9pkb: Difference between revisions

Latest revision as of 07:05, 15 July 2026

In situ HHT and CHX treated human hibernating state 80S ribosome

Structural highlights

9pkb is a 10 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Electron Microscopy, Resolution 3.05Å
Ligands:	1MA, 3HE, 4AC, 5MC, 6MZ, A2M, B8N, G7M, HMT, MA6, MG, OMC, OMG, OMU, PSU, SPD, SPM, UR3, UY1, ZN
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

SERB1_HUMAN Ribosome-binding protein that promotes ribosome hibernation, a process during which ribosomes are stabilized in an inactive state and preserved from proteasomal degradation (PubMed:36691768). Acts via its association with EEF2/eEF2 factor, sequestering EEF2/eEF2 at the A-site of the ribosome and promoting ribosome stabilization and storage in an inactive state (By similarity). May also play a role in the regulation of mRNA stability: binds to the 3'-most 134 nt of the SERPINE1/PAI1 mRNA, a region which confers cyclic nucleotide regulation of message decay (PubMed:11001948). Seems to play a role in PML-nuclear bodies formation (PubMed:28695742).[UniProtKB:Q9CY58]^[1] ^[2] ^[3]

References

↑ Heaton JH, Dlakic WM, Dlakic M, Gelehrter TD. Identification and cDNA cloning of a novel RNA-binding protein that interacts with the cyclic nucleotide-responsive sequence in the Type-1 plasminogen activator inhibitor mRNA. J Biol Chem. 2001 Feb 2;276(5):3341-7. PMID:11001948 doi:10.1074/jbc.M006538200
↑ Saito Â, Souza EE, Costa FC, Meirelles GV, Gonçalves KA, Santos MT, Bressan GC, McComb ME, Costello CE, Whelan SA, Kobarg J. Human Regulatory Protein Ki-1/57 Is a Target of SUMOylation and Affects PML Nuclear Body Formation. J Proteome Res. 2017 Sep 1;16(9):3147-3157. PMID:28695742 doi:10.1021/acs.jproteome.7b00001
↑ Shetty S, Hofstetter J, Battaglioni S, Ritz D, Hall MN. TORC1 phosphorylates and inhibits the ribosome preservation factor Stm1 to activate dormant ribosomes. EMBO J. 2023 Mar 1;42(5):e112344. PMID:36691768 doi:10.15252/embj.2022112344

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OCA

[1] Heaton JH, Dlakic WM, Dlakic M, Gelehrter TD. Identification and cDNA cloning of a novel RNA-binding protein that interacts with the cyclic nucleotide-responsive sequence in the Type-1 plasminogen activator inhibitor mRNA. J Biol Chem. 2001 Feb 2;276(5):3341-7. PMID:11001948 doi:10.1074/jbc.M006538200

[2] Saito Â, Souza EE, Costa FC, Meirelles GV, Gonçalves KA, Santos MT, Bressan GC, McComb ME, Costello CE, Whelan SA, Kobarg J. Human Regulatory Protein Ki-1/57 Is a Target of SUMOylation and Affects PML Nuclear Body Formation. J Proteome Res. 2017 Sep 1;16(9):3147-3157. PMID:28695742 doi:10.1021/acs.jproteome.7b00001

[3] Shetty S, Hofstetter J, Battaglioni S, Ritz D, Hall MN. TORC1 phosphorylates and inhibits the ribosome preservation factor Stm1 to activate dormant ribosomes. EMBO J. 2023 Mar 1;42(5):e112344. PMID:36691768 doi:10.15252/embj.2022112344

[1]

[2]

[3]

@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 9pkb is ON HOLD
+==In situ HHT and CHX treated human hibernating state 80S ribosome==
+<StructureSection load='9pkb' size='340' side='right'caption='[[9pkb]], [[Resolution|resolution]] 3.05&Aring;' scene=''>
-Authors:
+== Structural highlights ==
+<table><tr><td colspan='2'>[[9pkb]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=9PKB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9PKB FirstGlance]. <br>
-Description:
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 3.05&#8491;</td></tr>
-[[Category: Unreleased Structures]]
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1MA:6-HYDRO-1-METHYLADENOSINE-5-MONOPHOSPHATE'>1MA</scene>, <scene name='pdbligand=3HE:4-{(2R)-2-[(1S,3S,5S)-3,5-DIMETHYL-2-OXOCYCLOHEXYL]-2-HYDROXYETHYL}PIPERIDINE-2,6-DIONE'>3HE</scene>, <scene name='pdbligand=4AC:N(4)-ACETYLCYTIDINE-5-MONOPHOSPHATE'>4AC</scene>, <scene name='pdbligand=5MC:5-METHYLCYTIDINE-5-MONOPHOSPHATE'>5MC</scene>, <scene name='pdbligand=6MZ:N6-METHYLADENOSINE-5-MONOPHOSPHATE'>6MZ</scene>, <scene name='pdbligand=A2M:2-O-METHYLADENOSINE+5-(DIHYDROGEN+PHOSPHATE)'>A2M</scene>, <scene name='pdbligand=B8N:(2~{R})-2-azanyl-4-[5-[(2~{S},3~{R},4~{S},5~{R})-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]-3-methyl-2,6-bis(oxidanylidene)pyrimidin-1-yl]butanoic+acid'>B8N</scene>, <scene name='pdbligand=G7M:N7-METHYL-GUANOSINE-5-MONOPHOSPHATE'>G7M</scene>, <scene name='pdbligand=HMT:(3BETA)-O~3~-[(2R)-2,6-DIHYDROXY-2-(2-METHOXY-2-OXOETHYL)-6-METHYLHEPTANOYL]CEPHALOTAXINE'>HMT</scene>, <scene name='pdbligand=MA6:6N-DIMETHYLADENOSINE-5-MONOPHOSHATE'>MA6</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=OMC:O2-METHYLYCYTIDINE-5-MONOPHOSPHATE'>OMC</scene>, <scene name='pdbligand=OMG:O2-METHYLGUANOSINE-5-MONOPHOSPHATE'>OMG</scene>, <scene name='pdbligand=OMU:O2-METHYLURIDINE+5-MONOPHOSPHATE'>OMU</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene>, <scene name='pdbligand=SPD:SPERMIDINE'>SPD</scene>, <scene name='pdbligand=SPM:SPERMINE'>SPM</scene>, <scene name='pdbligand=UR3:3-METHYLURIDINE-5-MONOPHOSHATE'>UR3</scene>, <scene name='pdbligand=UY1:(1S)-1,4-anhydro-1-[(5S)-2,6-dioxo-1,2,5,6-tetrahydropyrimidin-5-yl]-2-O-methyl-5-O-phosphono-D-ribitol'>UY1</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=9pkb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9pkb OCA], [https://pdbe.org/9pkb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9pkb RCSB], [https://www.ebi.ac.uk/pdbsum/9pkb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9pkb ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/SERB1_HUMAN SERB1_HUMAN] Ribosome-binding protein that promotes ribosome hibernation, a process during which ribosomes are stabilized in an inactive state and preserved from proteasomal degradation (PubMed:36691768). Acts via its association with EEF2/eEF2 factor, sequestering EEF2/eEF2 at the A-site of the ribosome and promoting ribosome stabilization and storage in an inactive state (By similarity). May also play a role in the regulation of mRNA stability: binds to the 3'-most 134 nt of the SERPINE1/PAI1 mRNA, a region which confers cyclic nucleotide regulation of message decay (PubMed:11001948). Seems to play a role in PML-nuclear bodies formation (PubMed:28695742).[UniProtKB:Q9CY58]<ref>PMID:11001948</ref> <ref>PMID:28695742</ref> <ref>PMID:36691768</ref>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Homo sapiens]]
+[[Category: Large Structures]]
+[[Category: Wei Z]]
+[[Category: Yong X]]

9pkb: Difference between revisions

Latest revision as of 07:05, 15 July 2026

In situ HHT and CHX treated human hibernating state 80S ribosome

Structural highlights

Function

References

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