Structure of PDB 4v95 Chain D0 Binding Site BS01

Receptor Information

>4v95 Chain D0 (length=77) Species: 300852 (Thermus thermophilus HB8)

STRNGRDSQAKRLGVKRYEGQVVRAGNILVRQRGTRFKPGKNVGMGRDFT
LFALVDGVVEFQDRGRLGRYVHVRPLA

Ligand information

>4v95 Chain DA (length=2722)

agaugguaagggcccacgguggaugccucggcacccgagccgaugaagga
cguggcuaccugcgauaagccagggggagccgguagcgggcguggauccc
uggauguccgaaugggggaacccggccggcgggaacgccggucaccgcgc
ugcgcggggggaaccuggggaacugaaacaucucaguacccagaggagag
gaaagagaaaucgacucccugaguagcggcgagcgaaaggggaccagccu
aaaccguccggcuuguccgggcggggucguggggcccucgcgaaucccca
gccuagccgaagcuguugggaagcagcgccagagagggugaaagccccgu
aggcgaaagguggggggauaggugaggguacccgaguaccccgugguucg
uggagccaugggggaaucugggcggaccaccgccuaaggcuaaguacucc
gggugaccgauagcgcaccaguaccgugagggaaaggugaaaagaacccc
gggaggggagugaaauagagccugaaaccgugggcuuacaagcagucacg
gccccgcagggguuguggcgugccuauugaagcaugagccggcgacucac
ggucgugggcgagcuuaagccguugaggcggaggcguagggaaaccgagu
ccgaacagggcgcaagcgcgcaaaguccgcggccguggacccgaaaccgg
gcgagcuagcccuggccagggugaagcuggggugagacccaguggaggcc
cgaaccggugggggaugcaaaccccucggaugagcuggggcuaggaguga
aaagcuaaccgagcccggagauagcugguucuccccgaaaugacuuuagg
gucagccucaggcgcugacuggggccuguagagcacugauagggcuaggg
ggcccaccagccuaccaaacccugucaaacuccgaagggucccaggugga
gccugggagugagggcgcgagcgauaacguccgcguccgagcgcgggaac
aaccgagaccgccagcuaaggcccccaagucugggcuaagugguaaagga
uguggcgccgcguggcgccgcgccgaaaaugaucggggcuuaagcccagc
gccgaagcugcgggucuggggccccaggcgguaggggagcguucccgaug
ccgaugaaggccgacccgcgagggcggcuggagguaagggaagugcgaau
gccggcaugaguaacgauaaagagggugagaaucccucucgccguaagcc
caaggguuccuacgcaauggucgucagcguaggguuaggcgggaccuaag
gugaagccgaaaggcguagccgaagggcagccgguuaauauuccggcccu
ucccgcaggugcgauggggggacgcucuaggcuagggggaccggagccau
ggacgagcccggccagaagcgcagggugggagguaggcaaauccgccucc
caacaagcucugcgugguggggaagcccgcgggugacaaccccccgaagc
cagggagccaagaaaagccucuaagcacaaccugcgggaacccguaccgc
aaaccgacacaggugggcgggugcaagagcacucaggcgcgcgggagaac
ccucgccaaggaacucugcaaguuggccccguaacuucgggagaaggggu
gcucccuggggugaugagccccggggagccgcagugaacaggcucuggcg
acuguuuaccaaaaacacagcucucugcgaacucguaagaggagguauag
ggagcgacgcuugcccggugccggaaggucaaggggaggggugcaagccc
cgaaccgaagccccggugaacggcggccguaacuauaacgguccuaaggu
agcgaaauuccuugucggguaaguuccgaccugcacgaaaagcguaacga
ccggagcgcugucucggcgagggacccggugaaauugaacuggccgugaa
gaugcggccuacccguggcaggacgaaaagaccccguggagcuuuacugc
agccugguguuggcucuuggucgcgcgcggcugggggccuaacccucgga
uggggggacagcgcuuggcgggcaguuugacuggggcggucgccuccuaa
aagguaacggaggcgcccaaagguccccucaggcgggacggaaauccgcc
ggagagcgcaaggguagaagggggccugacugcgaggccugcaagccgag
caggggcgaaagccgggccuagugaaccgguggucccguguggaagggcc
aucgaucaacggauaaaaguuaccccggggauaacaggcugaucuccccc
gagcguccacagcggcggggagguuuggcaccucgaugucggcucgucgc
auccuggggcugaagaaggucccaaggguugggcuguucgcccauuaaag
cggcacgcgagcuggguucagaacgucgugagacaguucggucucuaucc
gccacgggcgcaggaggcuugaggggggcucuuccuaguacgagaggacc
ggaagggacgcaccucugguuucccagcugucccuccaggggcauaagcu
ggguagccaugugcggaagggauaaccgcugaaagcaucuaagcgggaag
cccgccccaagaugaggccucccacggcagccgguaaggacccgggaaga
ccacccgguggaugggccggggguguaagcgccgcgaggcguugagccga
ccggucccaaucguccgagucu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4v95 Structural basis for the rescue of stalled ribosomes: structure of YaeJ bound to the ribosome.
• Resolution: 3.2 Å
• Binding residue (original residue number in PDB): T10 N12 R14 D15 S16 Q17 A18 K19 R20 K24 R25 Y26 E27 Q29 R32 A33 G34 N35 I36 R39 R41 G42 T43 R44 F45 G54 R55 D56 F57 T58 F60 F69 R74 L75 R77
• Binding residue (residue number reindexed from 1): T2 N4 R6 D7 S8 Q9 A10 K11 R12 K16 R17 Y18 E19 Q21 R24 A25 G26 N27 I28 R31 R33 G34 T35 R36 F37 G46 R47 D48 F49 T50 F52 F61 R66 L67 R69

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0006412 translation

Cellular Component

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

External links

• PDB: RCSB:4v95, PDBe:4v95, PDBj:4v95
• PDBsum: 4v95
• PubMed: 22422986
• UniProt: P60493|RL27_THET8 Large ribosomal subunit protein bL27 (Gene Name=rpmA)