Structure of PDB 5t62 Chain p Binding Site BS01

Receptor Information

>5t62 Chain p (length=97) Species: 559292 (Saccharomyces cerevisiae S288C)

SINQKLALVIKSGKYTLGYKSTVKSLRQGKSKLIIIAANTPVLRKSELEY
YAMLSKTKVYYFQGGNNELGTAVGKLFRVGVVSILEAGDSDILTTLA

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): L25 G26 K28 S29 V50 R52 K53 S54 E57 F85 V87 G88
• Binding residue (residue number reindexed from 1): L17 G18 K20 S21 V42 R44 K45 S46 E49 F77 V79 G80

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0030627 pre-mRNA 5'-splice site binding

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006364 rRNA processing
• GO:0048025 negative regulation of mRNA splicing, via spliceosome

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5t62, PDBe:5t62, PDBj:5t62
• PDBsum: 5t62
• PubMed: 28179369
• UniProt: P14120|RL30_YEAST Large ribosomal subunit protein eL30 (Gene Name=RPL30)