Structure of PDB 8b6c Chain Z Binding Site BS01

Receptor Information

>8b6c Chain Z (length=135) Species: 9986 (Oryctolagus cuniculus)

GKFMKPGKVVLVLAGRYSGRKAVIVKNIDDGTSDRPYSHALVAGIDRYPR
KVTAAMGKKKIAKRSKIKSFVKVYNYNHLMPTRYSVDIPLDKTVVNKDVF
RDPALKRKARREAKVKFEERYKTGKNKWFFQKLRF

Ligand information

>8b6c Chain 5 (length=3619)

cgcgaccucagaucagacguggcgacccgcugaauuuaagcauauuaguc
agcggaggaaaagaaacuaaccaggauucccucaguaacggcgagugaac
agggaagagcccagcgccgaauccccgccccgcggcggggcgcgggaaau
guggcguacggaagacccacuccccggcgccgcucguggggggcccaagu
ccuucugaucgaggcccagcccguggacggugugaggccgguagcggccc
ccggcgcgccgggcccgggucuucccggagucggguugcuugggaaugca
gcccaaagcgggugguaaacuccaucuaaggcuaaauaccggcacgagac
cgauagucaacaaguaccguaagggaaaguugaaaagaacuuugaagaga
gaguucaagagggcgugaaaccguuaagagguaaacgggugggguccgcg
caguccgcccggaggauucaacccggcggcggccggccgugccggcgguc
ucggcggaucuuucccgcucccgggggcgggggaccgccccccggccggc
gaccggccgccgccgggcgcauuuccaccgcggcggugcgccgcgaccgg
cuccgggacggcugggaaggcccggcggggaagguggcccggggggacgc
cucgccggcgggcgcgaccccuccccggguguuacagccccgccccggca
gcagcagcucgccgaaucccggggccgagggagcgagaccugugucgccg
cgcucuccccccugggggggccgggccaccccucccacggcgcgaccgcu
ggggcggacuguccccagugcgccccgggcgggucgcgccgucgggcccg
ggggccacggcgcgucgcggcgcgcgcgagcgagcgcacggggucggcgg
cgaugucggcuacccacccgacccgucuugaaacacggaccaaggagucu
aacacgugcgcgagucgggggcucgcacgaaagccgccguggcgcaauga
aggugaaggccggcgucgccggccgaggugggaucccgaggccuuccagu
ccgccgagggcgcaccaccggcccgucucgcccgccgcgccggggaggug
gagcacgagcgcacguguuaggacccgaaagauggugaacuaugccuggg
cagggcgaagccagaggaaacucugguggagguccguagcgguccugacg
ugcgaaucggucguccgaccuggguauaggggcgaaagacuaaucgaacc
aucuaguagcugguucccuccaaaguuucccucaggauagcuggcgcucu
cgcccgcaguuuuauccgguaaagcgaaugauuagaggucuuggggccga
aacgaucucaaccuauucucaaacuuuaaauggguaagaagcccggcucg
cugguguggagccgggcguggaaugcgagugccuagugggccacuuuugg
uaagcagaacuggcgcugcgggaugaaccgaacgccggguuaaggcgccc
gaugccgacgcucaucagaccccagaaaagguguugguugauauagacag
caggaugguggccauggaagucggaauccgcuaaggaguguguaacaacu
caccugccgaaucaacuagcccugaaaauggauggcgcuggagcgucggg
cccauacccggccgucgcuggcagucggcagagcgagaaagagaguggcg
cggacgcuacgccgcgacgaguaggagggccgcugcggugagccuugaag
ccuagggcgcgggcccggguggagccgccgcaggugcagaucuugguggu
aguagcaaauauucaaacgagaacuuugaaggccgaaguggagaaggguu
ccaugugaacagcaguugaacaugggucagucgguccugagagaugggcg
agcgccguuccgaagggacgggcgauggccuccguugcccucagccgauc
gaaagggagucggguucagauccccgaauccggaguggcggagaugggcg
ccgcgaggcguccagugcgguaacgcgaccgaucccggagaagccggcgg
gagccccggggagaguucucuuuucuuugugaagggcagggcgcccugga
auggguucgccccgagagaggggcccgugccuuggaaagcgucgcgguuc
cggcggcguccggugagcucucgcuggcccuugaaaauccgggggagagg
guguaaaucucgcgccgggccguacccauauccgcagcaggucuccaagg
ugaacagccucuggcauguuggaacaauguagguaagggaagucggcaag
ccggauccguaacuucgggauaaggauuggcucuaagggcuggcagccga
cuuagaacuggugcggaccaggggaauccgacuguuuaauuaaaacaaag
caucgcgaaggcccgcggcggguguugacgcgaugugauuucugcccagu
gcucugaaugucaaagugaagaaauucaaugaagcgcggguaaacggcgg
gaguaacuaugacucucuuaagguagccaaaugccucgucaucuaauuag
ugacgcgcaugaauggaugaacgagauucccacugucccuaccuacuauc
cagcgaaaccacagccaagggaacgggcuuggcggaaucagcggggaaag
aagacccuguugagcuugacucuagucuggcacggugaagagacaugaga
acuccgaucguuuuuucacugacccggugaggcgggggggcgagccgggc
ucucgcuucuggcgccaagcgcccggccccggggccgggcgcgacccgcu
ccggggacagugccagguggggaguuugacuggggcgguacaccugucaa
acgguaacgcagguguccuaaggcgagcucagggaggacagaaaccuccc
guggagcagaagggcaaaagcucgcuugaucuugauuuucaguacgaaua
cagaccgugaaagcggggccucacgauccuucugaccuuuuggguuuuaa
gcaggaggugucagaaaaguuaccacagggauaacuggcuuguggcggcc
aagcguucauagcgacgucgcuuuuugauccuucgaugucggcucuuccu
aucauugugaagcagaauucaccaagcguuggauuguucacccacuaaua
gggaacgugagcuggguuuagaccgucgugagacagguuaguuuuacccu
acugaugauguguuguugccaugguaauccugcucaguacgagaggaacc
gcagguucagacauuugguguaugugcuuggcugaggagccaauggggcg
aagcuaccaucugugggauuaugacugaacgccucuaagucagaaucccg
cccaggcggaacgauacggcagcgccgaggagccucgguuggccucggau
agccggucccccgcgggguccggugcggagagcccuucgucccgggaaac
ggggcgcggccggaaagggggccgcccucucgcccgucacgcaccgcacg
uucguggggaaccuggcgcuaaaccauucguagacgaccugcuucugggu
cgggguuucguacguagcagagcagcugcugcgaucuauugaaagucagc
ccucgacacaaggguuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8b6c Structural insights into TRAP association with ribosome-Sec61 complex and translocon inhibition by a CADA derivative.
• Resolution: 2.79 Å
• Binding residue (original residue number in PDB): G16 R17 R36 Y38 R48 R51 T54 A55 G58 K59 K60 K64 R65 K67 K69 K73 V74 N76 H79 K107 R111 R112 K115 K133 R135 F136
• Binding residue (residue number reindexed from 1): G15 R16 R35 Y37 R47 R50 T53 A54 G57 K58 K59 K63 R64 K66 K68 K72 V73 N75 H78 K106 R110 R111 K114 K132 R134 F135

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0006364 rRNA processing
• GO:0006412 translation

Cellular Component

• GO:0005654 nucleoplasm
• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005783 endoplasmic reticulum
• GO:0005791 rough endoplasmic reticulum
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8b6c, PDBe:8b6c, PDBj:8b6c
• PDBsum: 8b6c
• PubMed: 36867692
• UniProt: G1TXF6|RL27_RABIT Large ribosomal subunit protein eL27 (Gene Name=RPL27)