Structure of PDB 8pv7 Chain CH Binding Site BS01

Receptor Information

>8pv7 Chain CH (length=627) Species: 759272 (Thermochaetoides thermophila DSM 1495)

TGWKDIPPVPTAQEFIDIVLSRTQRRLPTQIRPGFKISRIRAFYTRKVKF
TQETCSEKFGAIISSFPVLSDQHPFHRDLMNILYDADHFKVALGQISTAK
NLIETISRDYVRLLKYAQSLYQCKQLKRAALGRMATLIKRLKDPLIYLDQ
VRQHLARLPDINPTTRTLLVAGFPNVGKSSFVRSVTRADTPVEPYAFTTK
SLFVGHLDYKYLRYQVIDTPGILDHPLEEMNTIEMQSVTALAHLRAAVLY
FMDISEQCGFSLKAQINLFKSIKPLFANKMVFIVLNKMDIKKFEELDPEM
QQEINDLTKSGEVEILRASCATQEGVQEVKNHVCERLLVERVSQKLKAGT
HSNGNIGTRLQEVMARIHVATPMDGTTRETFIPEAVKNLKKYDKNDPNRR
VLARDIEEANGGAGVFNVDLRKDWILENPEWKYDKIPEIFDGKNVYDYID
PDIDAKLQALEEEEERLEKEGFYDEDDEEEEEILQKAEYIREQHALIRNE
AKMRKSLKNRAIIPRKAVKKPLSQLEDHLDQLGVDTEAIGLRARAQTSAK
ERLARSRSRARSVAATNRLQDGVQGTTLRSKAERQAKLAQRKMNRMARQG
EADRHIHASMPKHLFSGKRTIGKTDRR

Ligand information

>8pv7 Chain C1 (length=3078)

agguugaccucggaucagguaggaggacccgcugaacuuaagcauaucaa
uaagcggaggaaaagaaaccaacagggauugcccuaguaacggcgaguga
agcggcaacagcucaaauuugaaagcuggcuucggcccgcguuguaauuu
ggagaggaugcuuugggcgaggcuccuucugaguucccuggaacgggacg
ccacagagggugagagccccguauaguuggaagccaagccuguguaaagc
uccuucgacgagucgaguaguuugggaaugcugcucaaaaugggagguaa
auuucuucuaaagcuaaauaccggccagagaccgauagcgcacaaguaga
gugaucgaaagaugaaaagcacuuugaaaagaggguuaaauagcacguga
aauuguugaaagggaagcgcuugugaccagacuugcgcccggcggaucau
ccgguguucucaccggugcacuccgccgggcucaggccagcaucgguucu
ggcggggggauaaaggcccagggaauguggcuccuccgggaguguuauag
cccuggguguaauacccucgccgggaccgaggaccgcgcucugcaaggau
gcuggcguaauggucaccagcgacccgucuugaaacacggaccaaggagu
caagguuuugcgcgaguguuuggguguaaaacccgcacgcguaaugaaag
ugaacguaggugagagcuucggcgcaucaucgaccgauccugauguauuc
ggauggauuugaguaggagcguuaagccuuggacccgaaagauggugaac
uaugcuuggauagggugaagccagaggaaacucugguggaggcucgcagc
gguucugacgugcaaaucgaucgucaaaucugagcaugggggcgaaagac
uaaucgaaccaucuaguagcugguuaccgccgaaguuucccucaggauag
cagugucgaccuucaguuuuaugagguaaagcgaaugaacuuuaaauaug
uaagaagcccuuguuacuuaacugaacgugggcauucgaauguaucgaca
cuagugggccauuuuugguaagcagaacuggcgaugcgggaugaaccgaa
cgcgggguuaaggugccggaguggacgcucaucagacaccacaaaaggcg
uuaguacaucuugacagcaggacgguggccauggaagucggaauccgcua
aggacuguguaacaacucaccugccgaauguacuagcccugaaaauggau
ggcgcucaagcgucccacccauaccccgcccucaggguagaaacgaugcc
cugaggaguaggcggccguggaggucagugacgaagccuagggcgugagc
ccgggucgaacggccucuagugcagaucuuggugguaguagcaaauacuu
caaugagaacuugaaggaccgaaguggggaaagguuccaugugaacagcg
guuggacauggguuagucgauccuaagccauagggaaguuccguuucaaa
ggggcacucgugccccguguggcgaaagggaagccgguuaauauuccggc
accuggauguggguuuugcgcggcaacgcaacugaacgcggagacgacgg
cgggggccccgggcagaguucucuuuucuucuuaacggucuaucacccug
gaaacaguuugucuggagauaggguuuaauggccggaagagcccgacacu
ucugucggguccggugcgcucucgacgucccuugaaaauccgcgggaggg
aauaauucucacgccaggucguacucauaaccgcagcagguccccaaggu
gaacagccucugguugauagaacaauguagauaagggaagucggcaaaau
agauccguaacuucgggaaaaggauuggcucuaaggguugggcacgugcg
ugcgguuaacaaccaacuuagaacugguacggacagggggaaucugacug
ucuaauuaaaacauagcauugcgauggccagaaagugguguugacgcaau
gugauuucugcccagugcucugaaugucaaagugaagaaauucaaccaag
cgcggguaaacggcgggaguaacuaugacucucuguagccaaauggauua
acgagauucccacugucccuaucuacuaucuagcgaaaccacagccaagg
gaacgggcuuggcaaaaucagcggggaaagaagacccuguugagcuugac
ucuaguuugacauugugaaaagauuuuuuuacuuauucaaugaagcgggg
cuggacuugcguccaacuucuggaguuaagguccuucgcgggccgacccg
gguugaagacauugucagguggggaguuuggcuggggcggcacaucugug
cagguguccuaaggggggcucauggagaacagaaaucuccaguagaacaa
aaggguaaaaguccccuugauuuugauuuucagugugaauacaaaccaug
aaaguguggccuaucgauccuuuagucccucgaaauuugaggcuagaggu
gccagaaaaguuaccacagggauggcuuguggcggccaagcguucauagc
gacgucgcuuugauccuucgaugucggcucuuccuaucauaccgaagcag
aauucgguaagcguuggauuguucacccacuaauagggaacgugagcugg
guuuagaccgucgugagacagguuaguuuuacccuacugaugaacucguc
gcaaugguaauucagcuuaguacgagaggaaccgcugauucagauaauug
guuuuugcgguuguccgaccgggcagugccgcgaagcuaccaucugcugg
auaauggcugaacgccucuaagucagaauccaugccagaacgcgacgaua
cuacccgcacguuguagacguauaagaauaggcuccggccucguauccua
gcaggcgauuccuccgccggccucgaaguggccgucgguaauucgcguau
ugcaauuuagacacgcgcgggaucaaauccuuugcagacgacuuagaugu
gcgaaaggguccuguaagcaguagaguagccuuguuguuacgaucugcug
aggguaagcccuccuucgccuagauuuc

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8pv7 Structural insights into coordinating 5S RNP rotation with ITS2 pre-RNA processing during ribosome formation.
• Resolution: 2.12 Å
• Binding residue (original residue number in PDB): K5 D18 I19 L21 R23 T24 Q25 R26 R27 P29 T30 Q31 I32 R33 P34 G35 F36 K37 R40 R42 Y45 R47 K48 I64 F67 P68 V69 L70 D88 K91 V92 L94 G95 S98 T99 N102 R113 K116 Y117 L121 Y122 K125 K128 R129 A130 G133 R134 R153 R158 D161 R188 A189 Y196 F198 V205 H207 R214 N232 I234 G415 V416 H499 R503 R509 K510 K513 N514 R515 I517 P519 R520 K521 R595 A598 T600 N601 R602 Q619 K621 Q624 R625 N628 R629 A631 R632 Q633 R638 H639 A642 H647 K652 R653 I655 G656 K657 T658 D659 R660 R661
• Binding residue (residue number reindexed from 1): K4 D17 I18 L20 R22 T23 Q24 R25 R26 P28 T29 Q30 I31 R32 P33 G34 F35 K36 R39 R41 Y44 R46 K47 I63 F66 P67 V68 L69 D87 K90 V91 L93 G94 S97 T98 N101 R112 K115 Y116 L120 Y121 K124 K127 R128 A129 G132 R133 R152 R157 D160 R187 A188 Y195 F197 V204 H206 R213 N231 I233 G414 V415 H494 R498 R504 K505 K508 N509 R510 I512 P514 R515 K516 R561 A564 T566 N567 R568 Q585 K587 Q590 R591 N594 R595 A597 R598 Q599 R604 H605 A608 H613 K618 R619 I621 G622 K623 T624 D625 R626 R627

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003924 GTPase activity
• GO:0005525 GTP binding
• GO:0046872 metal ion binding

Biological Process

• GO:0042254 ribosome biogenesis
• GO:0042273 ribosomal large subunit biogenesis

Cellular Component

• GO:0005634 nucleus
• GO:0005730 nucleolus

External links

• PDB: RCSB:8pv7, PDBe:8pv7, PDBj:8pv7
• PDBsum: 8pv7
• PubMed: 37921038
• UniProt: G0S8F1|NOG1_CHATD Nucleolar GTP-binding protein 1 (Gene Name=NOG1)