Structure of PDB 5t62 Chain w Binding Site BS01

Receptor Information

>5t62 Chain w (length=87) Species: 559292 (Saccharomyces cerevisiae S288C)

GKGTPSFGKRHNKSHTLCNRCGRRSFHVQKKTCSSCGYPAAKTRSYNWGA
KAKRRHTTGTGRMRYLKHVSRRFKNGFQTGSASKASA

Ligand information

>5t62 Chain A (length=3204)

uugaccucaaaucagguaggaguacccgcugaacuuaagcauaucaauaa
gcggaggaaaagaaaccaaccgggauugccuuaguaacggcgagugaagc
ggcaaaagcucaaauuugaaaucugguaccuucggugcccgaguuguaau
uuggagagggcaacuuuggggccguuccuugucuauguuccuuggaacag
gacgucauagagggugagaaucccguguggcgaggagugcgguucuuugu
aaagugccuucgaagagucgaguuguuugggaaugcagcucuaagugggu
gguaaauuccaucuaaagcuaaauauuggcgagagaccgauagcgaacaa
guacagugauggaaagaugaaaagaacuuugaaaagagagugaaaaagua
cgugaaauuguugaaagggaagggcauuugaucagacaggccagcaucag
uuuugguggcaggauaaauccauaggaauguagcuugccucgguaaguau
uauagccugugggaauacugccagcugggacugaggacugcgacguaagu
caaggaugcuggcauaaugguuauaugccgcccgucuugaaacacggacc
aaggagucuaacgucuaugcgaguguuuggguguaaaacccauacgcgua
augaaagugaacguagguuggggccucgcaagaggugcacaaucgaccga
uccugaugucuucggauggauuugaguaagagcauagcuguugggacccg
aaagauggugaacuaugccugaauagggugaagccagaggaaacucuggu
ggaggcucguagcgguucugacgugcaaaucgaucgucgaauuuggguau
aggggcgaaagacuaaucgaaccaucuaguagcugguuccugccgaaguu
ucccucaggauagcagaagcucguaucaguuuuaugagguaaagcgaaug
auuagagguuccggggucgaaaugaccuugaccuauucucaaacuuuaaa
uauguaagaaguccuuguuacuuaauugaacguggacauuugaaugaaga
gcuuuuagugggccauuuuugguaagcagaacuggcgaugcgggaugaac
cgaacguagaguuaaggugccggaauacacgcucaucagacaccacaaaa
gguguuaguucaucuagacagccggacgguggccauggaagucggaaucc
gcuaaggaguguguaacaacucaccggccgaaugaacuagcccugaaaau
ggauggcgcucaagcguguuaccuauacucuaccgucaggguugauauga
ugcccugacgaguaggcaggcguggaggucagugacgaagccuagaccgu
aaggucgggucgaacggccucuagugcagaucuuggugguaguagcaaau
auucaaaugagaacuuugaagacugaaguggggaaagguuccacgucaac
agcaguuggacguggguuagucgauccuaagagauggggaagcuccguuu
caaaggccugauuuuaugcaggccaccaucgaaagggaauccgguuaaga
uuccggaaccuggauauggauucuucacgguaacguaacugaauguggag
acgucggcgcgagcccugggaggaguuaucuuuucuucuuaacagcuuau
caccccggaauugguuuauccggagauggggucuuauggcuggaagaggc
cagcaccuuugcuggcuccggugcgcuugugacggcccgugaaaauccac
aggaaggaauaguuuucaugccaggucguacugauaaccgcagcaggucu
ccaaggugaacagccucuaguugauagaauaauguagauaagggaagucg
gcaaaauagauccguaacuucgggauaaggauuggcucuaagggucgggu
acgaucaacuuagaacugguacggacaaggggaaucugacugucuaauua
aaacauagcauugcgauggucagaaagugauguugacgcaaugugauuuc
ugcccagugcucugaaugucaaagugaagaaauucaaccaagcgcgggua
aacggcgggaguaacuaugacucucuuaagguagccaaaugccucgucau
cuaauuagugacgcgcaugaauggauuaacgagauucccacugucccuau
cuacuaucuagcgaaaccacagccaagggaacgggcuuggcagaaucagc
ggggaaagaagacccuguugagcuugacucuaguuugacauugugaagag
acauagaggguguagaauaagugggagcuucggcgccagugaaauaccac
uaccuuuauaguuucuuuacuuauucaaugaagcggagcuggaauucauu
uuccacguucuagcauucaaggucccauucggggcugauccggguugaag
acauugucagguggggaguuuggcuggggcggcacaucuguuaaacgaua
acgcagauguccuaaggggggcucauggagaacagaaaucuccaguagaa
caaaaggguaaaagcccccuugauuuugauuuucagugugaauacaaacc
augaaaguguggccuaucgauccuuuagucccucggaauuugaggcuaga
ggugccagaaaaguuaccacagggauaacuggcuuguggcagucaagcgu
ucauagcgacauugcuuuuugauucuucgaugucggcucuuccuaucaua
ccgaagcagaauucgguaagcguuggauuguucacccacuaauagggaac
gugagcuggguuuagaccgucgugagacagguuaguuuuacccuacugau
gaauguuaccgcaauaguaauugaacuuaguacgagaggaacaguucauu
cggauaauugguuuuugcggcugucugaucaggcauugccgcgaagcuac
cauccgcuggauuauggcugaacgccucuaagucagaauccaugcuagaa
cgcggugauuucuuugcuccacacaauauagauggauacgaauaaggcgu
ccuuguggcgucgcugaaccauagcaggcuagcaacggugcacuuggcgg
aaaggccuugggugcuugcuggcgaauugcaaugucauuuugcgugggga
uaaaucauuuguauacgacuuagauguacaacgggguauuguaagcagua
gaguagccuuguuguuacgaucugcugagauuaagccuuuguugucugau
uugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5t62 Nmd3 is a structural mimic of eIF5A, and activates the cpGTPase Lsg1 during 60S ribosome biogenesis.
• Resolution: 3.3 Å
• Binding residue (original residue number in PDB): G2 K3 G4 T5 P6 S7 F8 G9 K10 R11 H12 N13 K14 S15 H16 R24 R25 H28 Q30 K31 S35 K43 T44 R45 Y47 N48 W49 K52 R55 R56
• Binding residue (residue number reindexed from 1): G1 K2 G3 T4 P5 S6 F7 G8 K9 R10 H11 N12 K13 S14 H15 R23 R24 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:5t62, PDBe:5t62, PDBj:5t62
• PDBsum: 5t62
• PubMed: 28179369
• UniProt: P49166|RL37A_YEAST Large ribosomal subunit protein eL37A (Gene Name=RPL37A)