Structure of PDB 8hfr Chain jh Binding Site BS01

Receptor Information

>8hfr Chain jh (length=87) Species: 559292 (Saccharomyces cerevisiae S288C)

GKGTPSFGKRHNKSHTLCNRCGRRSFHVQKKTCSSCGYPAAKTRSYNWGA
KAKRRHTTGTGRMRYLKHVSRRFKNGFQTGSASKASA

Ligand information

>8hfr Chain 1e (length=3274)

ugaccucaaaucagguaggaguacccgcugaacuuaagcauaucaauaag
cggaggaaaagaaaccaaccgggauugccuuaguaacggcgagugaagcg
gcaaaagcucaaauuugaaaucugguaccuucggugcccgaguuguaauu
uggagagggcaacuuuggggccguuccuugucuauguuccuuggaacagg
acgucauagagggugagaaucccguguggcgaggagugcgguucuuugua
aagugccuucgaagagucgaguuguuugggaaugcagcucuaagugggug
guaaauuccaucuaaagcuaaauauuggcgagagaccgauagcgaacaag
uacagugauggaaagaugaaaagaacuuugaaaagagagugaaaaaguac
gugaaauuguugaaagggaagggcauuugaucagacgccagcaucaguuu
ugguggcaggauaaauccauaggaauguagcuugccucgguaaguauuau
agccugugggaauacugccagcugggacugaggacugcgacguaagucaa
ggaugcuggcauaaugguuauaugccgcccgucuugaaacacggaccaag
gagucuaacgucuaugcgaguguuuggguguaaaacccauacgcguaaug
aaagugaacguagguuggggccucgcaagaggugcacaaucgaccgaucc
ugaugucuucggauggauuugaguaagagcauagcuguugggacccgaaa
gauggugaacuaugccugaauagggugaagccagaggaaacucuggugga
ggcucguagcgguucugacgugcaaaucgaucgucgaauuuggguauagg
ggcgaaagacuaaucgaaccaucuaguagcugguuccugccgaaguuucc
cucaggauagcagaagcucguaucaguuuuaugagguaaagcgaaugauu
agagguuccggggucgaaaugaccuugaccuauucucaaacuuuaaauau
guaagaaguccuuguuacuuaauugaacguggacauuugaaugaagagcu
uuuagugggccauuuuugguaagcagaacuggcgaugcgggaugaaccga
acguagaguuaaggugccggaauacacgcucaucagacaccacaaaaggu
guuaguucaucuagacagccggacgguggccauggaagucggaauccgcu
aaggaguguguaacaacucaccggccgaaugaacuagcccugaaaaugga
uggcgcucaagcguguuaccuauacucuaccgucaggguugauaugaugc
ccugacgaguaggcaggcguggaggucagugacgaagccuagaccguaag
gucgggucgaacggccucuagugcagaucuuggugguaguagcaaauauu
caaaugagaacuuugaagacugaaguggggaaagguuccacgucaacagc
aguuggacguggguuagucgauccuaagagauggggaagcuccguuucaa
aggccugauuuuaugcaggccaccaucgaaagggaauccgguuaagauuc
cggaaccuggauauggauucuucacgguaacguaacugaauguggagacg
ucggcgcgagcccugggaggaguuaucuuuucuucuuaacagcuuaucac
cccggaauugguuuauccggagauggggucuuauggcuggaagaggccag
caccuuugcuggcuccggugcgcuugugacggcccgugaaaauccacagg
aaggaauaguuuucaugccaggucguacugauaaccgcagcaggucucca
aggugaacagccucuaguugauagaauaauguagauaagggaagucggca
aaauagauccguaacuucgggauaaggauuggcucuaagggucggguagu
gagggccuuggucagacgcagcgggcgugcuuguggacugcuuggugggg
cuugcucugcuaggcggacuacuugcgugccuuguuguagacggccuugg
uaggucucuuguagaccgucgcuugcuacaauuaacgaucaacuuagaac
ugguacggacaaggggaaucugacugucuaauuaaaacauagcauugcga
uggucagaaagugauguugacgcaaugugauuucugcccagugcucugaa
ugucaaagugaagaaauucaaccaagcgcggguaaacggcguggauuaac
gagauucccacugucccuaucuacuaucuagcgaaaccacagccaaggga
acgggcuuggcagaaucagcggggaaagaagacccuguugagcuugacuc
uaguuugacauugugaagagacauagaggguguagaauaagugggagcuu
cggcgccagugaaauaccacuaccuuuauaguuucuuuacuuauucaaug
aagcggagcuggaauucauuuuccacguucuagcauucaaggucccauuc
ggggcugauccggguugaagacauugucagguggggaguuuggcuggggc
ggcacaucuguuaaacgauaacgcagauguccuaaggggggcucauggag
aacagaaaucuccaguagaacaaaaggguaaaagcccccuugauuuugau
uuucagugugaauacaaaccaugaaaguguggccuaucgauccuuuaguc
ccucggaauuugaggcuagaggugccagaaaaguuaccacagggauaacu
ggcuuguggcagucaagcguucauagcgacauugcuuuuugauucuucga
ugucggcucuuccuaucauaccgaagcagaauucgguaagcguuggauug
uucacccacuaauagggaacgugagcuggguuuagaccgucgugagacag
guuaguuuuacccuacugaugaauguuaccgcaauaguaauugaacuuag
uacgagaggaacaguucauucggauaauugguuuuugcggcugucugauc
aggcauugccgcgaagcuaccauccgcuggauuauggcugaacgccucua
agucagaauccaugcuagaacgcggugauuucuuugcuccacacaauaua
gauggauacgaauaaggcguccuuguggcgucgcugaaccauagcaggcu
agcaacggugcacuuggcggaaaggccuugggugcuugcuggcgaauugc
aaugucauuuugcguggggauaaaucauuuguauacgacuuagauguaca
acgggguauuguaagcaguagaguagccuuguuguuacgaucugcugaga
uuaagccuuuguugucugauuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8hfr Nuclear export of pre-60S particles through the nuclear pore complex.
• Resolution: 2.64 Å
• Binding residue (original residue number in PDB): G2 K3 T5 P6 F8 G9 K10 R11 H12 N13 K14 S15 H16 R24 S26 H28 Q30 K31 S35 K43 T44 R45 Y47 N48 W49 K52 R55 R56
• Binding residue (residue number reindexed from 1): G1 K2 T4 P5 F7 G8 K9 R10 H11 N12 K13 S14 H15 R23 S25 H27 Q29 K30 S34 K42 T43 R44 Y46 N47 W48 K51 R54 R55

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0008270 zinc ion binding
• GO:0019843 rRNA binding
• GO:0046872 metal ion binding

Biological Process

• GO:0000448 cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
• 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:0030687 preribosome, large subunit precursor
• GO:0044391 ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8hfr, PDBe:8hfr, PDBj:8hfr
• PDBsum: 8hfr
• PubMed: 37258668
• UniProt: P49166|RL37A_YEAST Large ribosomal subunit protein eL37A (Gene Name=RPL37A)