Structure of PDB 8pvl Chain CN Binding Site BS01

Receptor Information

>8pvl Chain CN (length=246) Species: 759272 (Thermochaetoides thermophila DSM 1495)

MAVRAQFENSNEVGVFATLTNSYCLVALGASENFYSVFEAELQDVIPICR
TTIAGTRIIGRLTAGNRKGLLVPTTTTDQELQHLRNSLPDDIRIQRIEER
LSALGNVIVCNDHTALIHPDLERETEEIIADVLGVEVFRQTIADHVLVGS
YMALSNQGGLVHPKTSIQDQDELSSLLGVPLVAGSVNRGSNVIGGGMVVN
DWLAVTGLDTTAPELSVIESVFRLGEGAGPGAINTSMKNTIVESFY

Ligand information

>8pvl Chain C1 (length=3078)

agguugaccucggaucagguaggaggacccgcugaacuuaagcauaucaa
uaagcggaggaaaagaaaccaacagggauugcccuaguaacggcgaguga
agcggcaacagcucaaauuugaaagcuggcuucggcccgcguuguaauuu
ggagaggaugcuuugggcgaggcuccuucugaguucccuggaacgggacg
ccacagagggugagagccccguauaguuggaagccaagccuguguaaagc
uccuucgacgagucgaguaguuugggaaugcugcucaaaaugggagguaa
auuucuucuaaagcuaaauaccggccagagaccgauagcgcacaaguaga
gugaucgaaagaugaaaagcacuuugaaaagaggguuaaauagcacguga
aauuguugaaagggaagcgcuugugaccagacuugcgcccggcggaucau
ccgguguucucaccggugcacuccgccgggcucaggccagcaucgguucu
ggcggggggauaaaggcccagggaauguggcuccuccgggaguguuauag
cccuggguguaauacccucgccgggaccgaggaccgcgcucugcaaggau
gcuggcguaauggucaccagcgacccgucuugaaacacggaccaaggagu
caagguuuugcgcgaguguuuggguguaaaacccgcacgcguaaugaaag
ugaacguaggugagagcuucggcgcaucaucgaccgauccugauguauuc
ggauggauuugaguaggagcguuaagccuuggacccgaaagauggugaac
uaugcuuggauagggugaagccagaggaaacucugguggaggcucgcagc
gguucugacgugcaaaucgaucgucaaaucugagcaugggggcgaaagac
uaaucgaaccaucuaguagcugguuaccgccgaaguuucccucaggauag
cagugucgaccuucaguuuuaugagguaaagcgaaugaacuuuaaauaug
uaagaagcccuuguuacuuaacugaacgugggcauucgaauguaucgaca
cuagugggccauuuuugguaagcagaacuggcgaugcgggaugaaccgaa
cgcgggguuaaggugccggaguggacgcucaucagacaccacaaaaggcg
uuaguacaucuugacagcaggacgguggccauggaagucggaauccgcua
aggacuguguaacaacucaccugccgaauguacuagcccugaaaauggau
ggcgcucaagcgucccacccauaccccgcccucaggguagaaacgaugcc
cugaggaguaggcggccguggaggucagugacgaagccuagggcgugagc
ccgggucgaacggccucuagugcagaucuuggugguaguagcaaauacuu
caaugagaacuugaaggaccgaaguggggaaagguuccaugugaacagcg
guuggacauggguuagucgauccuaagccauagggaaguuccguuucaaa
ggggcacucgugccccguguggcgaaagggaagccgguuaauauuccggc
accuggauguggguuuugcgcggcaacgcaacugaacgcggagacgacgg
cgggggccccgggcagaguucucuuuucuucuuaacggucuaucacccug
gaaacaguuugucuggagauaggguuuaauggccggaagagcccgacacu
ucugucggguccggugcgcucucgacgucccuugaaaauccgcgggaggg
aauaauucucacgccaggucguacucauaaccgcagcagguccccaaggu
gaacagccucugguugauagaacaauguagauaagggaagucggcaaaau
agauccguaacuucgggaaaaggauuggcucuaaggguugggcacgugcg
ugcgguuaacaaccaacuuagaacugguacggacagggggaaucugacug
ucuaauuaaaacauagcauugcgauggccagaaagugguguugacgcaau
gugauuucugcccagugcucugaaugucaaagugaagaaauucaaccaag
cgcggguaaacggcgggaguaacuaugacucucuguagccaaauggauua
acgagauucccacugucccuaucuacuaucuagcgaaaccacagccaagg
gaacgggcuuggcaaaaucagcggggaaagaagacccuguugagcuugac
ucuaguuugacauugugaaaagauuuuuuuacuuauucaaugaagcgggg
cuggacuugcguccaacuucuggaguuaagguccuucgcgggccgacccg
gguugaagacauugucagguggggaguuuggcuggggcggcacaucugug
cagguguccuaaggggggcucauggagaacagaaaucuccaguagaacaa
aaggguaaaaguccccuugauuuugauuuucagugugaauacaaaccaug
aaaguguggccuaucgauccuuuagucccucgaaauuugaggcuagaggu
gccagaaaaguuaccacagggauggcuuguggcggccaagcguucauagc
gacgucgcuuugauccuucgaugucggcucuuccuaucauaccgaagcag
aauucgguaagcguuggauuguucacccacuaauagggaacgugagcugg
guuuagaccgucgugagacagguuaguuuuacccuacugaugaacucguc
gcaaugguaauucagcuuaguacgagaggaaccgcugauucagauaauug
guuuuugcgguuguccgaccgggcagugccgcgaagcuaccaucugcugg
auaauggcugaacgccucuaagucagaauccaugccagaacgcgacgaua
cuacccgcacguuguagacguauaagaauaggcuccggccucguauccua
gcaggcgauuccuccgccggccucgaaguggccgucgguaauucgcguau
ugcaauuuagacacgcgcgggaucaaauccuuugcagacgacuuagaugu
gcgaaaggguccuguaagcaguagaguagccuuguuguuacgaucugcug
aggguaagcccuccuucgccuagauuuc

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8pvl Structural insights into coordinating 5S RNP rotation with ITS2 pre-RNA processing during ribosome formation.
• Resolution: 2.19 Å
• Binding residue (original residue number in PDB): N9 R188
• Binding residue (residue number reindexed from 1): N9 R188

Gene Ontology

Molecular Function

• GO:0003743 translation initiation factor activity
• GO:0043022 ribosome binding
• GO:0043023 ribosomal large subunit binding

Biological Process

• GO:0000054 ribosomal subunit export from nucleus
• GO:0000460 maturation of 5.8S rRNA
• GO:0000470 maturation of LSU-rRNA
• GO:0006412 translation
• GO:0006413 translational initiation
• GO:0042254 ribosome biogenesis
• GO:0042256 cytosolic ribosome assembly
• GO:0042273 ribosomal large subunit biogenesis
• GO:1902626 assembly of large subunit precursor of preribosome

Cellular Component

• GO:0005634 nucleus
• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0030687 preribosome, large subunit precursor

External links

• PDB: RCSB:8pvl, PDBe:8pvl, PDBj:8pvl
• PDBsum: 8pvl
• PubMed: 37921038
• UniProt: G0S683