Structure of PDB 6gzz Chain P1 Binding Site BS01

Receptor Information

>6gzz Chain P1 (length=117) Species: 300852 (Thermus thermophilus HB8)

PRAKTGVVRRRKHKKILKLAKGYWGLRSKSFRKARETLFAAGNYAYAHRK
RRKRDFRRLWIVRINAACRQHGLNYSTFIHGLKKAGIEVDRKNLADLAVR
EPQVFAELVERAKAAQG

Ligand information

>6gzz Chain A1 (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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...<<...........<<.<<<....<<..........>>.((......<
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.>>>............>>>..................<<....>>....>
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..<<<.<<.....<<<<<<<<.<<<..<<<...<<<.....>>>...>>>
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.....>>..<<<<<<....<<<<<....>>>>><<.<<<<<<.....<<<
<<<<<<....<<...<<<<<<.<.<.<<<...........>..>>.>..>
>>>>>>..>>.....>>>>>>>>>.....>>>>>>..>>..<<<<<<<.<
<......>>.>>>>>>>.....<<<......>>>...<<<<.<<<...<<
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<<<<.<<...<<<<<....<<.....>>..>>>>>....((<<<<.<<..
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>>.....<<......>>>>>>>.<<<........>>>..>>>>...<<<.
...<<<<<<<..<<...............<<<<<.....<..>......>
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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): P2 R3 A4 K5 T6 V8 R10 R11 K13 H14 K15 K16 K22 G23 Y24 W25 G26 L27 R28 S31 F32 R33 K34 E37 Y45 Y47 H49 K51 R53 R55 F57 W61 I62 N75 Y76 S77 I80 H81 R92 K93
• Binding residue (residue number reindexed from 1): P1 R2 A3 K4 T5 V7 R9 R10 K12 H13 K14 K15 K21 G22 Y23 W24 G25 L26 R27 S30 F31 R32 K33 E36 Y44 Y46 H48 K50 R52 R54 F56 W60 I61 N74 Y75 S76 I79 H80 R91 K92

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding

Biological Process

• GO:0000027 ribosomal large subunit assembly
• GO:0006412 translation

Cellular Component

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

External links

• PDB: RCSB:6gzz, PDBe:6gzz, PDBj:6gzz
• PDBsum: 6gzz
• PubMed: 30301898
• UniProt: P60491|RL20_THET8 Large ribosomal subunit protein bL20 (Gene Name=rplT)