Structure of PDB 8glp Chain Lg Binding Site BS01

Receptor Information

>8glp Chain Lg (length=114) Species: 9606 (Homo sapiens)

VQRLTYRRRLSYNTASNKTRLSRTPGNRIVYLYTKKVGKAPKSACGVCPG
RLRGVRAVRPKVLMRLSKTKKHVSRAYGGSMCAKCVRDRIKRAFLIEEQK
IVVKVLKAQAQSQK

Ligand information

>8glp Chain L5 (length=3546)

cgcgaccucagaucagacguggcgacccgcugaauuuaagcauauuaguc
agcggaggagaagaaacuaaccaggauucccucaguaacggcgagugaac
agggaagagcccagcgccgaauccccgccccgcggcggggcgcgggacau
guggcguacggaagacccgcuccccggcgccgcucguggggggcccaagu
ccuucugaucgaggcccagcccguggacggugugaggccgguagcggccc
ccggcgcgccgggcccgggucuucccggagucggguugcuugggaaugca
gcccaaagcgggugguaaacuccaucuaaggcuaaauaccggcacgagac
cgauagucaacaaguaccguaagggaaaguugaaaagaacuuugaagaga
gaguucaagagggcgugaaaccguuaagagguaaacgggugggguccgcg
caguccgcccggaggauucaacccggcggcggguccggccgugucggcgc
ggcggaucuuucccggcgggggaccgucccccgaccggcgaccggccgcc
gccgggcgcauuuccaccgcggcggugcgccgcgaccggcuccgggacgg
cugggaaggcccggcggggaagguggcucgggggcccccgaguguuacag
cccccccggcagcagcacucgccgaaucccggggccgagggagcgagacc
cgucgccgcgcucuccccccugggggggccgggccaccccucccacggcg
cgaccgcucggggcggacuguccccagugcgccccgggcgggucgcgccg
ucgggcccggggggccacgcgcgcgucccccgaagagggggacggcggag
cgagcgcacggggucggcggcgacgucggcuacccacccgacccgucuug
aaacacggaccaaggagucuaacacgugcgcgagucgggggcucgcacga
aagccgccguggcgcaaugaaggugaaggccggcgcgcucgccggccgag
gugggaucccgaggccucuccaguccgccgagggcgcaccaccggcccgu
cucgcccgccgcgccggggagguggagcacgagcgcacguguuaggaccc
gaaagauggugaacuaugccugggcagggcgaagccagaggaaacucugg
uggagguccguagcgguccugacgugcaaaucggucguccgaccugggua
uaggggcgaaagacuaaucgaaccaucuaguagcugguucccuccgaagu
uucccucaggauagcuggcgcucucgcagacccgagccacgcaguuuuau
ccgguaaagcgaaugauuagaggucuuggggccgaaacgaucucaaccua
uucucaaacuuuaaauggguaagaagcccggcucgcuggcguggagccgg
gcguggaaugcgagugccuagugggccacuuuugguaagcagaacuggcg
cugcgggaugaaccgaacgccggguuaaggcgcccgaugccgacgcucau
cagaccccagaaaagguguugguugauauagacagcaggaaccugccgaa
ucaacuagcccugaaaauggauggcgcuggagcgucgggcccauacccgg
ccgucgccggcagucgagaguggacgggagccccgcggacgcuacgccgc
gacgaguaggagggccgcugcggugagccuugaagccuagggcgcgggcc
cggguggagccgccgcaggugcagaucuuggugguaguagcaaauauuca
aacgagaacuuugaaggccgaaguggagaaggguuccaugugaacagcag
uugaacaugggucagucgguccugagagaugggcgagcgccguuccgaag
ggacgggcgauggccuccguugcccucggccgaucgaaagggagucgggu
ucagauccccgaauccggagcggagaugggcgccgcgaggcguccagugc
gguaacgcgaccgaucccggagaagccggcgggagccccggggagaguuc
ucuuuucuuugugaagggcagggcgcccuggaauggguucgccccgagag
aggggcccgugccuuggaaagcgucgcgguuccggcggcguccggugagc
ucucgcuggcccuugaaaauccgggggagaggguguaaaucucgcgccgg
gccguacccauauccgcagcaggucuccaaggugaacagccucuggcaug
uuggaacaauguagguaagggaagucggcaagccggauccguaacuucgg
gauaaggauuggcucuaagggcugguagcagccgacuuagaacuggugcg
gaccaggggaauccgacuguuuaauuaaaacaaagcaucgcgaaggcccg
cggcggguguugacgcgaugugauuucugcccagugcucugaaugucaaa
gugaagaaauucaaugaagcgcggguaaacggcgggaguaacuaugacuc
ucuuaagguagccaaaugccucgucaucuaauuagugacgcgcaugaaug
gaugaacgagauucccacugucccuaccuacuauccagcgaaaccacagc
caagggaacgggcuuggcggaaucagcggggaaagaagacccuguugagc
uugacucuagucuggcacggugaagagacguuuuuucacugacccgguga
ggcgggggggcgagccccgaggggcucucgcuucuggcgccaagcgcccg
gccgcgcgccggccgggcgcgacccgcuccggggacagugccaggugggg
aguuugacuggggcgguacaccugucaaacgguaacgcagguguccuaag
gcgagcucagggaggacagaaaccucccguggagcagaagggcaaaagcu
cgcuugaucuugauuuucaguacgaauacagaccgugaaagcggggccuc
acgauccuucugaccuuuuggguuuuaagcaggaggugucagaaaaguua
ccacagggauaacuggcuuguggcggccaagcguucauagcgacgucgcu
uuuugauccuucgaugucggcucuuccuaucauugugaagcagaauucac
caagcguuggauuguucacccacuaauagggaacgugagcuggguuuaga
ccgucgugagacagguuaguuuuacccuacugaugauguguuguugccau
gguaauccugcucaguacgagaggaaccgcagguucagacauuuggugua
ugugcuuggcugaggagccaauggggcgaagcuaccaucugugggauuau
gacugaacgccucuaagucagaaucccgcccaggcggaacgauacggcag
cgccgcggagccucgguuggccucggauagccggucccccgcgggguccg
gugcggagugcccuucguccugggaaacggggcgcggccggagaggcggc
cgcccccucgcccgucacgcaccgcacguucguggggaaccuggcgcuaa
accauucguagacgaccugcuucugggucgggguuucguacguagcagag
cagcgcugcgaucuauugaaagucagcccucgacacaaggguuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8glp mRNA decoding in human is kinetically and structurally distinct from bacteria.
• Resolution: 1.67 Å
• Binding residue (original residue number in PDB): V2 R4 L5 T6 Y7 R8 R9 R10 L11 S12 Y13 N14 T15 S17 R21 L22 R24 T25 P26 G27 N28 R29 Y32 L33 Y34 K36 K37 K40 P42 K43 A45 V48 R52 R54 G55 R57 R60 P61 K62 L64 M65 R66 S68 K69 T70 K72 H73 V74 S75 R76 Y78 G79 G80 S81 R88 R90 R93 A94 I97 E98 Q100 K101 K115
• Binding residue (residue number reindexed from 1): V1 R3 L4 T5 Y6 R7 R8 R9 L10 S11 Y12 N13 T14 S16 R20 L21 R23 T24 P25 G26 N27 R28 Y31 L32 Y33 K35 K36 K39 P41 K42 A44 V47 R51 R53 G54 R56 R59 P60 K61 L63 M64 R65 S67 K68 T69 K71 H72 V73 S74 R75 Y77 G78 G79 S80 R87 R89 R92 A93 I96 E97 Q99 K100 K114

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0045296 cadherin binding

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005783 endoplasmic reticulum
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:0045202 synapse
• GO:0070062 extracellular exosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8glp, PDBe:8glp, PDBj:8glp
• PDBsum: 8glp
• PubMed: 37020024
• UniProt: P49207|RL34_HUMAN Large ribosomal subunit protein eL34 (Gene Name=RPL34)