Structure of PDB 6gzz Chain C2 Binding Site BS01

Receptor Information

>6gzz Chain C2 (length=272) Species: 300852 (Thermus thermophilus HB8)

AVKKFKPYTPSRRFMTVADFSEITKTEPEKSLVKPLKKTGGRNNQGRITV
RFRGGGHKRLYRIIDFKRWDKVGIPAKVAAIEYDPNRSARIALLHYVDGE
KRYIIAPDGLQVGQQVVAGPDAPIQVGNALPLRFIPVGTVVHAVELEPKK
GAKLARAAGTSAQIQGREGDYVILRLPSGELRKVHGECYATVGAVGNADH
KNIVLGKAGRSRWLGRRPHVRGAAMNPVDHPHGGGEGRAPRGRPPASPWG
WQTKGLKTRKRRKPSSRFIIAR

Ligand information

>6gzz Chain A2 (length=2912)

ggucaagaugguaagggcccacgguggaugccucggcacccgagccgaug
aaggacguggcuaccugcgauaagccagggggagccgguagcgggcgugg
aucccuggauguccgaaugggggaacccggccggcgggaacgccggucac
cgcgcuuuuugcgcggggggaaccuggggaacugaaacaucucaguaccc
agaggagaggaaagagaaaucgacucccugaguagcggcgagcgaaaggg
gaccagccuaaaccguccggcuuguccgggcggggucguggggcccucgg
acaccgaauccccagccuagccgaagcuguugggaagcagcgccagagag
ggugaaagccccguaggcgaaagguggggggauaggugaggguacccgag
uaccccgugguucguggagccaugggggaaucugggcggaccaccgccua
aggcuaaguacuccgggugaccgauagcgcaccaguaccgugagggaaag
gugaaaagaaccccgggaggggagugaaauagagccugaaaccgugggcu
uacaagcagucacggccccgcaagggguuguggcgugccuauugaagcau
gagccggcgacucacggucgugggcgagcuuaagccguugaggcggaggc
guagggaaaccgaguccgaacagggcgcaaacggcccgcacgcgggccga
aaaguccgcggccguggacccgaaaccgggcgagcuagcccuggccaggg
ugaagcuggggugagacccaguggaggcccgaaccggugggggaugcaaa
ccccucggaugagcuggggcuaggagugaaaagcuaaccgagcccggaga
uagcugguucuccccgaaaugacuuuagggucagccucaggcgcugacug
gggccuguagagcacugauagggcuagggggcccaccagccuaccaaacc
cugucaaacuccgaagggucccagguggagccugggagugagggcgcgag
cgauaacguccgcguccgagcgcgggaacaaccgagaccgccagcuaagg
cccccaagucugggcuaagugguaaaggauguggcgccgcgaagacagcc
aggauguuggcuuagaagcagccaucauuuaaagagugcguaauagcuca
cuggucgaguggcgccgcgccgaaaaugaucggggcuuaagcccagcgcc
gaagcugcgggucugggggaugaccccaggcgguaggggagcguucccga
ugccgaugaaggccgacccgcgagggcggcuggagguaagggaagugcga
augccggcaugaguaacgauaaagagggugagaaucccucucgccguaag
cccaaggguuccuacgcaauggucgucagcguaggguuaggcgggaccua
aggugaagccgaaaggcguagccgaagggcagccgguuaauauuccggcc
cuucccgcaggugcgauggggggacgcucuaggcuagggggaccggagcc
auggacgagcccggccagaagcgcagggugggagguaggcaaauccgccu
cccaacaagcucugcgugguggggaagcccguacgggugacaaccccccg
aagccagggagccaagaaaagccucuaagcacaaccugcgggaacccgua
ccgcaaaccgacacaggugggcgggugcaagagcacucaggcgcgcggga
gaacccucgccaaggaacucugcaaguuggccccguaacuucgggagaag
gggugcucccuggggugaugagccccggggagccgcagugaacaggcucu
ggcgacuguuuaccaaaaacacagcucucugcgaacucguaagaggaggu
auagggagcgacgcuugcccggugccggaaggucaaggggaggggugcaa
gccccgaaccgaagccccggugaacggcggccguaacuauaacgguccua
agguagcgaaauuccuugucggguaaguuccgaccugcacgaaaagcgua
acgaccggagcgcugucucggcgagggacccggugaaauugaacuggccg
ugaagaugcggccuacccguggcaggacgaaaagaccccguggagcuuua
cugcagccugguguuggcucuuggucgcgccugcguaggauaggugggag
ccugugaacccccgccuccgggugggggggaggcgccggugaaauaccac
ccuggcgcggcugggggccuaacccucggauggggggacagcgcuuggcg
ggcaguuugacuggggcggucgccuccuaaaagguaacggaggcgcccaa
agguccccucaggcgggacggaaauccgccggagagcgcaaggguagaag
ggggccugacugcgaggccugcaagccgagcaggggcgaaagccgggccu
agugaaccgguggucccguguggaagggccaucgaucaacggauaaaagu
uaccccggggauaacaggcugaucucccccgagcguccacagcggcgggg
agguuuggcaccucgaugucggcucgucgcauccuggggcugaagaaggu
cccaaggguugggcuguucgcccauuaaagcggcacgcgagcuggguuca
gaacgucgugagacaguucggucucuauccgccacgggcgcaggaggcuu
gaggggggcucuuccuaguacgagaggaccggaagggacgcaccucuggu
uucccagcugucccuccaggggcauaagcuggguagccaugugcggaagg
gauaaccgcugaaagcaucuaagcgggaagcccgccccaagaugaggccu
cccacggcgucaagccgguaaggacccgggaagaccacccgguggauggg
ccggggguguaagcgccgcgaggcguugagccgaccggucccaaucgucc
gaggucuugacc

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6gzz Cryo-EM structure of the hibernating Thermus thermophilus 100S ribosome reveals a protein-mediated dimerization mechanism.
• Resolution: 4.13 Å
• Binding residue (original residue number in PDB): Y9 T10 S12 R13 R14 F15 F21 E30 K31 S32 V34 K38 K39 G41 G42 R43 N44 N45 G47 R48 I49 T50 R52 R54 H58 K59 L61 Y62 R63 K68 W70 K78 Y84 P86 R88 H96 Y97 V98 D99 E148 K151 L155 R157 A158 A159 L177 P178 S179 E181 V205 L206 G207 K208 A209 R211 R213 W214 R218 P219 H220 R222 G223 A225 M226 P228 G234 G235 G236 E237 G238 R239 A240 P241 R242 G243 R244 P246 A247 S248 P249 W250 Q253 T254 K255 G256 L257 K258 T259 R260 K261 R262 R263 R268 F269 I270 R273
• Binding residue (residue number reindexed from 1): Y8 T9 S11 R12 R13 F14 F20 E29 K30 S31 V33 K37 K38 G40 G41 R42 N43 N44 G46 R47 I48 T49 R51 R53 H57 K58 L60 Y61 R62 K67 W69 K77 Y83 P85 R87 H95 Y96 V97 D98 E147 K150 L154 R156 A157 A158 L176 P177 S178 E180 V204 L205 G206 K207 A208 R210 R212 W213 R217 P218 H219 R221 G222 A224 M225 P227 G233 G234 G235 E236 G237 R238 A239 P240 R241 G242 R243 P245 A246 S247 P248 W249 Q252 T253 K254 G255 L256 K257 T258 R259 K260 R261 R262 R267 F268 I269 R272

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0016740 transferase activity
• GO:0019843 rRNA binding

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• GO:0005840 ribosome
• GO:0015934 large ribosomal subunit
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6gzz, PDBe:6gzz, PDBj:6gzz
• PDBsum: 6gzz
• PubMed: 30301898
• UniProt: P60405|RL2_THET8 Large ribosomal subunit protein uL2 (Gene Name=rplB)