Structure of PDB 4v61 Chain B3 Binding Site BS01

Receptor Information

>4v61 Chain B3 (length=65) Species: 3562 (Spinacia oleracea)

MAKGKDVRVKVILECTGCVRKSVNKGSRGVSRYITQKNRHNTPSRLELRK
FCPYCYKHTIHGEIK

Ligand information

>4v61 Chain BA (length=2732)

uucaaacgaggaaaggcuuacgguggauaccuaggcacccagagacgagg
aagggcguauuaaucgacgaaaugcuucggggaguugaaaauaagcagag
auccggagauucccgaauaggucaaccuuucgaacuucugcugaauccau
gggcaggcaagagacaaccuggcgaacugaaacaucuuaguagccagagg
aaaagaaagcaaaagcgauucccguaguagcggcgagcgaaaugggagca
gccuagagcaauacaagcgucgugcugcuaggcgaaucaguggagugcgg
aacccuagauggugaaaguccaguagccgaaagcaucacuagcuuaugcu
cgaguagcauggggcacguggaaucccgugugaaucagcaaggaccaccu
ugcaaggcuaaauacuccugggugaccgauagcgaaguaguaccgugagg
gaagggugaaaagaacccccaucggggagugaaauagaacaugaaaccgu
aagcucucaagcagugggagggggaccagacccugaccgcgugccuguug
aagaaugagccggcgacucauaggcaguggcuugguuaagggaacccacc
ggagccguagcgaaagcgagucuucauagggcaauugucacugcuuaugg
acccgaaccugggugaucuauccaugaccaggaugaagcuugggugaaac
uaaguggagguccgaaccgacugauguugaagaaucagcggaugaguugu
gguuaggggugaaaugccacucgaacccagagcuagcugguucuccccga
aaugcguugaggcgcagcaguugacuggacaucuagggguaaagcacugu
uucggugcgggccgcgguaccaaaucgaggcaaacucugaauacuagaua
gucaaggucggccagugagacgaugggggauaagcuucaucgucgagagg
gaaacagcccggaucaccagcuaaggccccuaaaugaccgcucagugaua
aaggagguaggggugcagagacagccaggagguuugccuagaagcagcca
cccuugaaagagugcguaauagcucacugaucgagcgcucuugcgccgaa
gaugaacggggcuaagcggucugccgaagcugugggauguaaaaaaacau
cgguaggggagcguuccguguuagggagaaacgcgugcgugagccgcguu
ggacgaagcggaagcgagaaugucggcuugaguaacgcaaacauugguga
gaauccaaugccccgaaaaccuaaggguuccuccgcaagguucguccacg
gagggugagucagggccuaagaucaggccgaaaggcguagucgauggaca
acaggugaauauuccuguacuaccccuuguuggucccgagggacggagga
ggcuagguuagccgaaagaugguuaucgguucaaggacgcaagguggggu
agagaaaaugccucgagccaauguucgaguaccaggcgcuacggcgcuga
aguaaccgaugccauacucccaggaaaagcucgaaagaccuucaacaaaa
ggguaccuguacccgaaaccgacacagguagguagguagagaauaccuag
gggcgcgagacaacucucucuaaggaacucggcaaaauagccccguaacu
ucgggagaaggggugcccccucacaaagggggucgaagugaccaggcccg
ggcgacuguuuaccaaaaacacaggucuccgcaaagucguaagaccaugu
augggggcugacgccugcccagugccggaaggucaaggaaguuggugacc
ugaugacaggggagccggcgaccgaagccccggugaacggcggccguaac
uauaacgguccuaagguagcgaaauuccuugucggguaaguuccgacccg
cacgaaaggcguaacgaucugggcacugucucggagagaggcucggugaa
auagacaugucugugaagaugcggacuaccugcaccuggacagaaagacc
cuaugaagcuuuacuguucccugggauuggcuuugggcuuuuccugcgca
gcuuagguggaaggcgaagaaggcccccuuccgggggggcccgagccauc
agugagauaccacucuggaagagcuagaauucuaaccuugugucaggacc
uacgggccaagggacauucucagguagacaguuucuauggggcguaggcc
ucccaaaagguaacggaggcgugcaaagguuuccucgggccggacggaga
uuggcccucgagugcaaaggcagaagggagcuugacugcaagacccaccc
gucgagcagggacgaaagucggccuuagugauccgacggugccgagugga
agggccgucgcucaacggauaaaaguuacucuagggauaacaggcugauc
uuccccaagaguucacaucgacgggaagguuuggcaccucgaugucggcu
cuucgccaccuggggcuguaguauguuccaaggguugggcuguucgccca
uuaaagcgguacgugagcuggguucagaacgucgugagacaguucggucc
auauccggugugggcguuagagcauugagaggaccuuucccuaguacgag
aggaccgggaaggacgcaccucugguguaccaguuaucgugcccacggua
aacgcuggguagccaagugcggagcggauaacugcugaaagcaucuaagu
aguaagcccaccccaagaugagugcucuccua

..............<<<<<<<<<<.....<<..<<<<<<<<<<<......
..<<<<<<.....((.>>>.....<<<<<<.<.<<.))......>>....
.>>>>>>>...>>>....<<<....>>>........<<<<<<........
.>>>>>>..........<<<<<<.....<<....>>......>>>>>.>.
........<<....>>..<<<<<<.....<<.....>>....>>>>>>..
<<<..................<<<.<<<..<<<....<.<<.....>>.>
.((......<<<.....))>>>...>>>....>>>.>>>...........
......<<<<<<<<.........>>>>>>>>......<<<<<..((((>>
>>>..>>>......>>.>>>>>>>.>>...............<<....>>
....>>.........<<<<....>>>>..................>>>>>
>>>>>........<<<<..<.<<<......>>>>..>>>>...<.<....
....>.>.<<<<<<....<<<<<<<<<<<<<..<<<...<<.......>>
...>>>...<<....>>..<<<<.....>>>>....>>>>>>>>>>>>>.
.<<.<...<<<<<<.......<<<<<<<..<<<....<<<<<<......>
>>>>>.....>>>...<<<.<<<<<........>>>>>>>>....>>>>>
>>.....<<<.....>>>......>>>>>>......>.>>..<<<<<<..
..<<<<<....>>>>><<.<<<<<<..<<<<<<<<.<.....<<...<<<
<<<<<<.................>>>>>>>>>..>>.......>>>>>>.
>>>...>>>>>>..>>..<<<<<<<<<<......>>>>>>>>>>....<<
<......>>>...<<<<.<<<...<<<(((.....<<<<<<.........
..<<...<<<<.<<<<.....<.<.<<<.<<....<<.........>>..
..>>.........<<......>>...>>>.>.>.>>>.>>>>>..>>...
.......))).....>>>>>>.>>>...>>>>>>><<<<<......>>>>
>....>>>>>>..<<<<<...........<<<<<<.<<....>>>>>>>>
........>>>>>........>>>>>><......<<......<<<<<...
....>>>>>.<<<<....<<<<<.<<...<<<<<<...<<.....>>.>>
>>>>....((<<<<.<<...<<<...<<<....>>>...>>>...>>...
.<<<<........>>>>.))<<<<<.<<<<<<....<<<<.....<.<<.
.<...<<<<<<<<<<.....[[[..>>>>><...<<<<.....<<.<<<<
<.......>>>>>...>>....>>>>....><..<<<<<....>>>>>..
.>>>>>>....>....>>>..........>>>>.....>....>>>>>..
>>>>>>>>>..>>.....<<......>>>>>>>.<<<<.....>>>>..>
>>>..<<<<....<<<<<<<..<<...............<<<<<......
.........>>>>><<<<<<.......>>>>>>............<<<<<
<<<<..<<<.........>>>..<<<<<<<.....<<<....>>>.....
..>>>>>>>.<<<<<.<<<..<<<<<<<..<<<...<<..<<<<<<...<
<<....>>>....>>>>>>..>>...>>>>>>>>..>>>>><<<<<....
.....>>>>>........<...........<<<<<.......>>>>>...
..>....>>>>>..>>.>>>>>>>.....>>..>>>>>>>.>>>>>>...
..>.....<<<<..........>>>>..<<<<<<<<.<<...<......<
<<<.<<<<<<..<<<<...<<<<<<<..<<.<<<.<<<<<<<<<......
.....<<......<.......<<.<<<<.......>>>>.>>....>...
............>>..>>>>>>>>>.>>>.>.>..<<.<..<<<......
....>>>..>>>.....>>>>>>>....>>>>..<<<<.....>>>><<<
<<<...........>>>>>>..<<...<<<<<<<...<<<<<<.......
>>>>>>.....<<...(((>>....>>>>>>>...<<<<..<<<......
>>>..>>>>.<<<....>>>.>>))).......<<<<<<<.<<..)))).
.>>>>>>>>>.............>>>>..>>>>>>........<<<<..<
<<<<<...<<.......>>...>>>>>>...>>>>.........<.<<<.
<.<<<...<<<<<<<<........>>>>>..>>>..<<<.......>>>.
......>>>...>...>>>..>....<<<<<<<....>>>.>>>>....>
....>>>>>>>>>>....<<<<<<<...<.<<...<<<<<<.........
......>>>>>>..<<<<<...<<<<...<<<<<<<<<<<]]].>>>>>>
...>>>>>...>>>>.>>>>>....<<...<<<<...............>
>>>...>>..>>.>.......>>>>>>>....

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4v61 Cryo-EM study of the spinach chloroplast ribosome reveals the structural and functional roles of plastid-specific ribosomal proteins
• Resolution: 9.4 Å
• Binding residue (original residue number in PDB): K3 K10 K25 G26 S27 G29 V30 S31 R32 Y33 I34 T35 Q36 R39 S44 R45 L46 R49 K50 F51 K57 H58
• Binding residue (residue number reindexed from 1): K3 K10 K25 G26 S27 G29 V30 S31 R32 Y33 I34 T35 Q36 R39 S44 R45 L46 R49 K50 F51 K57 H58

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005840 ribosome
• GO:0009507 chloroplast
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:4v61, PDBe:4v61, PDBj:4v61
• PDBsum: 4v61
• PubMed: 18042701
• UniProt: P28805|RK33_SPIOL Large ribosomal subunit protein bL33c (Gene Name=rpl33)