Structure of PDB 5z3g Chain P Binding Site BS01

Receptor Information

>5z3g Chain P (length=108) Species: 559292 (Saccharomyces cerevisiae S288C)

RVKVHFDQAGKKVSRRNARATRAAKIAPRPLDLLRPVVRAPTVKYNRKVR
AGRGFTLAEVKAAGLTAAYARTIGIAVDHRRQNRNQEIFDANVQRLKEYQ
SKIIVFPR

Ligand information

>5z3g Chain A (length=1501)

guuugaccucaaaucagguaggaguacccgcugaacuuaagcauaucaau
aagcggaggaaaagaaaccaaccgggauugccuuaguaacggcgagugaa
gcggcaaaagcucaaauuugaaaucugguaccuucggugcccgaguugua
auuuggagagggcaacuuuggggccguuccuugucuauguuccuuggaac
aggacgucauagagggugagaaucccguguggcgaggagugcgguucuuu
guaaagugccuucgaagagucgaguuguuugggaaugcagcucuaagugg
guggccaucuaaagcuaaauauuggcgagagaccgauagcgaacaaguac
agugauggaaagaugaaaagaacuuugaaaagagagugaaaaaguacgug
aaauuguugaaagggaagggcauuugaucagacaugguguuuugugcccu
cugcuccuuguggguaggggacgcauuucacugggccagcaucaguuuug
guggcaggauaaauccauaggaauguagcuugccucgguaaguauuauag
ccugugggaauacugccagcugggacugaggacugcgacguaagucaagg
augcuggcauaaugguuauaugccgcccgucuugaaacacggaccaagga
gucuaacgucuaugcgaguguuuggguguaaaacccauacgcguaagguu
ggggccucgcaagaggugcacaaucgaccgauccggauuugaguaagagc
auagcuguugggacccgaaagauggugaccaucuaguagcugguuccugc
cgaaguuucccucaggauagcagaagcucguaucaguuuuaugguaagga
augaagagcuuuuagugggccauuuuuggagaacuggcgaugcgggauga
accgaacguagaguuaaggugccggaauacacgcucacaaaagguguuag
uucaucugaacuagcccugggcgcucaagcguguuaccuauacucuaccg
ucaggguugauaugaugcccugacgaguaggcaggcguggaggucaguga
cgaagccuagaccguaaggucgggucgaacggccucuagugcagaucuug
gugguaguagcuagaucuagcgaaaccacagccaaggcuuggguuaccgc
aauaguaauugaacuuaguacgagaggaacaguucauucggauaauuggu
uuuugcggcugucugaucaggcauugccgcgaagcuaccauccgcuggau
uauggcugaacgccucuaagucagaauccaugcuagaacgcggugaugcu
ccacacaaagauggauacgaauaaggcguccuuguggcgucgcugaacca
uagcaggcuagcaacggugcacuuggcggaaaggccuugggugcuugcug
gcgaauugcaaugucagcguggggauaaaucauuuguauacgacuuagau
guacaacgggguauuguaagcgcugagauuaagccuuuguugucugauuu
g

..........................<<<<<<.....<......>.....
.>>>>>.>.........<<....>>..<<<<<......<<.....>>...
..>>>>>..<<<..<........<<.<<<<<<...>>>>>>.>>......
..>....<<<<<<.<<<<<<<<<<<<<<<<<<<<<.....<<<<......
>>>>.(.......<<<......)>>>....>>>>>>>>..>>>>>>>>..
..>>>>>>>>>>>........<<<<<<<........>>>>>>>.....<<
<<<..>>>>>..>>>..................................<
<....>>...............<<<......>>>................
..................<<<<<.<<<<<<.....<<<<...<<<..<<<
<<<<<.......>>>>>>>>..>>>...>>>>..<<<<<<<.<<<<<<<<
<<<<<<<.....<<<<<<<<<......<<<<<<....>>>>>>.......
>>>>>>>.>.>.>>>>>.>>>>>>>>>>........<<<....>>>....
.>>>>>>>....>>>>>>.>>>>>..<<<<........>>>><<<<<<..
...<<<<<.<<<<<<..<<<...<<<<.....>>>>...>>>....<<<<
<..<<<<<....>>>>>...>>>>>.<<....<..>......>>....>>
>>>>.>>>>>...<<.<...<<<<<<.>>>>>>......>.>>..<<<<<
<......<<<....>>>..<<<<<<<<.....<<<.<<<<<<.>>>>..>
>>>>...>>>>>>.>>..<<<<.<<<....>>>.>>>>....<<<.....
.>>>...<<<<<<<..<<<<(((.....<<<<<<.......<<<.<<<<<
<<<<..>>>>>>>>>>>>.)))......>>>>>>.>>>>..>>>>>>><<
<<<<<<<.........>>>>>>>>>....>>>>>><<<<<<<<<<.<<..
....<<<<.<<<<....>>>>>>>>...>>>>>>>>>>.>>.....>>>>
>><<.....<<<<<..>>>>>....>>....<<<<<.>>>>>.<<<<<<<
..<<<<...<<<<<<...............>>>>>>..<<<<<...<<<<
....<<<<<<<<<......>>>>..>>>>>...>>>>..>>>>>.<<<<.
..<<<<<...........>>>>>...>>>>.>>>>....>>>>>>>..<<
<<<<........<<..........<<<<<<.....>>>>>>......>>.
......<<<<<<...<<<<<.<..<<<......>>>..>.>>>>>.>>>>
>>................>>>>>>.<<<<<<.<..<.......>..>...
..<<<<<.<<<.<<.....<..>....>>....>>>..>>>>>..>>>>>
>

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5z3g Cryo-EM structure of an early precursor of large ribosomal subunit reveals a half-assembled intermediate.
• Resolution: 3.65 Å
• Binding residue (original residue number in PDB): Q28 A29 K32 R35 R36 R39 R42 R55 V58 R59 P61 T62 V63 Y65 N66 K68 R70 G72 R73 R91 D98 H99 R100 R104 N105
• Binding residue (residue number reindexed from 1): Q8 A9 K12 R15 R16 R19 R22 R35 V38 R39 P41 T42 V43 Y45 N46 K48 R50 G52 R53 R71 D78 H79 R80 R84 N85

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome

Biological Process

• 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:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5z3g, PDBe:5z3g, PDBj:5z3g
• PDBsum: 5z3g
• PubMed: 29557065
• UniProt: Q12690|RL13A_YEAST Large ribosomal subunit protein eL13A (Gene Name=RPL13A)