Structure of PDB 7ss9 Chain D Binding Site BS01

Receptor Information

>7ss9 Chain D (length=46) Species: 83333 (Escherichia coli K-12)

MKRTFQPSVLKRNRSHGFRARMATKNGRQVLARRRAKGRARLTVSK

Ligand information

>7ss9 Chain 1 (length=2903)

gguuaagcgacuaagcguacacgguggaugcccuggcagucagaggcgau
gaaggacgugcuaaucugcgauaagcgucgguaaggugauaugaaccguu
auaaccggcgauuuccgaauggggaaacccaguguguuucgacacacuau
cauuaacugaauccauagguuaaugaggcgaaccgggggaacugaaacau
cuaaguaccccgaggaaaagaaaucaaccgagauucccccaguagcggcg
agcgaacggggagcagcccagagccugaaucaguguguguguuaguggaa
gcgucuggaaaggcgcgcgauacagggugacagccccguacacaaaaaug
cacaugcugugagcucgaugaguagggcgggacacgugguauccugucug
aauauggggggaccauccuccaaggcuaaauacuccugacugaccgauag
ugaaccaguaccgugagggaaaggcgaaaagaaccccggcgaggggagug
aaaaagaaccugaaaccguguacguacaagcagugggagcacgcuuaggc
gugugacugcguaccuuuuguauaaugggucagcgacuuauauucuguag
caagguuaaccgaauaggggagccgaagggaaaccgagucuuaacugggc
guuaaguugcaggguauagacccgaaacccggugaucuagccaugggcag
guugaagguuggguaacacuaacuggaggaccgaaccgacuaaugucgaa
aaauuagcggaugacuuguggcugggggugaaaggccaaucaaaccggga
gauagcugguucuccccgaaagcuauuuagguagcgccucgugaauucau
cuccggggguagagcacuguuucggcaagggggucaucccgacuuaccaa
cccgaugcaaacugcgaauaccggagaauguuaucacgggagacacacgg
cgggugcuaacguccgucgugaagagggaaacaacccagaccgccagcua
aggucccaaagucaugguuaagugggaaacgaugugggaaggcccagaca
gccaggauguuggcuuagaagcagccaucauuuaaagaaagcguaauagc
ucacuggucgagucggccugcgcggaagauguaacggggcuaaaccaugc
accgaagcugcggcagcgacgcuuaugcguuguuggguaggggagcguuc
uguaagccugcgaaggugugcugugaggcaugcuggagguaucagaagug
cgaaugcugacauaaguaacgauaaagcgggugaaaagcccgcucgccgg
aagaccaaggguuccuguccaacguuaaucggggcagggugagucgaccc
cuaaggcgaggccgaaaggcguagucgaugggaaacagguuaauauuccu
guacuugguguuacugcgaaggggggacggagaaggcuauguuggccggg
cgacgguugucccgguuuaagcguguaggcugguuuuccaggcaaauccg
gaaaaucaaggcugaggcgugaugacgaggcacuacggugcugaagcaac
aaaugcccugcuuccaggaaaagccucuaagcaucagguaacaucaaauc
guaccccaaaccgacacagguggucagguagagaauaccaaggcgcuuga
gagaacucgggugaaggaacuaggcaaaauggugccguaacuucgggaga
aggcacgcugauauguaggugaggucccucgcggauggagcugaaaucag
ucgaagauaccagcuggcugcaacuguuuauuaaaaacacagcacugugc
aaacacgaaaguggacguauacggugugacgccugcccggugccggaagg
uuaauugaugggguuagcgcaagcgaagcucuugaucgaagccccgguaa
acggcggccguaacuauaacgguccuaagguagcgaaauuccuugucggg
uaaguuccgaccugcacgaauggcguaaugauggccaggcugucuccacc
cgagacucagugaaauugaacucgcugugaagaugcaguguacccgcggc
aagacggaaagaccccgugaaccuuuacuauagcuugacacugaacauug
agccuugauguguaggauaggugggaggcuuugaaguguggacgccaguc
ugcauggagccgaccuugaaauaccacccuuuaauguuugauguucuaac
guugacccguaauccggguugcggacagugucugguggguaguuugacug
gggcggucuccuccuaaagaguaacggaggagcacgaagguuggcuaauc
cuggucggacaucaggagguuagugcaauggcauaagccagcuugacugc
gagcgugacggcgcgagcaggugcgaaagcaggucauagugauccggugg
uucugaauggaagggccaucgcucaacggauaaaagguacuccggggaua
acaggcugauaccgcccaagaguucauaucgacggcgguguuuggcaccu
cgaugucggcucaucacauccuggggcugaaguaggucccaaggguaugg
cuguucgccauuuaaagugguacgcgagcuggguuuagaacgucgugaga
caguucggucccuaucugccgugggcgcuggagaacugaggggggcugcu
ccuaguacgagaggaccggaguggacgcaucacugguguucggguuguca
ugccaauggcacugcccgguagcuaaaugcggaagagauaagugcugaaa
gcaucuaagcacgaaacuugccccgagaugaguucucccugacccuuuaa
ggguccugaaggaacguugaagacgacgacguugauaggccgggugugua
agcgcagcgaugcguugagcuaaccgguacuaaugaaccgugaggcuuaa
ccu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7ss9 Time-resolved cryo-EM visualizes ribosomal translocation with EF-G and GTP.
• Resolution: 3.9 Å
• Binding residue (original residue number in PDB): M1 R3 T4 F5 Q6 P7 S8 V9 L10 K11 R12 H16 F18 R19 R21 M22 K25 N26 V30 R33 R35 K37 G38 R39 R41 S45 K46
• Binding residue (residue number reindexed from 1): M1 R3 T4 F5 Q6 P7 S8 V9 L10 K11 R12 H16 F18 R19 R21 M22 K25 N26 V30 R33 R35 K37 G38 R39 R41 S45 K46

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:7ss9, PDBe:7ss9, PDBj:7ss9
• PDBsum: 7ss9
• PubMed: 34903725
• UniProt: P0A7P5|RL34_ECOLI Large ribosomal subunit protein bL34 (Gene Name=rpmH)