Structure of PDB 4v8i Chain DF Binding Site BS01

Receptor Information

>4v8i Chain DF (length=202) Species: 274 (Thermus thermophilus)

VYQIPVLSPSGRRELAADLPAEINPHLLWEVVRWQLAKRRRGTASTKTRG
EVAYSGRKIWPQKHTGRARHGDIGAPIFVGGGVVFGPKPRDYSYTLPKKV
RKKGLAMAVADRAREGKLLLVEAFAGVNGKTKEFLAWAKEAGLDGSESVL
LVTGNELVRRAARNLPWVVTLAPEGLNVYDIVRTERLVMDLDAWEVFQNR
IG

Ligand information

>4v8i Chain DA (length=2798)

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
agccugguguuggcucuuggucgcgccugcguaggauaggugggagccug
ugaacccccgccuccgggugggggggaggcgccggugaaauaccacccug
gcgcggcugggggccuaacccucggauggggggacagcgcuuggcgggca
guuugacuggggcggucgccuccuaaaagguaacggaggcgcccaaaggu
ccccucaggcgggacggaaauccgccggagagcgcaaggguagaaggggg
ccugacugcgaggccugcaagccgagcaggggcgaaagccgggccuagug
aaccgguggucccguguggaagggccaucgaucaacggauaaaaguuacc
ccggggauaacaggcugaucucccccgagcguccacagcggcggggaggu
uuggcaccucgaugucggcucgucgcauccuggggcugaagaagguccca
aggguugggcuguucgcccauuaaagcggcacgcgagcuggguucagaac
gucgugagacaguucggucucuauccgccacgggcgcaggaggcuugagg
ggggcucuuccuaguacgagaggaccggaagggacgcaccucugguuucc
cagcugucccuccaggggcauaagcuggguagccaugugcggaagggaua
accgcugaaagcaucuaagcgggaagcccgccccaagaugaggccuccca
cggcagccgguaaggacccgggaagaccacccgguggaugggccgggggu
guaagcgccgcgaggcguugagccgaccggucccaaucguccgagucu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4v8i How hibernation factors RMF, HPF, and YfiA turn off protein synthesis.
• Resolution: 2.7 Å
• Binding residue (original residue number in PDB): N29 H31 E35 R38 Q40 L41 A42 K43 R44 R45 R46 T48 A49 S50 T51 T53 R54 G55 V57 A58 Y59 S60 G61 R62 K63 Q67 K68 H69 G71 R72 A73 R74 H75 G76 P81 I82 F83 V84 V89 F90 P92 P94 R95 Y99 T100 P102 K103 K104 V105 R106 K108 G134 K135 T136 R165 R168 N169 L170 P171 E179 G180 N182 Y184 R205
• Binding residue (residue number reindexed from 1): N24 H26 E30 R33 Q35 L36 A37 K38 R39 R40 R41 T43 A44 S45 T46 T48 R49 G50 V52 A53 Y54 S55 G56 R57 K58 Q62 K63 H64 G66 R67 A68 R69 H70 G71 P76 I77 F78 V79 V84 F85 P87 P89 R90 Y94 T95 P97 K98 K99 V100 R101 K103 G129 K130 T131 R160 R163 N164 L165 P166 E174 G175 N177 Y179 R200

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:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:4v8i, PDBe:4v8i, PDBj:4v8i
• PDBsum: 4v8i
• PubMed: 22605777
• UniProt: Q5SHN9|RL4_THET8 Large ribosomal subunit protein uL4 (Gene Name=rplD)