Structure of PDB 4v8u Chain DW Binding Site BS01

Receptor Information

>4v8u Chain DW (length=113) Species: 300852 (Thermus thermophilus HB8)

MEAKAIARYVRISPRKVRLVVDLIRGKSLEEARNILRYTNKRGAYFVAKV
LESAAANAVNNHDMLEDRLYVKAAYVDEGPALKRVLPRARGRADIIKKRT
SHITVILGEKHGK

Ligand information

>4v8u Chain DA (length=2901)

agaugguaagggcccacgguggaugccucggcacccgagccgaugaagga
cguggcuaccugcgauaagccagggggagccgguagcgggcguggauccc
uggauguccgaaugggggaacccggccggcgggaacgccggucaccgcgc
uuuugcgcggggggaaccuggggaacugaaacaucucaguacccagagga
gaggaaagagaaaucgacucccugaguagcggcgagcgaaaggggaccag
ccuaaaccguccggcuuguccgggcggggucguggggcccucggacaccg
aauccccagccuagccgaagcuguugggaagcagcgccagagagggugaa
agccccguaggcgaaagguggggggauaggugaggguacccgaguacccc
gugguucguggagccaugggggaaucugggcggaccaccgccuaaggcua
aguacuccgggugaccgauagcgcaccaguaccgugagggaaaggugaaa
agaaccccgggaggggagugaaauagagccugaaaccgugggcuuacaag
cagucacggccccgcaagggguuguggcgugccuauugaagcaugagccg
gcgacucacggucgugggcgagcuuaagccguugaggcggaggcguaggg
aaaccgaguccgaacagggcgcaagcgggccgcacgcggcccgcaaaguc
cgcggccguggacccgaaaccgggcgagcuagcccuggccagggugaagc
uggggugagacccaguggaggcccgaaccggugggggaugcaaaccccuc
ggaugagcuggggcuaggagugaaaagcuaaccgagcccggagauagcug
guucuccccgaaaugacuuuagggucagccucaggcgcugacuggggccu
guagagcacugauagggcuagggggcccaccagccuaccaaacccuguca
aacuccgaagggucccagguggagccugggagugagggcgcgagcgauaa
cguccgcguccgagcgcgggaacaaccgagaccgccagcuaaggccccca
agucugggcuaagugguaaaggauguggcgccgcgaagacagccaggagg
uuggcuuagaagcagccauccuuuaaagagugcguaauagcucacugguc
gaguggcgccgcgccgaaaaugaucggggcuuaagcccagcgccgaagcu
gcgggucugggggaugaccccaggcgguaggggagcguucccgaugccga
ugaaggccgacccgcgagggcggcuggagguaagggaagugcgaaugccg
gcaugaguaacgauaaagagggugagaaucccucucgccguaagcccaag
gguuccuacgcaauggucgucagcguaggguuaggcgggaccuaagguga
agccgaaaggcguagccgaagggcagccgguuaauauuccggcccuuccc
gcaggugcgauggggggacgcucuaggcuagggggaccggagccauggac
gagcccggccagaagcgcagggugggagguaggcaaauccgccucccaac
aagcucugcgugguggggaagcccguacgggugacaaccccccgaagcca
gggagccaagaaaagccucuaagcacaaccugcgggaacccguaccgcaa
accgacacaggugggcgggugcaagagcacucaggcgcgcgggagaaccc
ucgccaaggaacucugcaaguuggccccguaacuucgggagaaggggugc
ucccuggggugaugagccccggggagccgcagugaacaggcucuggcgac
uguuuaccaaaaacacagcucucugcgaacucguaagaggagguauaggg
agcgacgcuugcccggugccggaaggucaaggggaggggugcaagccccg
aaccgaagccccggugaacggcggccguaacuauaacgguccuaagguag
cgaaauuccuugucggguaaguuccgaccugcacgaaaagcguaacgacc
ggagcgcugucucggcgagggacccggugaaauugaacuggccgugaaga
ugcggccuacccguggcaggacgaaaagaccccguggagcuuuacugcag
ccugguguuggcucuuggucgcgccugcguaggauaggugggagccugug
aacccccgccuccgggugggggggaggcgccggugaaauaccacccuggc
gcggcugggggccuaacccucggauggggggacagcgcuuggcgggcagu
uugacuggggcggucgccuccuaaaagguaacggaggcgcccaaaggucc
ccucaggcgggacggaaauccgccggagagcgcaaggguagaagggggcc
ugacugcgaggccugcaagccgagcaggggcgaaagccgggccuagugaa
ccgguggucccguguggaagggccaucgaucaacggauaaaaguuacccc
ggggauaacaggcugaucucccccgagcguccacagcggcggggagguuu
ggcaccucgaugucggcucgucgcauccuggggcugaagaaggucccaag
gguugggcuguucgcccauuaaagcggcacgcgagcuggguucagaacgu
cgugagacaguucggucucuauccgccacgggcgcaggaggcuugagggg
ggcucuuccuaguacgagaggaccggaagggacgcaccucugguuuccca
gcugucccuccaggggcauaagcuggguagccaugugcggaagggauaac
cgcugaaagcaucuaagcgggaagcccgccccaagaugaggccucccacg
gcgucaagccgguaaggacccgggaagaccacccgguggaugggccgggg
guguaagcgccgcgaggcguugagccgaccggucccaaucguccgagguc
u

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4v8u Crystal structure of 70S ribosome with both cognate tRNAs in the E and P sites representing an authentic elongation complex.
• Resolution: 3.7 Å
• Binding residue (original residue number in PDB): A5 I6 A7 R8 R11 S13 R15 K16 R18 R25 N40 K41 R42 K49 S53 A56 N57 N60 N61 H62 Y75 D77 E78 P80 R84 P87 R88 A89 R90 G91 R92 A93 D94 I96 K97 K98 R99 H102
• Binding residue (residue number reindexed from 1): A5 I6 A7 R8 R11 S13 R15 K16 R18 R25 N40 K41 R42 K49 S53 A56 N57 N60 N61 H62 Y75 D77 E78 P80 R84 P87 R88 A89 R90 G91 R92 A93 D94 I96 K97 K98 R99 H102

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:0015934 large ribosomal subunit
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:4v8u, PDBe:4v8u, PDBj:4v8u
• PDBsum: 4v8u
• PubMed: 23527033
• UniProt: Q5SHP3|RL22_THET8 Large ribosomal subunit protein uL22 (Gene Name=rplV)