Structure of PDB 4v97 Chain DE Binding Site BS01

Receptor Information

>4v97 Chain DE (length=204) Species: 300852 (Thermus thermophilus HB8)

MKGILGVKVGMTRIFRDDRAVPVTVILAGPCPVVQRRTPEKDGYTAVQLG
FLPQNPKRVNRPLKGHFAKAGVEPVRILREIRDFNPEGDTVTVEIFKPGE
RVDVTGTSKGRGFAGVMKRWNFAGGPDSHGAHKIHRHPGSIGNRKTPGRV
YKGKKMAGHYGAERVTVMNLEVVDVIPEENLLLVKGAVPGPNGGLVIVRE
TKKA

Ligand information

>4v97 Chain DA (length=2824)

agaugguaagggcccacgguggaugccucggcacccgagccgaugaagga
cguggcuaccugcgauaagccagggggagccgguagcgggcguggauccc
uggauguccgaaugggggaacccggccggcgggaacgccggucaccgcgc
gcgcggggggaaccuggggaacugaaacaucucaguacccagaggagagg
aaagagaaaucgacucccugaguagcggcgagcgaaaggggaccagccua
aaccguccggcuuguccgggcggggucguggggcccucgcgaauccccag
ccuagccgaagcuguugggaagcagcgccagagagggugaaagccccgua
ggcgaaagguggggggauaggugaggguacccgaguaccccgugguucgu
ggagccaugggggaaucugggcggaccaccgccuaaggcuaaguacuccg
ggugaccgauagcgcaccaguaccgugagggaaaggugaaaagaaccccg
ggaggggagugaaauagagccugaaaccgugggcuuacaagcagucacgg
ccccgcaagggguuguggcgugccuauugaagcaugagccggcgacucac
ggucgugggcgagcuuaagccguugaggcggaggcguagggaaaccgagu
ccgaacagggcgcaguccgcggccguggacccgaaaccgggcgagcuagc
ccuggccagggugaagcuggggugagacccaguggaggcccgaaccggug
ggggaugcaaaccccucggaugagcuggggcuaggagugaaaagcuaacc
gagcccggagauagcugguucuccccgaaaugacuuuagggucagccuca
ggcgcugacuggggccuguagagcacugauagggcuagggggcccaccag
ccuaccaaacccugucaaacuccgaagggucccagguggagccugggagu
gagggcgcgagcgauaacguccgcguccgagcgcgggaacaaccgagacc
gccagcuaaggcccccaagucugggcuaagugguaaaggauguggcgccg
cgaagacagccagauagcucacuggucgaguggcgccgcgccgaaaauga
ucggggcuuaagcccagcgccgaagcugcgggucugggggaugaccccag
gcgguaggggagcguucccgaugccgaugaaggccgacccgcgagggcgg
cuggagguaagggaagugcgaaugccggcaugaguaacgauaaagagggu
gagaaucccucucgccguaagcccaaggguuccuacgcaauggucgucag
cguaggguuaggcgggaccuaaggugaagccgaaaggcguagccgaaggg
cagccgguuaauauuccggcccuucccgcaggugcgauggggggacgcuc
uaggcuagggggaccggagccauggacgagcccggccagaagcgcagggu
gggagguaggcaaauccgccucccaacaagcucugcgugguggggaagcc
cgggugacaaccccccgaagccagggagccaagaaaagccucuaagcaca
accugcgggaacccguaccgcaaaccgacacaggugggcgggugcaagag
cacucaggcgcgcgggagaacccucgccaaggaacucugcaaguuggccc
cguaacuucgggagaaggggugcucccuggggugaugagccccggggagc
cgcagugaacaggcucuggcgacuguuuaccaaaaacacagcucucugcg
aacucguaagaggagguauagggagcgacgcuugcccggugccggaaggu
caaggggaggggugcaagccccgaaccgaagccccggugaacggcggccg
uaacuauaacgguccuaagguagcgaaauuccuugucggguaaguuccga
ccugcacgaaaagcguaacgaccggagcgcugucucggcgagggacccgg
ugaaauugaacuggccgugaagaugcggccuacccguggcaggacgaaaa
gaccccguggagcuuuacugcagccugguguuggcucuuggucgcgccug
cguaggauaggugggagccugugaacccccgccuccgggugggggggagg
cgccggugaaauaccacccuggcgcggcugggggccuaacccucggaugg
ggggacagcgcuuggcgggcaguuugacuggggcggucgccuccuaaaag
guaacggaggcgcccaaagguccccucaggcgggacggaaauccgccgga
gagcgcaaggguagaagggggccugacugcgaggccugcaagccgagcag
gggcgaaagccgggccuagugaaccgguggucccguguggaagggccauc
gaucaacggauaaaaguuaccccggggauaacaggcugaucucccccgag
cguccacagcggcggggagguuuggcaccucgaugucggcucgucgcauc
cuggggcugaagaaggucccaaggguugggcuguucgcccauuaaagcgg
cacgcgagcuggguucagaacgucgugagacaguucggucucuauccgcc
acgggcgcaggaggcuugaggggggcucuuccuaguacgagaggaccgga
agggacgcaccucugguuucccagcugucccuccaggggcauaagcuggg
uagccaugugcggaagggauaaccgcugaaagcaucuaagcgggaagccc
gccccaagaugaggccucccacggcgucaagccgguaaggacccgggaag
accacccgguggaugggccggggguguaagcgccgcgaggcguugagccg
accggucccaaucguccgaggucu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4v97 Reorganization of an intersubunit bridge induced by disparate 16S ribosomal ambiguity mutations mimics an EF-Tu-bound state.
• Resolution: 3.516 Å
• Binding residue (original residue number in PDB): K8 M11 T12 R13 P22 R37 K41 D42 Y44 R58 N60 R61 P62 K64 I77 R79 E80 R82 K109 G110 R111 G112 F113 G115 K118 R119 F122 A123 P126 D127 S128 H129 G130 A131 H132 K133 I134 H135 R136 H137 P138 G139 S140 I141 G142 N143 R144 K145 T146 P147 G148 R149 V150 Y151 K152 K154 M156 A157 H159 R164 V165 T166 M168 N169 K185 A187 V188 P189 K202 K203
• Binding residue (residue number reindexed from 1): K8 M11 T12 R13 P22 R37 K41 D42 Y44 R58 N60 R61 P62 K64 I77 R79 E80 R82 K109 G110 R111 G112 F113 G115 K118 R119 F122 A123 P126 D127 S128 H129 G130 A131 H132 K133 I134 H135 R136 H137 P138 G139 S140 I141 G142 N143 R144 K145 T146 P147 G148 R149 V150 Y151 K152 K154 M156 A157 H159 R164 V165 T166 M168 N169 K185 A187 V188 P189 K202 K203

Gene Ontology

Molecular Function

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

Biological Process

• GO:0006412 translation

Cellular Component

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

External links

• PDB: RCSB:4v97, PDBe:4v97, PDBj:4v97
• PDBsum: 4v97
• PubMed: 23630274
• UniProt: Q5SHN8|RL3_THET8 Large ribosomal subunit protein uL3 (Gene Name=rplC)