Structure of PDB 8c8x Chain 3 Binding Site BS01

Receptor Information

>8c8x Chain 3 (length=64) Species: 562 (Escherichia coli)

PKIKTVRGAAKRFKKTGKGGFKHKHANLRHILTKKATKRKRHLRPKAMVS
KGDLGLVIACLPYA

Ligand information

>8c8x Chain A (length=2705)

gguuaagcgacuaagcguacacgguggaugcccuggcagucagaggcgau
gaaggacgugcuaaucugcgauaagcgucgguaaggugauaugaaccguu
auaaccggcgauuuccgaauggggaaacccaguguguuucgacacacuau
cauuaacugaauccauagguuaaugaggcgaaccgggggaacugaaacau
cuaaguaccccgaggaaaagaaaucaaccgagauucccccaguagcggcg
agcgaacggggagcagcccagagccugaaucaguguguguguuaguggaa
gcgucuggaaaggcgcgcgauacagggugacagccccguacacaaaaaug
cacaugcugugagcucgaugaguagggcgggacacgugguauccugucug
aauauggggggaccauccuccaaggcuaaauacuccugacugaccgauag
ugaaccaguaccgugagggaaaggcgaaaagaaccccggcgaggggagug
aaaaagaaccugaaaccguguacguacaagcagugggagcacgcuuaggc
gugugacugcguaccuuuuguauaaugggucagcgacuuauauucuguag
caagguuaaccgaauaggggagccgaagggaaaccgagucuuaacugggc
guuaaguugcaggguauagacccgaaacccggugaucuagccaugggcag
guugaagguuggguaacacuaacuggaggaccgaaccgacuaauguugaa
aaauuagcggaugacuuguggcugggggugaaaggccaaucaaaccggga
gauagcugguucuccccgaaagcuauuuagguagcgccucgugaauucau
cuccggggguagagcacuguuucggcaagggggucaucccgacuuaccaa
cccgaugcaaacugcgaauaccggagaauguuaucacgggagacacacgg
cgggugcuaacguccgucgugaagagggaaacaacccagaccgccagcua
aggucccaaagucaugguuaagugggaaacgaugugggaaggcccgucgg
ccugcgcggaagauguaacggggcuaaaccaugcaccgaagcugcggcag
cgacgcuuaugcguuguuggguaggggagcguucuguaagccugcgaagg
ugugcugugaggcaugcuggagguaucagaagugcgaaugcugacauaag
uaacgauaaagcgggugaaaagcccgcucgccggaagaccaaggguuccu
guccaacguuaaucggggcagggugagucgaccccuaaggcgaggccgaa
aggcguagucgaugggaaacagguuaauauuccuguacuugguguuacug
cgaaggggggacggagaaggcuauguuggccgggcgacgguugucccggu
uuaagcguguaggcugguuuuccaggcaaauccggaaaaucaaggcugag
gcgugaugacgaggcacuacggugcugaagcaacaaaugcccugcuucca
ggaaaagccucuaagcaucagguaacaucaaaucguaccccaaaccgaca
cagguggucagguagagaauaccaaggcgcuugagagaacucgggugaag
gaacuaggcaaaauggugccguaacuucgggagaaggcacgcugauaugu
aggugaggucccucgcggauggagcugaaaucagucgaagauaccagcug
gcugcaacuguuuauuaaaaacacagcacugugcaaacacgaaaguggac
guauacggugugacgccugcccggugccggaagguuaauugaugggguua
gcgcaagcgaagcucuugaucgaagccccgguaaacggcggccguaacua
uaacgguccuaagguagcgaaauuccccugcacgaauggcguaaugaugg
ccaggcugucuccacccgagacucagugaaauugaacucgcugugaagau
gcaguguacccgcggcaagacggaaagaccccgugaaccuuuacuauagc
uugacacugaacauugagccuugauguguaggauaggugggaggcuuuga
aguguggacgccagucugcauggagccgaccuugaaauaccacccuuuaa
uguuugauguucuaacguugacccguaauccggguugcggacagugucug
guggguaguuugacuggggcggucuccuccuaaagaguaacggaggagca
cgaagguuggcuaauccuggucggacaucaggagguuagugcaauggcau
aagccagcuugacugcgagcgugacggcgcgagcaggugcgaaagcaggu
cauagugauccggugguucugaauggaagggccaucgcucaacggauaaa
agguacuccggggaggcugauaccgcccaagaguucauaucgacggcggu
guuuggcacgucccuaucugccgugggcgcuggagaacugaggggggcug
cuccuaguacgagaggaccggaguggacgcaucacugguguucggguugu
caugccaauggcacugcccgguagcuaaaugcggaagagauaagugcuga
aagcaucuaagcacgaaacuugccccgagaugaguucucccugacccuuu
aaggguccugaaggaacguugaagacgacgacguugauaggccgggugug
uaagcgcagcgaugcguugagcuaaccgguacuaaugaaccgugaggcuu
aaccu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8c8x Cryo-EM captures early ribosome assembly in action.
• Resolution: 3.93 Å
• Binding residue (original residue number in PDB): P1 K2 I3 K4 T5 R7 R12 T16 K18 K22 K24 H25 N27 R29 H30 I31 L32 T33 K34 K35 K38 R39 K40 R41 H42 S50 Y63
• Binding residue (residue number reindexed from 1): P1 K2 I3 K4 T5 R7 R12 T16 K18 K22 K24 H25 N27 R29 H30 I31 L32 T33 K34 K35 K38 R39 K40 R41 H42 S50 Y63

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome

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:8c8x, PDBe:8c8x, PDBj:8c8x
• PDBsum: 8c8x
• PubMed: 36797249
• UniProt: P0A7Q1|RL35_ECOLI Large ribosomal subunit protein bL35 (Gene Name=rpmI)