Structure of PDB 6vwm Chain B Binding Site BS01

Receptor Information

>6vwm Chain B (length=209) Species: 562 (Escherichia coli)

MIGLVGKKVGMTRIFTEDGVSIPVTVIEVEANRVTQVKDLANDGYRAIQV
TTGAKKANRVTKPEAGHFAKAGVEAGRGLWEFRLAEGEEFTVGQSISVEL
FADVKKVDVTGTSKGKGFAGTVKRWNFRTQDATHGNSLSHRVPGSIGQNQ
TPGKVFKGKKMAGQMGNERVTVQSLDVVRVDAERNLLLVKGAVPGATGSD
LIVKPAVKA

Ligand information

>6vwm Chain 2 (length=2833)

gguuaagcgacuaagcguacacgguggaugcccuggcagucagaggcgau
gaaggacgugcuaaucugcgauaagcgucgguaaggugauaugaaccguu
auaaccggcgauuuccgaauggggaaacccaguguguuucgacacacuau
cauuaacugaauccauagguuaaugaggcgaaccgggggaacugaaacau
cuaaguaccccgaggaaaagaaaucaaccgagauucccccaguagcggcg
agcgaacggggagcagcccagagccugaaucaguguguguguuaguggaa
gcgucuggaaaggcgcgcgauacagggugacagccccguacacaaaaaug
cacaugcugugagcucgaugaguagggcgggacacgugguauccugucug
aauauggggggaccauccuccaaggcuaaauacuccugacugaccgauag
ugaaccaguaccgugagggaaaggcgaaaagaaccccggcgaggggagug
aaaaagaaccugaaaccguguacguacaagcagugggagcacgcuuaggc
gugugacugcguaccuuuuguauaaugggucagcgacuuauauucuguag
caagguuaaccgaauaggggagccgaagggaaaccgagucuuaacugggc
guuaaguugcaggguauagacccgaaacccggugaucuagccaugggcag
guugaagguuggguaacacuaacuggaggaccgaaccgacuaaugucgaa
aaauuagcggaugacuuguggcugggggugaaaggccaaucaaaccggga
gauagcugguucuccccgaaagcuauuuagguagcgccucgugaauucau
cuccggggguagagcacuguuucggcaagggggucaucccgacuuaccaa
cccgaugcaaacugcgaauaccggagaauguuaucacgggagacacacgg
cgggugcuaacguccgucgugaagagggaaacaacccagaccgccagcua
aggucccaaagucaugguuaagugggaaacgaugugggaaggucggccug
cgcggaagauguaacggggcuaaaccaugcaccgaagcugcggcagcgac
gcuuaugcguuguuggguaggggagcguucuguaagccugcgaaggugug
cugugaggcaugcuggagguaucagaagugcgaaugcugacauaaguaac
gauaaagcgggugaaaagcccgcucgccggaagaccaaggguuccugucc
aacguuaaucggggcagggugagucgaccccuaaggcgaggccgaaaggc
guagucgaugggaaacagguuaauauuccuguacuugguguuacugcgaa
ggggggacggagaaggcuauguuggccgggcgacgguugucccgguuuaa
gcguguaggcugguuuuccaggcaaauccggaaaaucaaggcugaggcgu
gaugacgaggcacuacggugcugaagcaacaaaugcccugcuuccaggaa
aagccucuaagcaucagguaacaucaaaucguaccccaaaccgacacagg
uggucagguagagaauaccaaggcgcuugagagaacucgggugaaggaac
uaggcaaaauggugccguaacuucgggagaaggcacgcugauauguaggu
gaggucccucgcggauggagcugaaaucagucgaagauaccagcuggcug
caacuguuuauuaaaaacacagcacugugcaaacacgaaaguggacguau
acggugugacgccugcccggugccggaagguuaauugaugggguuagcgc
aagcgaagcucuugaucgaagccccgguaaacggcggccguaacuauaac
gguccuaagguagcgaaauuccuugucggguaaguuccgaccugcacgaa
uggcguaaugauggccaggcugucuccacccgagacucagugaaauugaa
cucgcugugaagaugcaguguacccgcggcaagacggaaagaccccguga
accuuuacuauagcuugacacugaacauugagccuugauguguaggauag
gugggaggcuuugaaguguggacgccagucugcauggagccgaccuugaa
auaccacccuuuaauguuugauguucuaacguugacccguaauccggguu
gcggacagugucugguggguaguuugacuggggcggucuccuccuaaaga
guaacggaggagcacgaagguuggcuaauccuggucggacaucaggaggu
uagugcaauggcauaagccagcuugacugcgagcgugacggcgcgagcag
gugcgaaagcaggucauagugauccggugguucugaauggaagggccauc
gcucaacggauaaaagguacuccggggauaacaggcugauaccgcccaag
aguucauaucgacggcgguguuuggcaccucgaugucggcucaucacauc
cuggggcugaaguaggucccaaggguauggcuguucgccauuuaaagugg
uacgcgagcuggguuuagaacgucgugagacaguucggucccuaucugcc
gugggcgcuggagaacugaggggggcugcuccuaguacgagaggaccgga
guggacgcaucacugguguucggguugucaugccaauggcacugcccggu
agcuaaaugcggaagagauaagugcugaaagcaucuaagcacgaaacuug
ccccgagaugaguucucccugacccuuuaaggguccugaaggaacguuga
agacgacgacguugauaggccggguguguaagcgcagcgaugcguugagc
uaaccgguacuaaugaaccgugaggcuuaaccu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6vwm mRNA stem-loops can pause the ribosome by hindering A-site tRNA binding.
• Resolution: 3.4 Å
• Binding residue (original residue number in PDB): M11 T12 P23 Q36 D43 Y45 Q49 N58 R59 T61 K62 P63 G66 H67 K70 L79 E81 R83 K114 G115 K116 G117 F118 G120 K123 R124 F127 R128 T129 Q130 D131 T133 H134 G135 N136 S137 L138 S139 H140 R141 P143 G144 S145 I146 G147 Q148 N149 Q150 T151 P152 K154 V155 F156 K157 K159 M161 Q164 N167 R169 V170 T171 Q173 S174 K190 A192 V193 P194 T197 K208 A209
• Binding residue (residue number reindexed from 1): M11 T12 P23 Q36 D43 Y45 Q49 N58 R59 T61 K62 P63 G66 H67 K70 L79 E81 R83 K114 G115 K116 G117 F118 G120 K123 R124 F127 R128 T129 Q130 D131 T133 H134 G135 N136 S137 L138 S139 H140 R141 P143 G144 S145 I146 G147 Q148 N149 Q150 T151 P152 K154 V155 F156 K157 K159 M161 Q164 N167 R169 V170 T171 Q173 S174 K190 A192 V193 P194 T197 K208 A209

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0019843 rRNA binding

Biological Process

• GO:0000027 ribosomal large subunit assembly
• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6vwm, PDBe:6vwm, PDBj:6vwm
• PDBsum: 6vwm
• PubMed: 32427100
• UniProt: P60438|RL3_ECOLI Large ribosomal subunit protein uL3 (Gene Name=rplC)