Structure of PDB 8pfr Chain JV Binding Site BS01

Receptor Information

>8pfr Chain JV (length=203) Species: 4932 (Saccharomyces cerevisiae)

GAYKYLEELQRKKQSDVLRFLQRVRVWEYRQKNVIHRAARPTRPDKARRL
GYKAKQGFVIYRVRVRRGNRKRPVPKGATYGKPTNQGVNELKYQRSLRAT
AEERVGRRAANLRVLNSYWVNQDSTYKYFEVILVDPQHKAIRRDARYNWI
CDPVHKHREARGLTATGKKSRGINKGHKFNNTKAGRRKTWKRQNTLSLWR
YRK

Ligand information

>8pfr Chain A (length=3038)

uugaccucaaaucagguaggaguacccgcugaacuuaagcauaucaauaa
gcggaggaaaagaaaccaaccgggauugccuuaguaacggcgagugaagc
ggcaaaagcucaaauuugaaaucugguaccuucggugcccgaguuguaau
uuggagagggcaacuuuggggccguuccuugucuauguuccuuggaacag
gacgucauagagggugagaaucccguguggcgaggagugcgguucuuugu
aaagugccuucgaagagucgaguuguuugggaaugcagcucuaagugggu
gguaaauuccaucuaaagcuaaauauuggcgagagaccgauagcgaacaa
guacagugauggaaagaugaaaagaacuuugaaaagagagugaaaaagua
cgugaaauuguugaaagggaagggcauuugaucagacaggccagcaucag
uuuugguggcaggauaaauccauaggaauguagcuugccucgguaaguau
uauagccugugggaauacugccagcugggacugaggacugcgacguaagu
caaggaugcuggcauaaugguuauaugccgcccgucuugaaacacggacc
aaggagucuaacgucuaugcgaguguuuggguguaaaacccauacgcgua
augaaagugaacguagguuggggccucgcaagaggugcacaaucgaccga
uccugaugucuucggauggauuugaguaagagcauagcuguugggacccg
aaagauggugaacuaugccugaauagggugaagccagaggaaacucuggu
ggaggcucguagcgguucugacgugcaaaucgaucgucgaauuuggguau
aggggcgaaagacuaaucgaaccaucuaguagcugguuccugccgaaguu
ucccucaggauagcagaagcucguaucaguuuuaugagguaaagcgaaug
auuagagguuccggggucuugaccuauucucaaacuuuaaauauguaaga
aguccuuguuacuuaauugaacguggacauuugaaugaagagcuuuuagu
gggccauuuuugguaagcagaacuggcgaugcgggaugaaccgaacguag
aguuaaggugccggaauacacgcucaucagacaccacaaaagguguuagu
ucaucuagacaggaaugaacuagcccugaaaauggauggcgcucaagcgu
guuaccuauacucuaccgucaggguugauaugaugcccugacgaguaggc
aggcguggaggucagugacgaagccuagaccguaaggucgggucgaacgg
ccucuagugcagaucuuggugguaguagcaaauauucaaaugagaacuuu
gaagacugaaguggggaaagguuccacgucaacagcaguuggacgugggu
uagucgauccuaagagauggggaagcuccguuucaaaggccugauuuuau
gcaggccaccaucgaaagggaauccgguuaagauuccggaaccuggauau
ggauucuucacgguaacguaacugaauguggagacgucggcgcgagcccu
gggaggaguuaucuuuucuucuuaacagcuuaucaccccggaauugguuu
auccggagauggggucuuauggcuggaagaggccagcaccuuugcuggcu
ccggugcgcuugugacggcccgugaaaauccacaggaaggaauaguuuuc
augccaggucguacugauaaccgcagcaggucuccaaggugaacagccuc
uaguugauagaauaauguagauaagggaagucggcaaaauagauccguaa
cuucgggauaaggauuggcucuaagggucggacgaucaacuuagaacugg
uacggacaaggggaaucugacugucuaauuaaaacauagcauugcgaugg
ucagaaagugauguugacgcaaugugauuucugcccagugcucugaaugu
caaagugaagaaauucaaccaagcgcggguaaacggcggaagguagccaa
augccucgucaucuaauuagugacgcgcaugaauggauuaacgagauucc
cacugucccuaucuacuaucuagcgaaaccacagccaagggaacgggcuu
ggcagaaucagcggggaaagaagacccuguugagcuugacucuaguuuga
cauugugaaguacuuauucaaugaagcggagcuggaccacguucuagcau
ucaaggucccauucggggcugauccggguugaagacauugucaggugggg
aguuuggcuggggcggcacaucuguuaaacgauaacgcagauguccuaag
gggggcucauggagaacagaaaucuccaguagaacaaaaggguaaaagcc
cccuugauuuugauuuucagugugaauacaaaccaugaaaguguggccua
ucgauccuuuagucccucggaauuugaggcuagaggugccagaaaaguua
ccacagggauaacuggcuuguggcagucaagcguucauagcgacauugcu
uuuugauucuucgaugucggcucuuccuaucauaccgaagcagaauucgg
uaagcguuggauuguucacccacuaauagggaacgugagcuggguuuaga
ccgucgugagacagguuaguuuuacccuacugaugaauguuaccgcaaua
guaauugaacuuaguacgagaggaacaguucauucggauaauugguuuuu
gcggcugucugaucaggcauugccgcgaagcuaccauccgcuggauuaug
gcugaacgccucuaagucagaauccaugcuagaacgcggugauuucuuug
cuccacacaauauagauggauacgaauaaggcguccuuguggcgucgcug
aaccauagcaggcuagcaacggugcacuuggcggaaaggccuugggugcu
ugcuggcgaauugcaaugucauuuugcguggggauaaaucauuuguauac
gacuuagauguacaacgggguauuguaagcaguagaguagccuuguuguu
acgaucugcugagauuaagccuuuguugucugauuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8pfr Real-space refinement in PHENIX for cryo-EM and crystallography.
• Resolution: 2.15 Å
• Binding residue (original residue number in PDB): G2 Y4 K5 E8 R12 K14 Q15 R31 N34 V35 R41 R44 K47 R49 R50 A55 Q57 R67 R68 G69 N70 R71 K72 R73 P74 K77 G78 Y81 G82 K83 T85 N86 Q87 N90 E91 K93 Y94 Q95 R96 S97 L98 R105 R108 N112 S125 Y127 K128 Q138 H139 K140 R144 R147 W150 P154 V155 H156 K157 H158 A161 R162 A166 K169 K170 S171 R172 I174 K176 G177 H178 K179 F180 N181 N182 R187 R188 K189 W191 K192 R193 Q194 W200 R201 Y202 R203 K204
• Binding residue (residue number reindexed from 1): G1 Y3 K4 E7 R11 K13 Q14 R30 N33 V34 R40 R43 K46 R48 R49 A54 Q56 R66 R67 G68 N69 R70 K71 R72 P73 K76 G77 Y80 G81 K82 T84 N85 Q86 N89 E90 K92 Y93 Q94 R95 S96 L97 R104 R107 N111 S124 Y126 K127 Q137 H138 K139 R143 R146 W149 P153 V154 H155 K156 H157 A160 R161 A165 K168 K169 S170 R171 I173 K175 G176 H177 K178 F179 N180 N181 R186 R187 K188 W190 K191 R192 Q193 W199 R200 Y201 R202 K203

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0002181 cytoplasmic translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8pfr, PDBe:8pfr, PDBj:8pfr
• PDBsum: 8pfr
• UniProt: P05748|RL15A_YEAST Large ribosomal subunit protein eL15A (Gene Name=RPL15A)