Structure of PDB 5mlc Chain N Binding Site BS01

Receptor Information

>5mlc Chain N (length=182) Species: 3562 (Spinacia oleracea)

TRFRLDNLGPQPGSRKKGKRKGRGHAAGQGGSCGFGMRGQKSRSGPGIMR
GFEGGQMPLYRRIPKLRGIAGGMRAGLPKYVPINLRDIEVAGFKEGEEVS
LESLKAKGIINPSGRERRLPLKILGEGELSTKLQIKARAFSGSAKEKLEA
AGCSVTVLPGRKKYIKESVRKNLARADEYFAK

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): D83 N84 L85 Q88 G90 S91 R92 K93 G95 K96 R97 K98 G99 R100 A103 Q106 G108 S109 G111 F112 G113 M114 R115 G116 Q117 K118 S119 R120 S121 G122 F129 E130 G131 G132 Q133 M134 Y137 R138 R139 P141 K142 R144 G145 G148 M150 R151 A152 G153 N161 I186 N188 S190 G191 R194 K199 L201 G202 S218 G219 K239 Y241 I242 K243 V246 N249 R252 Y256 F257
• Binding residue (residue number reindexed from 1): D6 N7 L8 Q11 G13 S14 R15 K16 G18 K19 R20 K21 G22 R23 A26 Q29 G31 S32 G34 F35 G36 M37 R38 G39 Q40 K41 S42 R43 S44 G45 F52 E53 G54 G55 Q56 M57 Y60 R61 R62 P64 K65 R67 G68 G71 M73 R74 A75 G76 N84 I109 N111 S113 G114 R117 K122 L124 G125 S141 G142 K162 Y164 I165 K166 V169 N172 R175 Y179 F180

Gene Ontology

Molecular Function

• GO:0003729 mRNA binding
• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005762 mitochondrial large ribosomal subunit
• GO:0005840 ribosome
• GO:0009507 chloroplast
• GO:0015934 large ribosomal subunit
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5mlc, PDBe:5mlc, PDBj:5mlc
• PDBsum: 5mlc
• PubMed: 27986857
• UniProt: P22798|RK15_SPIOL Large ribosomal subunit protein uL15c (Gene Name=RPL15)