacuagugggc
cauuuuugguaagcagaacuggcgaugcgggaugaaccgaacgcgggguu
aaggugccggaguggacgcucaucagacaccacaaaaggcguuaguacau
cuugacagcaggacgguggccauggaagucggaauccgcuaaggacugug
uaacaacucaccugccgaauguacuagcccugaaaauggauggcgcucaa
gcgucccacccauaccccgcccucaggguagaaacgaugcccugaggagu
aggcggccguggaggucagugacgaagccuagggcgugagcccgggucga
acggccucuagugcagaucuuggugguaguagcaaauuugauagaacaau
guagauaagggaagucggcuccguaacuugguacggacaggggaaucugc
gagauucccacugucccuaucuacuaucuagcgaaaccacagccaaggga
acgggcuuggcaaaaucagcggggaagacccuguugagcuugacucuagu
uugacauugugaaaagacauaggagguguagaauaggugggagcuucggc
gccagugaaauaccacuacuccuauuguuuuuuuacuuauucaauugaag
acauugucagguggggaguuccuuuagucccucgaaauuugaggcuagag
gagaaaaguuaccacagggauaacuggcuuguggcggccaagcguucaua
gcgacgucgcuuuuuggaugucggcucuuccuaucauaccgaagcagaau
ucgguaagcguuggauuguucacccacuaauagggaacguggaccgucgu
gagacagguuagucccuacugaugaacucgucgcaaugguaauucagcuu
aguacgagaggaaccgcugauucagauaauugguuuuugcgguuguccga
ccgggcagugccgcgaagcuaccaucugcuggauaauggcugaacgccuc
uaagucagaauccaugccagaacgcgacgauaacccgcacguagacguau
aagaauaggcuccggccucguauccuagcaggcgauuccuccgccggccu
cgaaguggccgucgguaauucgcguauugcaaagacacgcgcgggaucaa
auccuuugcagacgacuuagaugugcgaaaggguccuguaagcaguagag
uagccuuguuguuacgaucugcugaggguaagcccuccuucgccuagauu
uc

........................<<<<<<.....<......>......>
>>>>.>...<.....<<....>>..<<<<<......<<.....>>.....
>>>>>..<<<..<<.......<<.<<<....>>>.>>.......>>....
<<<<<.<<<<<<<<<..<<<<<<..<<....<<<<......>>>>.((..
....<<<.....))>>>....>>..>>>.>>>..>>>>....>>>>>>>>
.>>........<<<<<<<........>>>>>>>.....<<<<<<......
>>>>>>..>>>....>.............................<<...
.>>...............<<<<....>>>>....................
..............<<<<.<<<<<<<....<<.<<<<<<<<<<.<<.<<<
<<<....>>>>>>>>...>>>>>>>>>>.>>.<<<<<<<.<<<<<<<<<<
<<<<<.......<<<<<<<<......<<<<<....>>>>>.......>>>
>>>>>......>>>>>>>>>>>>>>>........<<...>>.....>>>>
>>>....>>>>>>>.>>>>..<<<<.<....>.>>>><<<<<<...<<<<
<<<<<.<<<<..<<<...<<<<.....>>>>...>>>...<<....>>..
.....<<<<<..<<....>>...>>>>>.<<<<<<<<....<....>...
.>>>.>>>.>>....>>>>.>>>>>>>>>.<<.<..<<<<<<<.....>>
>>>>...>..>.>>...<<<<<....<.<<<....>>>.><<<<<<<<<<
....<<.<<<<<<<.....<<<........>>.>.....>>>>>....<<
..<<<<.<......>>>>>.>>.......>>>>..>>>>>>>>.>>..<<
<<.<<<<<.....>>>>>.>>>>....<<<......>>>...<<<<<<<.
..<<<(((.....<<<<<<.....<<..........<<<.<<<<<<<<<<
.......<<<<<.<<<...<<.........>>...>>>.........<<.
.....>>...>>>>>...>>>>>>>>>>>>>..........))).>>...
>>>>>>.>>>...>>>>>>><<<<<<<<<.........>>>>>>>>>...
.>>>>>.<.<<<<<<<<.<<......<<<<.<<<<....>>>>>>>>...
>>>>>>>>>>..>.....>>>>>><<.....<<........<<<<.....
<<<<<<.<<<<<<<<....<<<<<<.<..>.>>>>>>...<<<<<<<<<>
>.>>>>>>>>>>.>>>>>>>>>>>..>>>>>>....>>....<<<<<...
.....>>>>>....<<<<<.<<<.....<<<<<<.<<<<<<.<<<<<.<<
<<<<<<..<<<<<<<<<<<<<<<<<..........<<<<<..........
............>>>>>.>>>>>>>.>>>>>>>>>>...<<<<..>>>>.
....>>>>>>>>..>>>>>.<<<<<<<..<<<<<<...>>>>>>>>>>>>
>....>>>>>.>.>>>>>>.............<<<<<<...<<.......
>>...>>>>>>.....((........<<<<<<..<.<<<<<<<......>
>>>>>>...>.<<<.....))..>>>.....>>>>>..>...<<<<<<..
..>>>.>>>.....>>>.>>>>>....<<<<<<<..<<<<.<.<<<<<..
...............>>>>>.><<<<<...<<<<....<<<<<<<<<<..
..>>>>>..>>>>>...>>>>..>>>>>.<<<<...<<<<<.........
..>>>>>...>>>>.>>>>....>>>>>>>...<<<<<.<<.......<<
.......<<<<..>>>>....>>........<<<<.....<<<.<<<<<.
......>>>>>.>>>....>>>>..............>>.>>>>>...<<
<<<<<.............>>....<<<<<<<<<.<<<....<<<<....<
<<<<......>>>>>...>>>>...>>>....>>>>..>>>>>...>>>>
>.

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8i9v Mechanism of 5S RNP recruitment and helicase-surveilled rRNA maturation during pre-60S biogenesis.
• Resolution: 3.1 Å
• Binding residue (original residue number in PDB): P2 S3 E4 H7 R8 Y10 K12 Q19 R20 G21 R22 R23 N24 T25 H26 P27 K28 L47 Y55 R56 A57 K59 R62 R67 K72 T74 R75 H77 G78 N79 S80 R84 P90 P92 A93 R94 S99 R101
• Binding residue (residue number reindexed from 1): P1 S2 E3 H6 R7 Y9 K11 Q18 R19 G20 R21 R22 N23 T24 H25 P26 K27 L46 Y54 R55 A56 K58 R61 R66 K71 T73 R74 H76 G77 N78 S79 R83 P89 P91 A92 R93 S98 R100

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0042273 ribosomal large subunit biogenesis

Cellular Component

• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8i9v, PDBe:8i9v, PDBj:8i9v
• PDBsum: 8i9v
• PubMed: 37129998
• UniProt: G0SCL3