Structure of PDB 7mpj Chain Aj Binding Site BS01

Receptor Information

>7mpj Chain Aj (length=87) Species: 4932 (Saccharomyces cerevisiae)

GKGTPSFGKRHNKSHTLCNRCGRRSFHVQKKTCSSCGYPAAKTRSYNWGA
KAKRRHTTGTGRMRYLKHVSRRFKNGFQTGSASKASA

Ligand information

>7mpj Chain A1 (length=3137)

uugaccucaaaucagguaggaguacccgcugaacuuaagcauaucaauaa
gcggaggaaaagaaaccaaccgggauugccuuaguaacggcgagugaagc
ggcaaaagcucaaauuugaaaucugguaccuucggugcccgaguuguaau
uuggagagggcaacuuuggggccguuccuugucuauguuccuuggaacag
gacgucauagagggugagaaucccguguggcgaggagugcgguucuuugu
aaagugccuucgaagagucgaguuguuugggaaugcagcucuaagugggu
gguaaauuccaucuaaagcuaaauauuggcgagagaccgauagcgaacaa
guacagugauggaaagaugaaaagaacuuugaaaagagagugaaaaagua
cgugaaauuguugaaagggaagggcauuugaucagacaggccagcaucag
uuuugguggcaggauaaauccauaggaauguagcuugccucgguaaguau
uauagccugugggaauacugccagcugggacugaggacugcgacguaagu
caaggaugcuggcauaaugguuauaugccgcccgucuugaaacacggacc
aaggagucuaacgucuaugcgaguguuuggguguaaaacccauacgcgua
augaaagugaacguagguuggggccucgcaagaggugcacaaucgaccga
uccugaugucuucggauggauuugaguaagagcauagcuguugggacccg
aaagauggugaacuaugccugaauagggugaagccagaggaaacucuggu
ggaggcucguagcgguucugacgugcaaaucgaucgucgaauuuggguau
aggggcgaaagacuaaucgaaccaucuaguagcugguuccugccgaaguu
ucccucaggauagcagaagcucguaucaguuuuaugagguaaagcgaaug
auuagagguuccggggucaccuugaccuauucucaaacuuuaaauaugua
agaaguccuuguuacuuaauugaacguggacauuugaaugaagagcuuuu
agugggccauuuuugguaagcagaacuggcgaugcgggaugaaccgaacg
uagaguuaaggugccggaauacacgcucaucagacaccacaaaagguguu
aguucaucuagacagccggacgguggccauggaagucggaauaggagugu
guaacaacucaccggccgaaugaacuagcccugaaaauggauggcgcuca
agcguguuaccuauacucuaccgucaggguugauaugaugcccugacgag
uaggcaggcguggaggucagugacgaagccuagaccguaaggucgggucg
aacggccucuagugcagaucuuggugguaguagcaaauauucaaaugaga
acuuugaagacugaaguggggaaagguuccacgucaacagcaguuggacg
uggguuagucgauccuaagagauggggaagcuccguuucaaaggccugau
uuuaugcaggccaccaucgaaagggaauccgguuaagauuccggaaccug
gauauggauucuucacgguaacguaacugaauguggagacgucggcgcga
gcccugggaggaguuaucuuuucuucuuaacagcuuaucaccccggaauu
gguuuauccggagauggggucuuauggcuggaagaggccagcaccuuugc
uggcuccggugcgcuugugacggcccgugaaaauccacaggaaggaauag
uuuucaugccaggucguacugauaaccgcagcaggucuccaaggugaaca
gccucuaguugauagaauaauguagauaagggaagucggcaaaauagauc
cguaacuucgggauaaggauuggcucuaagggucggguacgaucaacuua
gaacugguacggacaaggggaaucugacugucuaauuaaaacauagcauu
gcgauggucagaaagugauguugacgcaaugugauuucugcccagugcuc
ugaaugucaaagugaagaaauucaaccaagcgcggguaaacggcgggagu
aacuaugacucucuuaagguagccaaaugccucgucaucuaauuagugac
gcgcaugaauggauuaacgagauucccacugucccuaucuacuaucuagc
gaaaccacagccaagggaacgggcuuggcagaaucagcggggaaagaaga
cccuguugagcuugacucuaguuugacauugugaagagacauaguuucuu
uacuuauucaaugaagcggagcuggaauucauuuuccacguucuagcauu
caaggucccauucggggcugauccggguugaagacauugucaggugggga
guuuggcuggggcggcacaucuguuaaacgauaacgcagauguccuaagg
ggggcucauggagaacagaaaucuccaguagaacaaaaggguaaaagccc
ccuugauuuugauuuucagugugaauacaaaccaugaaaguguggccuau
cgauccuuuagucccucggaauuugaggcuagaggugccagaaaaguuac
cacagggauaacuggcuuguggcagucaagcguucauagcgacauugcuu
uuugauucuucgaugucggcucuuccuaucauaccgaagcagaauucggu
aagcguuggauuguucacccacuaauagggaacgugagcuggguuuagac
cgucgugagacagguuaguuuuacccuacugaugaauguuaccgcaauag
uaauugaacuuaguacgagaggaacaguucauucggauaauugguuuuug
cggcugucugaucaggcauugccgcgaagcuaccauccgcuggauuaugg
cugaacgccucuaagucagaauccaugcuagaacgcggugauuucuuugc
uccacacaauauagauggauacgaauaaggcguccuuguggcgucgcuga
accauagcaggcuagcaacggugcacuuggcggaaaggccuugggugcuu
gcuggcgaauugcaaugucauuuugcguggggauaaaucauuuguauacg
acuuagauguacaacgggguauuguaagcaguagaguagccuuguuguua
cgaucugcugagauuaagccuuuguugucugauuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7mpj CryoEM structures of pseudouridine-free ribosome suggest impacts of chemical modifications on ribosome conformations.
• Resolution: 2.7 Å
• Binding residue (original residue number in PDB): G2 K3 G4 T5 P6 F8 G9 K10 R11 H12 N13 K14 S15 H16 R24 R25 S26 H28 Q30 K31 S35 S36 K43 T44 R45 Y47 N48 W49 K52 R55 R56
• Binding residue (residue number reindexed from 1): G1 K2 G3 T4 P5 F7 G8 K9 R10 H11 N12 K13 S14 H15 R23 R24 S25 H27 Q29 K30 S34 S35 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:7mpj, PDBe:7mpj, PDBj:7mpj
• PDBsum: 7mpj
• PubMed: 35489333
• UniProt: P49166|RL37A_YEAST Large ribosomal subunit protein eL37A (Gene Name=RPL37A)