Structure of PDB 8pv4 Chain CR Binding Site BS01

Receptor Information

>8pv4 Chain CR (length=390) Species: 759272 (Thermochaetoides thermophila DSM 1495)

ADLVNLQYKIRRDPKSYAQEFYDQWLAYDAQRQIFFSSPATASSEDIKKF
HDLVDLVAHVADLYPDITAPFPDHLKQLLTQHHTTLDKDLREKVVGSLVL
LRRKDVIDSVSLLTTLFPILISSPSKSLRTLIYTKIISDLRESNAKATNH
KLNRTIQTVLHNLLTSDRTSSKGLWACRITRELWRRQIWTDARPCDVMKE
ACLSDNEKVVVGGCRFFLGGDKNFSALHLINDPQGFAEKLFQKHLQNLKN
KFTLENRLLVLQLVTRLVGLHKLTVLPLYSWFVRYLTPKQLNVTTFLACL
AQATHNLVPPDVIEPLVVKIANEFVSEASAAEVAAAGLNAIREVAMRQPL
CMSETLLQDLVLYQKSKDKGVMMAAKGLQSLYREVYPEML

Ligand information

>8pv4 Chain C1 (length=3136)

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
ucuaguuugacauugugaaaagacauaggagguguagaauaggugggagc
uucggcgccagugaaauaccacuacuccuauuguuuuuuuacuuauucaa
ugaagcggggcuggacuugcguccaacuucuggaguuaagguccuucgcg
ggccgacccggguugaagacauugucagguggggaguuuggcuggggcgg
cacaucugugcagguguccuaaggggggcucauggagaacagaaaucucc
aguagaacaaaaggguaaaaguccccuugauuuugauuuucagugugaau
acaaaccaugaaaguguggccuaucgauccuuuagucccucgaaauuuga
ggcuagaggugccagaaaaguuaccacagggauggcuuguggcggccaag
cguucauagcgacgucgcuuugauccuucgaugucggcucuuccuaucau
accgaagcagaauucgguaagcguuggauuguucacccacuaauagggaa
cgagcuggguuuagaccgucgugagacagguuaguuuuacccuacugaug
aacucgucgcaaugguaauucagcuuaguacgagaggaaccgcugauuca
gauaauugguuuuugcgguuguccgaccgggcagugccgcgaagcuacca
ucugcuggauaauggcugaacgccucuaagucagaauccaugccagaacg
cgacgauacuacccgcacguuguagacguauaagaauaggcuccggccuc
guauccuagcaggcgauuccuccgccggccucgaaguggccgucgguaau
ucgcguauugcaauuuagacacgcgcgggaucaaauccuuugcagacgac
uuagaugugcgaaaggguccuguaagcaguagaguagccuuguuguuacg
aucugcugaggguaagcccuccuucgccuagauuuc

...........................<<<<<<.....<...<..>....
..>>>>>.>.........<<....>>..<<<<<......<<.>...>>..
...>>>>>..<<<..<<.......<<.<<<....>>>.>>.......>>.
...<<<<<.<<<<<<<<<..<<<<<<..<<<...<<<<......>>>>.(
(......<<<.....))>>>.>..>>..>>.>>>>..>>>>....>>>>>
>>>.>>........<<<<<<<........>>>>>>>.....<<<<<..((
((((>>>>>..>>>..................................<<
....>>...............<<<<....>>>>.................
.................<<<<.<<<<<<.<...<<.<<<<<<<<<.....
<<<<<<....>>>>>>......>>>>>>>>>.>>.<<<<<<<.<<<<<<<
<<<<<<<<.......<<<<<<<<......<<<<<....>>>>>.......
>>>>>>>>......>>>>>>>>>>>>>>>........<<...>>.....>
>>>>>>....>>>>>>>.>>>>..<<<<.<....>.>>>><<<<<<...<
<<<<<<<<.<<<<..<<<..<<<<<.....>>>>>..>>>...<<....>
>.......<<<<<..<<....>>...>>>>>.<<<<<<<<...<<....>
>...>>>>.>>.>>....>>>>.>>>>>>>>>.<<.<...<<<<<<....
.<<<<<<<<<..<<<....<<<<<<<....>>>>>>>.....>>>...<<
<<.<<.<<........>>>>>>>>....>>>>>>>>>...<<.......>
>......>>>>>>......>.>>...<<<<<......<<<....>>>..<
<<<<<<<<.....<<.<<<<<<<.....<<<........>>.>.....>>
>>>...<<<<.<<<<.<......>>>>>.>>>>.....>>>>...>>>>>
>>.>>..<<<<.<<<<<.....>>>>>.>>>>....<<<......>>>..
.<<<<<<<...<<<(((.....<<<<<<.....<<..........<<<.<
<<<<<<<<<.......<<<<<.<<<...<<.........>>...>>>...
......<<......>>...>>>>>...>>>>>>>>>>>>>..........
))).>>...>>>>>>.>>>...>>>>>>><<<<<<<<<.........>>>
>>>>>>....>>>>>.<.<<<<<<<<.<<......<<<<.<<<<....>>
>>>>>>...>>>>>>>>>>..>.....>>>>>><<<....<<.....<<<
<<<.......>>>>>><<<<.....<<<<<.<<...<<<<<<...<<...
..>>.>>>>>>....((<<<<<<...<<<<..<<<....>>>........
<<<<<......>>>>>...>>>>....>>...<<<<<........>>>>>
))<<<<.<<<<.<<<....<<<....>>>...<.((<<<<<<...<<<<.
<<<<<<<.<<<<<.<<<<...[[..>>>>.><...<<<<<....<<<<<<
....<<<.....>>>....>>>>>>.....>>>>>....><<<<<<<...
...>>>>>>>>>>>...>>>>>>>.>>>>.........>>>>>>...>..
...>>>...>>>>>>>>>>>>..>>.....<<......>>>>>>>.<<<<
.....>>>>..>>>>..<<<<.....<<<<<<<.<<.........<....
.<<<<<....<....>.....>>>>><<.<<<<<<<<<<<.<<<<<..>>
>>>......>>>>>..>>>>>>.>>............<<<<<<<<<..<<
<.........>>>..<<<<<<<....<<<<.....>>>>......>>>>>
>>.........<<.<<<<<.....<<<.....<<<<....>>>>.....>
>>..>>>..>>>>.<<<<<<.......>>>>>>......<<..>>.....
.>>.>>>>>>>..>..>>.>>>>>>>..>>>>>>...>>>....<<<<<.
.......>>>>>....<<<<<..<<<........<<<<<.<<<<<<..<<
<<<.<<<<<<<<..<<<<<<<<<<<<<<<<<..........<<<<<..<<
....>>............>>>>>.>>>>>>>.>>>>>>>>>>...<<<<<
.....<<<<..<<<<<....>>>>>..........))..<<<<<.....>
>>>>..>>>>..>>>>>.....>>>>>>>>..>>>>>.......<<<<<<
.<<<<<<....>>>>>>>>...<<<<<<<...<<<<<<.......>>>>>
>.....<<......>>....>>>>>>>....<<<<.<.<<<.....>>>.
>>>>><<<<....>>>.>>>>>.<<...<<<<<<<..<<<<.))))))>>
>>>>>>>>>.....>>..>>>>..>>>>>>>.........<<<<<<...<
<.......>>...>>>>>>...............<<<<..<<<<<..<.<
<<<<<<......>>>>>>>...>.<<<.........>>>.....>>>>>.
...>>>>......<<<<<<<....>>>.>>>>........>>>.>>>>>.
...<<<<<<<..<<<<.<.<<<<<.................>>>>>.><<
<<<...<<<<....<<<<<<<<<<]]..>>>>>..>>>>>...>>>>..>
>>>>.<<<<...<<<<<...........>>>>>...>>>>.>>>>....>
>>>>>>.....<<<<<.<<.<<<......<<.......<<<....>>>..
..>>........<<<<.....<<<.<<<<<.......>>>>>.>>>....
>>>>..............>>>>>.>>>>>...<<<<<<<...........
..>>....<<<<<<<<<.<<<....<<<<....<<<<<......>>>>>.
..>>>>...>>>....>>>>..>>>>>...>>>>>.

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8pv4 Structural insights into coordinating 5S RNP rotation with ITS2 pre-RNA processing during ribosome formation.
• Resolution: 2.9 Å
• Binding residue (original residue number in PDB): K148 S151 R154 K159 H163 K164 R198 R199 N292
• Binding residue (residue number reindexed from 1): K135 S138 R141 K146 H150 K151 R185 R186 N223

Gene Ontology

Biological Process

• GO:0000055 ribosomal large subunit export from nucleus
• GO:0015031 protein transport
• GO:0042254 ribosome biogenesis
• GO:0042273 ribosomal large subunit biogenesis

Cellular Component

• GO:0005634 nucleus
• GO:0005730 nucleolus

External links

• PDB: RCSB:8pv4, PDBe:8pv4, PDBj:8pv4
• PDBsum: 8pv4
• PubMed: 37921038
• UniProt: G0S215|SDA1_CHATD Protein SDA1 (Gene Name=SDA1)