Structure of PDB 4v8p Chain GM Binding Site BS02

Receptor Information

>4v8p Chain GM (length=300) Species: 5911 (Tetrahymena thermophila)

GFVKVLKTKAYFKRFQTKYRRRREGLTDYYARKRLIIQDKDKYNTPKYRL
VARATNTRIIAQIVYATLKCDRVLCAADSYELKRFGVSTGLASYAAAYAT
GLLLARRLLKQIGLDTVYAGQTKVDGAYFNVDEDQKEKKPFKAILDAGLV
RTTTGNRVFGVLKGACDGGINIPHSESRFPGYVRASDEGESSKYKPEDHK
ARIFGKHIDAYMKHLKGQSNEAFQKQFSKWSKTLEAAKVDSVEKLFTKVH
AEIRKNPERVKSTKKNDKPKRDHKKFYPTKLTAAQRKDRVKTKFQLALSQ

Ligand information

>4v8p Chain H1 (length=3119)

cuacaccugaaacaagcaagauuacccgcugaacuuaagcauaucaguaa
gcggaggaaaagaaacuaacuaggauagccccaguaauggcgaaugaaca
ggcuaaagcucaaagugaaaaucugaaguggucaacacaacagaauugua
aucuaaagggucaaccugaaacuaagcuccucucauaaguuccuuggaac
aggacgucaaagagggugacaaccccguagucggagaggaaggcuggugu
aagggagauuucaaagagucggguuguuugggauugcagcccuaaguggg
agauaaacuucuucuaaagcuaaauauacacgggagaccgauagcgaaca
aguacugcgaaggaaagaugaaaagaacuuugaaaagagggcuaaaagac
uugaaaccguugagaaggaagcuguagaagagcaauaaacuggacggcgc
auaagggggaaguacuaaucacugcagagucgauacguaaaaggucgaug
aguaaggaaaugguacagaacuugcuacgccggucagaagacaaaauggg
uucagauugaaggagucaccugagaucgggcagcaaugcagaucaaaagg
aaaacuucaaacuggacugaggggccuaagggcgauuuugucaaaauggc
uucuacugacccgucuugaaacacggaccaaggagucuaucaauuaagcg
agugauaggguggaaaaacccguccgcgaaacgaaagugaguacaaggug
ccaagccgcaagguagcagcaucacccgaccuugagucuccgacgaaggg
uucgaggaagagcuuaauuguuaggacccgaaagauggugaacuacgcuu
gaauagggugaagccaggggaaacucugguggaagcucguagcgauacug
acgugcaaaucguucgucaaauuugaguguaggggcgaaagacuaaucga
accaucuaguagcugguucccuccgaaguuucucucaggauagcaagagc
aaguacgcaguuuuauuagguaaagcgaaugauuagaggacucgggguuc
caagaaucucgaccuauucucaaacuuuaaauugguaagagccgcggagu
uuacuuaaaugaacucucgggaagaaugcagugcucuuagugggccauuu
uugguaagcagaacuggcgaugagggaugaaccuaacguugagauaaggc
gcccaaaugcacgcucaucagauaccacaaaagguguugguucauacgga
cagcaggccugccgaaugaacuagcccugaaaauggauggcgcugaagcg
uguugccgauacucaaccaucagagcaaaugcgaggcuuugaugaguagg
agggcgugaucguugccuagaaguauugggcgugagccuauauggagcag
cgauuagugcagaucuuggugguaguagcaaauauucaaaugagaacuuu
gaagaccgaaguggagaaggguuccaugagaacagcaauuguucaugggu
uacucgauccuaagacauagguuaacuccuugcaauacaagaagacauuc
guuuucguugucaaaagggaaugagguuaauauuccucaagcuggacgug
guauagagcgguaacgcaaagaaacccggagacgucagcaggugucacug
gaagaguuaucuuuucuuuuuaacauacuauggccaugaaauuggauuau
ccagagauaucggcuguauguauggcagagcagcucagagcugucaguug
cgcaccugaugacccuugaaaaucugggggagacauaauuucacgccagu
ucguacccauaaccgcaucaggucuccaagguuagcagccucugguccau
agaacaauguagauaagggaagucggcaaauuggauccguaacuucggga
uaaggauuggcucugaggaucucagaacugaagcggacaaagguaauccg
acuguuuaauaaaaacaaagcauugugacggccucaacaggugaugacac
aaugugauuucugcccagugcucugaaugucaaagugacgcaauucaacc
aagcgcggguaaacggcgggaguaacuaugacucucuuaagguagccaaa
ugccucgucaucuaauuagugacgcgcaugaauggauuaaugagauuacc
acugucccuaucuacuaucuagcgaacccacagcuaagggaacgggcuua
gaauaaucagcggggaaagaagacccuguugagcuugacucuagucuaac
uuugugaaauggcagucauuuugcuuauuucgugaagaaaagacuggugc
aaaccaguucuaaaguuaaggucauuuauugacugauuuuugcgaaagac
augguuagggggggaguuugucuggggcggaaugccuguuaaaccauaac
gcaggcguccuaaguguagcucagugagaacggaaaucucacguagaaca
aaaggguaaaagcuacauugauuuugauuuucaguaggaauacaaaccgc
gaaagcguggccuaucgauccuuuaacuuuacaaguuuuaagcuagaggu
gucagaaaaguuaccacagggauaacuggcuuguggcagccaagaguuca
uaucgacguugcuuuuugauccuucgaugucggcucuuccuaucauugug
aagcagaauucacaacgugucggauuguucacccgcuaauagggaacgug
agcuggguuuagaccgucgugagacagguuaguuuuacccuacugaugaa
acgauguugcgacaguaauuuaaguuaguacgagaggaacacuuaaauca
gauaauugguaaauacgguugucugaaaagacaaugccgugaagcuacca
ucuguuggauuaugacugaaggccucuaagucagaauccaugcuggaaag
caaugucuaagugugaugauaaacgaaaaaaaauaaaaauuaaguucgaa
agguagagcggggaagagcgaaaaagcuugaccuuaacugcuaaucguaa
uuccaaauuaucaucuacguaaaucuuuuguagacgacuuaacauggaac
ggguauuguaagcaugagaguagaauuuccuacgaucugcugagauucag
cccgucuccuuagauuuau

........................<<<<<<.....<......>......>
>>>>.>...{.....<<....>>..<<<<<......<<.....>>.....
>>>>>..[[[...........<<<<..<<<.....>>>..>>>>......
.......<<<<<..<<<...<<<.<<<<<<<<<<......<<<<......
>>>>.((......<<<.....))>>>.......>>>>>>>..>>>>>>..
.>>>..>>>>.>........<<<<<<<........>>>>>>>.....(((
((..<<<<<<)))))..]]]....}.........................
....<<....>>...............<<<<....>>>>...........
.....................<.<<<<<<<....<<...<<<<.<<<<<.
....<<<....<<<<<.<<..<<<<...<<<<<<.<......>>>>>>>.
.>>.>>...>>>>>>>....>>>....>>>>>.>>>>..<<<<<<<<.<<
<<<<<.<<<<<<......<<<..<<<<..<<<....>>>.>>>>...>>>
....>>>>>>.>>>>>>>.....<<<....>>>.>>>>>>>>...>>..>
>>>>>>.>..<<<<........>>>><<<<<<...<<<<.<<<<<<<<<.
.<<<...<<<<......>>>>...>>>...<<....>>........<<<<
<...<<<....>>>....>>>>>.<<<<<<<....<<<...>>>....>>
.>>>.>>....>>>>>>>>>.>>>>.<<.<...<<<<<<.....<<<<<<
<<<..<<<....<<<<<<<....>>>>>>>.....>>>...<<<<.<<.<
<........>>>>>>>>....>>>>>>>>>...<<.......>>......
>>>>>>......>.>>..<<<<<<....<.<<<....>>>.><<<<<<<<
<.....<<<.<<<<<<<<<...<<<....<<<....<<<..<<<<<<<<<
...>>>>>>>>>>>>....>>>..>.>>...>>>>>>>...<<<.<<<<<
<..........>>>>>>>>>....>>>>>..>>>>>>>.>>..<<<<.<<
<<<.....>>>>>.>>>>....<<<......>>>...<<<<<<....<<<
(((.....<<<<<<......<..........<<<.<<<<<<<<<......
..<<<<..>>>>....>>>>>>>>>>>>..........))).>....>>>
>>>.>>>....>>>>>><<<<<<<<<.........>>>>>>>>>....>>
>>>><.<<<<<<<<<<......<<<<.<<<<....>>>>>>>>...>>>>
>>>>>>..>.....>>>>>><<.....<<.....<<<<<<.......>>>
>>><<<<.....<<<<<.<<...<<<<<<...<<.....>>.>>>>>>..
..((<<<<<<...<<<..<<<......>>>..........<<<<<<....
>>>>>>...>>>....>>>..<<<<<........>>>>>))<<<<.<<<<
..<<...<<<....>>>.......<<<<<<...<<<<.<<<<<<<<<<<<
<<<<<<.......>>>>>><...<<<<<...<<<<<<<....<<<<...>
>>>....>>>.>>>>....>>>>>....><<<<<<<.>>>>>>>>>>>.>
.>>>>>>>.>>>>.........>>>>>>.........>>..>>>>>>>>.
>>>..>>.....<<......>>>>>>>.<<<<.....>>>>..>>>>..<
<<<.....<<<<<<<.<<...............<<<<<............
...>>>>><<.<<<<<<...>>>>>>.>>............<<<<<<<<<
..<<<.........>>>..<<<<<<<....<<<<....>>>>......>>
>>>>>...<<..<<<..<<<<<<....<<<.....<<<......>>>...
..>>>.>>>>..>>>>><<<<<<.......>>>>>>........<.....
......<<<<<.......>>>>>.....>.....>>....>>.>>>>>>>
.....>>.>>>>>>>..>>>>>>....>>....<<<<<........>>>>
>....(((((..{{{.{{......[[[[.{{[[[[..<<<<<..<<<<<<
<..<<<<<<<<<<.>>>>>>>>>>...<<<<<.....<<<<..<<<<<..
..>>>>>............<<<<<.....>>>>>..>>>>..>>>>>...
..>>>>>>>...>>>>>...<<<.....>>>..<<<<<<...........
>>>>>>..<<...<<<<<<<...<<<<<<.......>>>>>>.....<<.
..(((>>....>>>>>>>...<<<.<<<<<.......>>>>.>>>>.<<<
....>>>.>>))).......(((((.[.(((.>>>>>>)))].)))))..
........]]]]..}}]]]].......<<.<...<<<<<<...<<.....
..>>...>>>>>>....>.>.>.......<<<<<.<<<<<<..<<<<<<<
<<......>>>>>>>..>>.<<<.........>>>.....>>>>>..>..
.>>>.>>....<<<<<<<....>>>.>>>>....}}..}}}.)))))...
..<<<<<<<<..<<<<.<<<<<<<<...............>>>>>>>><<
<<<...<<<<....<<<<<<<<<<....>>>>>..>>>>>...>>>>..>
>>>>.<<<<...<<<<<...........>>>>>...>>>>.>>>>....>
>>>>>>>.....<<<<<<<<......<<................>>....
..<<<<...<<<...<<<<......>>>>..>>>...>>>>.........
......>>>>>>>>....<<<<<<<<<.............>....<<<<<
<<<.<<<....<<<.<<..<<<<......>>>>..>>>>>...>>>....
>>>>>.>>>..>>>>>>>>

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4v8p Crystal Structure of the Eukaryotic 60S Ribosomal Subunit in Complex with Initiation Factor 6.
• Resolution: 3.52 Å
• Binding residue (original residue number in PDB): F3 K5 V6 L7 K8 K10 Y12 K14 R15 F16 Q17 K19 R23 T28 D29 Y31 R35 L36 I38 K43 Y44 T46 K48 Y49 I113 K140 P141 F142 I145 L146 L150 T153 H175 S176 S178 R179
• Binding residue (residue number reindexed from 1): F2 K4 V5 L6 K7 K9 Y11 K13 R14 F15 Q16 K18 R22 T27 D28 Y30 R34 L35 I37 K42 Y43 T45 K47 Y48 I112 K139 P140 F141 I144 L145 L149 T152 H174 S175 S177 R178

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome
• GO:0008097 5S rRNA binding
• GO:0019843 rRNA binding

Biological Process

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

Cellular Component

• GO:0005634 nucleus
• GO:0005737 cytoplasm
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:4v8p, PDBe:4v8p, PDBj:4v8p
• PDBsum: 4v8p
• PubMed: 22052974
• UniProt: Q231U7|RL5_TETTS Large ribosomal subunit protein uL18 (Gene Name=RPL5)