Structure of PDB 6hcf Chain F3 Binding Site BS01

Receptor Information

>6hcf Chain F3 (length=225) Species: 9986 (Oryctolagus cuniculus)

NFAELKIKRLRKKFAQKMLRKARRKLIYEKAKHYHKEYRQMYRTEIRMAR
MARKAGNFYVPAEPKLAFVIRIRGINGVSPKVRKVLQLLRLRQIFNGTFV
KLNKASINMLRIVEPYIAWGYPNLKSVNELIYKRGYGKINKKRIALTDNT
LIARSLGKYNIICMEDLIHEIYTVGKHFKEANNFLWPFKLSSPRGGMKKK
TTHFVEGGDAGNREDQINRLIRRMN

Ligand information

>6hcf Chain 52 (length=3634)

cgcgaccucagaucagacguggcgacccgcugaauuuaagcauauuaguc
agcggaggaaaagaaacuaaccaggauucccucaguaacggcgagugaac
agggaagagcccagcgccgaauccccgccccgcggcggggcgcgggaaau
guggcguacggaagacccacuccccggcgccggggggcccaaguccuucu
gaucgaggcccagcccguggacggugugaggccgguagcggcccccggcg
cgccgggcccgggucuucccggagucggguugcuugggaaugcagcccaa
agcgggugguaaacuccaucuaaggcuaaauaccggcacgagaccgauag
ucaacaaguaccguaagggaaaguugaaaagaacuuugaagagagaguuc
aagagggcgugaaaccguuaagagguaaacgggugggguccgcgcagucc
gcccggaggauucaacccggcggcgcgguccggccgugccggcggggcgg
aucucccgcucccgucggcgggggaccgccccccggccggcgaccggccg
ccgccgggcgcauuuccaccgcggcggugcgccgcgaccggcuccgggac
ggcugggaaggccccggcggggaagguggcccgggggccccggguguuac
agccccgccccggcagcagcagcucgccgaaucccggggccgagggagcg
agacccgugcgccgcgcucuccccccucgggggggccgggccaccccucc
cacggcgcgaccgcucucccacccggggggcggggcggacuguccccagu
gcgccccgggcgggucgcgccgucgggcccgggggagguucucucggggc
cacgcgucccccgcgagcgcacggggucggcggcgaugucggcuacccac
ccgacccgucuugaaacacggaccaaggagucuaacacgugcgcgagucg
ggggcuacgaaagccgccguggcgcaaugaaggugaaggccggcggcgcg
ccgccggccgaggugggaucccgaggccuuccaguccgccgagggcgcac
caccggcccgucucgcccgccgcgccggggagguggagcacgagcgcacg
uguuaggacccgaaagauggugaacuaugccugggcagggcgaagccaga
ggaaacucugguggagguccguagcgguccugacgugcgaaucggucguc
cgaccuggguauaggggcgaaagacuaaucgaaccaucuaguagcugguu
cccuccaaaguuucccucaggauagcuggcgcucuccgcaguuuuauccg
guaaagcgaaugauuagaggucuuggggccgaaacgaucucaaccuauuc
ucaaacuuuaaauggguaagaagcccggcucgcugguguggagccgggcg
uggaaugcgagugccuagugggccacuuuugguaagcagaacuggcgcug
cgggaugaaccgaacgccggguuaaggcgcccgaugccgacgcucaucag
accccagaaaagguguugguugauauagacagcaggaugguggccaugga
agucggaauccgcuaaggaguguguaacaacucaccugccgaaucaacua
gcccugaaaauggauggcgcuggagcgucgggcccauacccggccgucgc
uggcagucggcagagcgagaaagagaguggcgcggacgcuacgccgcgac
gaguaggagggccgcugcggugagccuugaagccuagggcgcgggcccgg
guggagccgccgcaggugcagaucuuggugguaguagcaaauauucaaac
gagaacuuugaaggccgaaguggagaaggguuccaugugaacagcaguug
aacaugggucagucgguccugagagaugggcgagcgccguuccgaaggga
cgggcgauggccuccguugcccucagccgaucgaaagggagucggguuca
gauccccgaauccggaguggcggagaugggcgccgcgaggcguccagugc
gguaacgcgaccgaucccggagaagccggcgggagccccggggagaguuc
ucuuuucuuugugaagggcagggcgcccuggaauggguucgccccgagag
aggggcccgugccuuggaaagcgucgcgguuccggcggcguccggugagc
ucucgcuggcccuugaaaauccgggggagaggguguaaaucucgcgccgg
gccguacccauauccgcagcaggucuccaaggugaacagccucuggcaug
uuggaacaauguagguaagggaagucggcaagccggauccguaacuucgg
gauaaggauuggcucuaagggcuggcagccgacuuagaacuggugcggac
caggggaauccgacuguuuaauuaaaacaaagcaucgcgaaggcccgcgg
cggguguugacgcgaugugauuucugcccagugcucugaaugucaaagug
aagaaauucaaugaagcgcggguaaacggcgggaguaacuaugacucucu
uaagguagccaaaugccucgucaucuaauuagugacgcgcaugaauggau
gaacgagauucccacugucccuaccuacuauccagcgaaaccacagccaa
gggaacgggcuuggcggaaucagcggggaaagaagacccuguugagcuug
acucuagucuggcacggugaagagacaugagagguguagaauaaguggga
ggcccgggccgccggugaaauaccacuacucugaucguuuuuucacugac
ccggugaggcgggggggcgagccgggcucucgcuucuggcgccaagcgcc
cggccggccgggcgcgacccgcuccggggacagugccagguggggaguuu
gacuggggcgguacaccugucaaacgguaacgcagguguccuaaggcgag
cucagggaggacagaaaccucccguggagcagaagggcaaaagcucgcuu
gaucuugauuuucaguacgaauacagaccgugaaagcggggccucacgau
ccuucugaccuuuuggguuuuaagcaggaggugucagaaaaguuaccaca
gggauaacuggcuuguggcggccaagcguucauagcgacgucgcuuuuug
auccuucgaugucggcucuuccuaucauugugaagcagaauucaccaagc
guuggauuguucacccacuaauagggaacgugagcuggguuuagaccguc
gugagacagguuaguuuuacccuacugaugauguguuguugccaugguaa
uccugcucaguacgagaggaaccgcagguucagacauuugguguaugugc
uuggcugaggagccaauggggcgaagcuaccaucugugggauuaugacug
aacgccucuaagucagaaucccgcccaggcggaacgauagcgccggagcc
ucgguuggccucggauagccggucccccgccgggguccggugcggagagc
ccuucgucccgggaaacggggcggccggaaagggggccgcccucucgccc
gucacgcaccgcacguucguggggaaccuggcgcuaaaccauucguagac
gaccugcuucugggucgggguuucguacguagcagagcagcugcugcgau
cuauugaaagucagcccucgacacaaggguuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6hcf ZNF598 Is a Quality Control Sensor of Collided Ribosomes.
• Resolution: 3.9 Å
• Binding residue (original residue number in PDB): F24 K28 K30 R31 R33 R42 R45 K47 Y50 H57 K58 R61 Y64 R65 R69 R72 R75 I97 N98 G99 P102 K106 L110 A127 N130 N145 R165 T172 A175 G179 I184 E187 K201 K211 S213 S214 R216 G217 G218 M219 K222 R241 R244
• Binding residue (residue number reindexed from 1): F2 K6 K8 R9 R11 R20 R23 K25 Y28 H35 K36 R39 Y42 R43 R47 R50 R53 I75 N76 G77 P80 K84 L88 A105 N108 N123 R143 T150 A153 G157 I162 E165 K179 K189 S191 S192 R194 G195 G196 M197 K200 R219 R222

Gene Ontology

Molecular Function

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

Biological Process

• GO:0000463 maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)

Cellular Component

• GO:0005737 cytoplasm
• GO:0022625 cytosolic large ribosomal subunit

External links

• PDB: RCSB:6hcf, PDBe:6hcf, PDBj:6hcf
• PDBsum: 6hcf
• PubMed: 30293783
• UniProt: G1TUB1