Structure of PDB 5mlc Chain W Binding Site BS01

Receptor Information

>5mlc Chain W (length=129) Species: 3562 (Spinacia oleracea)

RIKRWERKDCKPNSLPKLHKRHVKVGDTVKVISGGEKGKIGEISKIHKHN
STVIIKDLNFKTKHVKSKEEGEQGQIIKIEAAIHSSNVMLILKEQEVADR
VGHKILEDVRKVRYLIKTGEIVDTPDRWK

Ligand information

>5mlc Chain A (length=2750)

uucaaacgaggaaaggcuuacgguggauaccuaggcacccagagacgagg
aagggcguauuaaucgacgaaaugcuucggggaguugaaaauaagcagag
auccggagauucccgaauaggucaaccuuucgaacuucugcugaauccau
gggcaggcaagagacaaccuggcgaacugaaacaucuuaguagccagagg
aaaagaaagcaaaagcgauucccguaguagcggcgagcgaaaugggagca
gccuaaaccgugaaaacgggguugugggagaggcugcuaggcgaaucagu
ggagugcggaacccuagauggugaaaguccaguagccgaaagcaucacuc
ugacccgaguagcauggggcacguggaaucccgugugaaucagcaaggac
caccuugcaaggcuaaauacuccugggugaccgauagcgaaguaguaccg
ugagggaagggugaaaagaacccccaucggggagugaaauagaacaugaa
accguaagcucucaagcagugggagggggaccagacccugaccgcgugcc
uguugaagaaugagccggcgacucauaggcaguggcuugguuaagggaac
ccaccggagccguagcgaaagcgagucuucauagggcaauugucacugcu
uauggacccgaaccugggugaucuauccaugaccaggaugaagcuugggu
gaaacuaaguggagguccgaaccgacugauguugaagaaucagcggauga
guugugguuaggggugaaaugccacucgaacccagagcuagcugguucuc
cccgaaaugcguugaggcgcagcaguugacuggacaucuagggguaaagc
acuguuucggugcgggccgcgagagcgguaccaaaucgaggcaaacucug
aauacuagauaugaccuaggggucaaggucggccagugagacgauggggg
auaagcuucaucgucgagagggaaacagcccggaucaccagcuaaggccc
cuaaaugaccgcucagugauaaaggagguaggggugcagagacagccagg
agguuugccuagaagcagccacccuugaaagagugcguaauagcucacug
aucgagcgcucuugcgccgaagaugaacggggcuaagcggucugccgaag
cugugggauguaaaaaaacaucgguaggggagcguuccguguuagggaga
aacgcgugcgugagccgcguuggacgaagcggaagcgagaaugucggcuu
gaguaacgcaaacauuggugagaauccaaugccccgaaaaccuaaggguu
ccuccgcaagguucguccacggagggugagucagggccuaagaucaggcc
gaaaggcguagucgauggacaacaggugaauauuccuguacuaccccuug
uuggucccgagggacggaggaggcuagguuagccgaaagaugguuaucgg
uucaaggacgcaaggugaagggguagagaaaaugccucgagccaauguuc
gaguaccaggcgcuacggcgcugaaguaaccgaugccauacucccaggaa
aagcucgaacgaccuucaacaaaaggguaccuguacccgaaaccgacaca
gguagguagguagagaauaccuaggggcgcgagacaacucucucuaagga
acucggcaaaauagccccguaacuucgggagaaggggugcccccucacaa
agggggucgaagugaccaggcccgggcgacuguuuaccaaaaacacaggu
cuccgcaaagucguaagaccauguaugggggcugacgccugcccagugcc
ggaaggucaaggaaguuggugaccugaugacaggggagccggcgaccgaa
gccccggugaacggcggccguacgguccuaagguagcgaaauuccuuguc
ggguaaguuccgacccgcacgaaaggcguaacgaucugggcacugucucg
gagagaggcucggugaaauagacaugucugugaagaugcggacuaccugc
accuggacagaaagacccuaugaagcuuuacuguucccugggauuggcuu
ugggcuuuuccugcgcagcuuagguggaaggcgaagaaggcccccuuccg
ggggggcccgagccaucagugagauaccacucuggaagagcuagaauucu
aaccuugugucaggaccuacgggccaagggacauucucagguagacaguu
ucuauggggcguaggccucccaaaagguaacggaggcgugcaaagguuuc
cucgggccggacggagauuggcccucgagugcaaaggcagaagggagcuu
gacugcaagacccacccgucgagcagggacgaaagucggccuuagugauc
cgacggugccgaguggaagggccgucgcucaacggauaaaaguuacucua
gggauaacaggcugaucuuccccaagaguucacaucgacgggaagguuug
gcaccucgaugucggcucuucgccaccuggggcuguaguauguuccaagg
guugggcuguucgcccauuaaagcgguacgugagcuggguucagaacguc
gugagacaguucgguccauauccggugugggcguuagagcauugagagga
ccuuucccuaguacgagaggaccgggaaggacgcaccucugguguaccag
uuaucgugcccacgguaaacgcuggguagccaagugcggagcggauaacu
gcugaaagcaucuaaguaguaagcccaccccaagaugagugcucuccuau

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5mlc Cryo-EM structure of the spinach chloroplast ribosome reveals the location of plastid-specific ribosomal proteins and extensions.
• Resolution: 3.6 Å
• Binding residue (original residue number in PDB): R47 I48 K49 R50 W51 R53 K54 S60 L61 K66 H68 V71 G80 G81 I92 K94 K107 T108 K109 H110 V111 K112 Q119 G120 Q121 H130 S132 N133 M135 R146 H149 K157 R173
• Binding residue (residue number reindexed from 1): R1 I2 K3 R4 W5 R7 K8 S14 L15 K20 H22 V25 G34 G35 I46 K48 K61 T62 K63 H64 V65 K66 Q73 G74 Q75 H84 S86 N87 M89 R100 H103 K111 R127

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005739 mitochondrion
• GO:0005840 ribosome
• GO:0009507 chloroplast
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5mlc, PDBe:5mlc, PDBj:5mlc
• PDBsum: 5mlc
• PubMed: 27986857
• UniProt: P27683|RK24_SPIOL Large ribosomal subunit protein uL24c (Gene Name=RPL24)