Structure of PDB 5x8t Chain T Binding Site BS01

Receptor Information

>5x8t Chain T (length=144) Species: 3562 (Spinacia oleracea)

PGKCDEITTRGYSISMSVDKARRVIDQIRGRSYAETLMILELMPYRACYP
IFKLIYSAAANASHNKQFNKANLIISKAEVNKGITLKKVKPRARGRSYMI
KRPTCHITIVLRDITHFDSYDKFLESLTPKKLIALLGLMSTGRR

Ligand information

>5x8t Chain A (length=2809)

ucaaacgaggaaaggcuuacgguggauaccuaggcacccagagacgagga
agggcguauuaaucgacgaaaugcuucggggaguugaaaauaagcagaga
uccggagauucccgaauaggucaaccuuucgaacuucugcugaauccaug
ggcaggcaagagacaaccuggcgaacugaaacaucuuaguagccagagga
aaagaaagcaaaagcgauucccguaguagcggcgagcgaaaugggagcag
ccuaaaccgugaaaacgggguugugggagagcaauacaagcgucgugcug
cuaggcgaaucaguggagugcggaacccuagauggugaaaguccaguagc
cgaaagcaucacuagcuuaugcucugacccgaguagcauggggcacgugg
aaucccgugugaaucagcaaggaccaccuugcaaggcuaaauacuccugg
gugaccgauagcgaaguaguaccgugagggaagggugaaaagaaccccca
ucggggagugaaauagaacaugaaaccguaagcucucaagcagugggagg
gggaccagacccugaccgcgugccuguugaagaaugagccggcgacucau
aggcaguggcuugguuaagggaacccaccggagccguagcgaaagcgagu
cuucauagggcaauugucacugcuuauggacccgaaccugggugaucuau
ccaugaccaggaugaagcuugggugaaacuaaguggagguccgaaccgac
ugauguugaagaaucagcggaugaguugugguuaggggugaaaugccacu
cgaacccagagcuagcugguucuccccgaaaugcguugaggcgcagcagu
ugacuggacaucuagggguaaagcacuguuucggugcgggccgcgagagc
gguaccaaaucgaggcaaacucugaauacuagauaugaccuccaaauaac
aggggucaaggucggccagugagacgaugggggauaagcuucaucgucga
gagggaaacagcccggaucaccagcuaaggccccuaaaugaccgcucagu
gauaaaggagguaggggugcagagacagccaggagguuugccuagaagca
gccacccuugaaagagugcguaauagcucacugaucgagcgcucuugcgc
cgaagaugaacggggcuaagcggucugccgaagcugugggauguaaaaaa
acaucgguaggggagcguuccguguuagggagaaacgcgugcgugagccg
cguuggacgaagcggaagcgagaaugucggcuugaguaacgcaaacauug
gugagaauccaaugccccgaaaaccuaaggguuccuccgcaagguucguc
cacggagggugagucagggccuaagaucaggccgaaaggcguagucgaug
gacaacaggugaauauuccuguacuaccccuuguuggucccgagggacgg
aggaggcuagguuagccgaaagaugguuaucgguucaaggacgcaaggug
acccuguuuuucaggguaagaagggguagagaaaaugccucgagccaaug
uucgaguaccaggcgcuacggcgcugaaguaaccgaugccauacucccag
gaaaagcucgaacgaccuucaacaaaaggguaccuguacccgaaaccgac
acagguagguagguagagaauaccuaggggcgcgagacaacucucucuaa
ggaacucggcaaaauagccccguaacuucgggagaaggggugcccccuca
caaagggggucgaagugaccaggcccgggcgacuguuuaccaaaaacaca
ggucuccgcaaagucguaagaccauguaugggggcugacgccugcccagu
gccggaaggucaaggaaguuggugaccugaugacaggggagccggcgacc
gaagccccggugaacggcggccguaacuauaacgguccuaagguagcgaa
auuccuugucggguaaguuccgacccgcacgaaaggcguaacgaucuggg
cacugucucggagagaggcucggugaaauagacaugucugugaagaugcg
gacuaccugcaccuggacagaaagacccuaugaagcuuuacuguucccug
ggauuggcuuugggcuuuuccugcgcagcuuagguggaaggcgaagaagg
cccccuuccgggggggcccgagccaucagugagauaccacucuggaagag
cuagaauucuaaccuugugucaggaccuacgggccaagggacauucucag
guagacaguuucuauggggcguaggccucccaaaagguaacggaggcgug
caaagguuuccucgggccggacggagauuggcccucgagugcaaaggcag
aagggagcuugacugcaagacccacccgucgagcagggacgaaagucggc
cuuagugauccgacggugccgaguggaagggccgucgcucaacggauaaa
aguuacucuagggauaacaggcugaucuuccccaagaguucacaucgacg
ggaagguuuggcaccucgaugucggcucuucgccaccuggggcuguagua
uguuccaaggguugggcuguucgcccauuaaagcgguacgugagcugggu
ucagaacgucgugagacaguucgguccauauccggugugggcguuagagc
auugagaggaccuuucccuaguacgagaggaccgggaaggacgcaccucu
gguguaccaguuaucgugcccacgguaaacgcuggguagccaagugcgga
gcggauaacugcugaaagcaucuaaguaguaagcccaccccaagaugagu
gcucuccua

.............<<<<<<<<<<.....<<..<<<<<<<<<<<.<.....
.<<<<<<.....((.>>>.....<<<<<<<..<<.))......>>.....
>>>>>>>...>>>....<<<....>>>......<<<<<<<<.........
>>>>>..>>>.>....<<<<<<.....<<....>>......>>>>>.>..
.......<<....>>..<<<<<<.....<<.....>>....>>>>>>..<
<<....<<<<....>>>>......<<<<<<<<<....<<<<...<<<.<<
<<.<<<...<<.<<.....>>.>>((......<<<.....))>>>...>>
>...>>>>.>>>..>>>>.>>>>>>..>>>.....<<<<<<<<.......
..>>>>>>>>......<<<<<..<<<<>>>>>..>>>......>>.>>>>
>>>.>>...............<<....>>....>>.........<<<<..
..>>>>..................>>>>>>>>>>........<<<<..<<
<<.......>>>>..>>>>...<.<........>.>.<<<<<<....<<<
<<<<<<<<<...<<<...<<.......>>...>>>...<<....>>..<<
<<.....>>>>.....>>>>>>>>>>>>..<<.<...<<<<<<.....<.
<<<<<<<..<<<....<<<<<<......>>>>>>.....>>>...<<<.<
<<<<........>>>>>>>>....>>>>>>>.>...<<<.....>>>...
...>>>>>>......>.>>..<<<<<<....<<<<<....>>>>><<.<<
<<<<<....<<<<<<.....<<<...<<<<<<<<...<<<<<........
>>>.>>...>>>>>>>>..>>.>.....>>>>>>..<<<<<<........
.>>>>>>..>>>>>>>..>>..<<<<<<<<<<......>>>>>>>>>>..
..<<<......>>>...<<<<.<<<...<<<(((.....<<<<<<.....
......<<..<<<<<<<<<<.........<<<.<<....<<.........
>>....>>.........<<......>>...>>>.....>>>>>>>>>>.>
>..........))).....>>>>>>.>>>...>>>>>>><<<<<......
>>>>>....>>>>>><.<<<<<<...........<<<<<.<<....>>>>
>>.>.......>>>>>>..>.....>>>>>><......<<.....<<<<<
<.......>>>>>><<<<....<<<<<.<<...<<<<<<...<<.....>
>.>>>>>>....((<<<<.<<...<<<...<<<....>>>...>>>...>
>...<<<<<........>>>>>))<<<<<.<<<<.<<<<.<<<<....<<
<<..<<<..<<<<<<<<<<.....(((..>>>>>....<<<<<...<<<.
<<<<<<.....>>>>>>.....<<<<<<.......>>>>>>..>>>..>>
>>>.....<..<<<<<....>>>>>...>>>>>>...>>>...>>>>...
......>>>>...>>>>....>>>>..>>>>>>>>>..>>.....<<...
...>>>>>>>.<<<<.....>>>>..>>>>..<<<<....<<<<<<<<.<
<.........<.....<<<<<....<....>.....>>>>><<<<<<<..
...>>>>>>>............<<<<<<<<<..<<<.........>>>..
<<<<<<<.....<<<....>>>.......>>>>>>>.<<<<<.<<<..<<
<<<<<..<<<...<<..<<<<<<..<<<<....>>>>...>>>>>>..>>
...>>>>>>>>..>>>>><<<<<<.......>>>>>>........<....
.......<<<<<<.....>>>>>>.....>....>>>>>..>>.>>>>>>
>..>..>>.>>>>>>>>.>>>>>>.....>.....<<<<<........>>
>>>..<<<<<<<<.<<<..<......<<<<.<<<<<<..<<<<<..<<<<
<<<..<<.<<<.<<<<<<<<..............<<<..<<<......<<
<<<<.......>.>>>>>...>>>............>>>.....>>>>>>
>>.>>>.>>...<<<<<.<<<..........>>>>>>>>.....>>>>>>
>...>>>>>..<<<<.....>>>><<<<<<...........>>>>>>..<
<...<<<<<<<..<<<<<<<.......>>>>>>>....<<...(((>>..
..>>>>>>>...<<<<..<<<......>>>..>>>>.<<<....>>>.>>
))).......<<<<<<<.<<..>>>>..>>>>>>>>>.............
>>>>..>>>>>>.......<<<<.<.<<<<<<...<<.......>>...>
>>>>>...>>>>.>.......<<<<<...<<<<..<<<<<<<<.......
.>>>>>..>>>.<<<<<.....>>>>>.....>>>>.......>>>>>..
...<<<<<<<....>>>.>>>>....>...>>>>>>>>>>>....<<<<<
<<...<.<<..<<<<<<<...............>>>>>>>.<<<<<...<
<<<...<<<<<<<<<<<))).>>>>>>...>>>>>...>>>>.>>>>>..
<.<<...<<<<<<...........>>>>>>...>>>.>>.>.......>>
>>>>>....

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5x8t Unique localization of the plastid-specific ribosomal proteins in the chloroplast ribosome small subunit provides mechanistic insights into the chloroplastic translation
• Resolution: 3.3 Å
• Binding residue (original residue number in PDB): Y37 S38 S40 S42 K45 R47 R48 R54 P69 R71 K78 Y81 S82 N86 H89 N90 E104 N106 K107 I109 L111 K113 P116 R117 A118 R119 G120 R121 S122 Y123 I125 K126 R127 P128
• Binding residue (residue number reindexed from 1): Y12 S13 S15 S17 K20 R22 R23 R29 P44 R46 K53 Y56 S57 N61 H64 N65 E79 N81 K82 I84 L86 K88 P91 R92 A93 R94 G95 R96 S97 Y98 I100 K101 R102 P103

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:0009507 chloroplast
• GO:0015934 large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5x8t, PDBe:5x8t, PDBj:5x8t
• PDBsum: 5x8t
• PubMed: 28582576
• UniProt: P09594|RK22_SPIOL Large ribosomal subunit protein uL22c (Gene Name=rpl22)