Michal Harel at 08:31, 2 November 2023

2023-11-02T08:31:47Z

Michal Harel: New page: == 3D Structures of Ribozymes == Updated on {{REVISIONDAY2}}-{{MONTHNAME|{{REVISIONMONTH}}}}-{{REVISIONYEAR}} {{#tree:id=OrganizedByTopic|openlevels=0| Hepatitis delta virus ribozyme ...

2022-03-03T10:07:45Z

New page: == 3D Structures of Ribozymes == Updated on {{REVISIONDAY2}}-{{MONTHNAME|{{REVISIONMONTH}}}}-{{REVISIONYEAR}} {{#tree:id=OrganizedByTopic|openlevels=0| *Hepatitis delta virus ribozyme *...

New page

== 3D Structures of Ribozymes ==

Updated on {{REVISIONDAY2}}-{{MONTHNAME|{{REVISIONMONTH}}}}-{{REVISIONYEAR}}
{{#tree:id=OrganizedByTopic|openlevels=0|

*Hepatitis delta virus ribozyme

**[[3nkb]] – HDVRZ + DNA/RNA – Hepatitis delta virus 
**[[4prf]] – HDVRZ 
**[[1ato]] – HDVRZ - NMR 
**[[2oih]], [[4pr6]] - HDVRZ + U1 small nuclear ribonucleoprotein A 
**[[1vc5]], [[4prf]] - HDVRZ + U1 small nuclear ribonucleoprotein A (mutant) 
**[[2oj3]], [[1sj3]], [[1sj4]], [[1sjf]], [[1vbx]], [[1vby]], [[1vbz]], [[1vc0]] - HDVRZ (mutant) + U1 small nuclear ribonucleoprotein A 
**[[1vc6]], [[4prf]], [[1pr6]], [[1drz]]- HDVRZ (mutant) + U1 small nuclear ribonucleoprotein A (mutant)

*glmS ribozyme

**[[4meg]], [[4meh]] - glmS RZ – synthetic 
**[[3l3c]], [[3g8s]], [[3g8t]], [[3g96]], [[3g9c]] – glmS RZ + RNA + U1 small nuclear ribonucleoprotein A 
**[[2nz4]] - glmS RZ + substrate RNA 13-mer+ U1 small nuclear ribonucleoprotein A (mutant) 
**[[3b4a]], [[3b4b]], [[3b4c]], [[2z74]], [[2z75]] – Tt-glmS RZ (mutant) + glmS RZ substrate RNA + glmS – ''Thermoanaerobacter tengcongensis'' 
**[[2ho6]], [[2ho7]] - Tt-glmS RZ + glmS RZ substrate RNA 
**[[2gcs]], [[2h0s]], [[2h0x]], [[2h0z]] - Tt-glmS RZ + Tt-glmS RZ amino RNA inhibitor 
**[[2gcv]], [[2h0w]] - Tt-glmS RZ + Tt-glmS RZ product oligonucleotide

*Hairpin ribozyme

**[[3i2q]], [[3i2r]], [[3i2s]], [[3i2u]], [[3cqs]], [[2d2k]], [[2d2l]], [[4g6p]], [[4g6r]], [[4g6s]] – Hairpin RZ 
**[[3gs1]], [[3gs5]], [[3gs8]], [[2bcy]], [[2bcz]], [[2fgp]], [[1x9c]], [[1x9k]] - Hairpin RZ (mutant) 
**[[3cr1]] – Hairpin RZ + RNA 
**[[2m24]], [[2m23]], [[2k65]], [[2k66]] - Hairpin RZ 29-mer – NMR 
**[[3b58]], [[3b5a]], [[3b5f]], [[3b5s]], [[3b91]], [[3bbi]], [[3bbk]], [[3bbm]] - Hairpin RZ 29-mer + RNA 
**[[2npy]], [[2npz]] - Hairpin RZ + RZ domain linking strand 
**[[2p7d]], [[2p7e]], [[2p7f]], [[2oue]], [[1m5o]], [[1m5p]], [[1m5v]] - Hairpin RZ strands I, II, III +substrate strand – Tobacco ringspot virus 
**[[1m5k]] - Hairpin RZ + RNA inhibitor substrate + U1 small nuclear ribonucleoprotein A

*Hammerhead ribozyme

**[[1nyi]], [[1q29]], [[379d]], [[359d]], [[299d]], [[300d]], [[301d]], [[1mme]], [[1hmh]], [[5di2]], [[5di4]], [[5dh6]], [[5dh7]], [[5dh8]], [[5eao]], [[5eaq]] - Hammerhead RZ 
**[[1rmn]] - Hammerhead RZ – fluorescence measurements 
**[[2ro2]], [[2rpk]] – Hammerhead RZ domain I 
**[[3czw]], [[3d0m]] - Hammerhead RZ shorter strands 
**[[2qus]], [[2quw]] - Hammerhead RZ (mutant) 
**[[2oeu]], [[5dqk]] - Hammerhead RZ + RNA 
**[[488d]] – Hammerhead RZ + RNA products 
**[[3zd5]], [[3zp8]] - Hammerhead RZ enzyme+substrate strands 
**[[3zd4]] - Hammerhead RZ enzyme strand

*Leadzyme

**[[2ldz]], [[1ldz]], [[1nuj]], [[1nuv]], [[429d]] – Leadzyme – NMR 

*Group I intron ribozymes

**[[1u6b]], [[1zzn]], [[3bo2]], [[3bo3]], [[3bo4]], [[3iin]] - RZ P9 + RNA + U1 small nuclear ribonucleoprotein 
**[[2r8s]] – RZ P4-P6 domain + antibody – mouse 
**[[1y0q]] – RZ group I + RNA – Staphylococcus phage twort 
**[[1x8w]] – TtRZ – ''Tetrahymena thermophilia'' 
**[[6wls]], [[7ez0]], [[7ez2]] – TtRZ – Cryo EM 
**[[1grz]], [[6bjx]], [[6d8l]], [[6d8m]], [[6d8n]], [[6d8o]] – TtRZ (mutant) 
**[[1l8v]], [[1gid]] – TtRZ P4-P6 domain 
**[[1hr2]] - TtRZ P4-P6 domain (mutant) 
**[[3hhn]] – ligase RZ + U1 small nuclear ribonucleoprotein A 
**[[3r1h]], [[3r1l]] - ligase RZ (mutant) + U1 small nuclear ribonucleoprotein A+ RNA 

*Group II intron ribozymes

**[[6ez0]] – yRZ - NMR 
**[[5j01]], [[5j02]] - OiRZ - ''Oceanobacillus iheyensis'' 
**[[6t3k]], [[6t3n]], [[6t3r]], [[6t3s]] - OiRZ (mutant) 
**[[3fs0]], [[3ftm]] - ligase RZ 

*Various ribozymes

**[[1b36]] – RZ loop B - NMR 
**[[5v3i]] – VS RZ – ''Neurospora'' 
**[[2l5z]], [[1e4p]], [[2mis]] – 26-mer of VS RZ – NMR 
**[[1yn1]], [[1yn2]], [[1tbk]], [[1tjz]], [[1hwq]] - VS RZ stem-loop V – NMR 
**[[5v3i]] - VS RZ 
**[[4r4p]], [[4r4v]] - VS RZ (mutant) 
**[[3hhn]] – Class I ligase RZ + U1 small nuclear ribonucleoprotein A 
**[[3r1h]], [[3r1l]] - Class I ligase RZ (mutant) + U1 small nuclear ribonucleoprotein A+ RNA 
**[[3fs0]], [[3ftm]] - Class II ligase RZ 
**[[3cul]], [[3cun]] – Aminoacyl tRNA synthetase RZ 92-mer + U1 small nuclear ribonucleoprotein A 
**[[2cd1]], [[2cd5]], [[1xsg]], [[1f6x]], [[1f78]], [[1f7f]], [[1f7h]] – RNase P RZ P4 domain 
**[[2cd3]], [[2cd6]], [[1xsh]], [[1xst]], [[1xsu]], [[1f6z]], [[1f79]], [[1f7g]], [[1f7i]] - RNase P RZ P4 domain (mutant) 
**[[2oiu]] – L1 RZ RNA ligase 
**[[2hoj]], [[2hok]], [[2hol]], [[2hom]], [[2hoo]], [[2hop]] – THI-box riboswitch + thiamine pyrophosphate analog 
**[[2f88]] – RZ domain 5 – ''Pyaiella litorralis'' 
**[[1ykq]] – Diels-Alder RZ 
**[[1ykv]], [[1yls]] - Diels-Alder RZ + reaction products 
**[[4qjh]], [[5dun]] – twister sRZ – synthetic 
**[[4rge]], [[4rgf]] – twister sRZ env22 
**[[5t5a]], [[5y85]], [[5y87]] – twister sister RZ – Metagenome 
**[[5k7c]],[[5k7d]],[[5k7e]], [[5ktj]], [[6ufj]], [[6ufk]] - pistol sRZ 
**[[6uey]], [[6uf1]] – pistol EcRZ 
**[[6r47]] – pistol RZ – Alistipes putredinis 
**[[6g7z]], [[6gyv]] – lariat-capping RZ – ''Didymium iridis'' 
**[[6jq5]], [[6jq6]] – hatchet sRZ 
**[[6xjq]], [[6xjw]], [[6xjy]], [[6xjz]] – self-alkylating RZ + antibody – ''Aeropyrum pernix'' 
**[[7dlz]], [[7dwh]] – SAM-dependent methyltransferase sRZ + U1A 
**[[6wll]], [[6wlm]] – Gly RZ – ''Fusobacterium nucleatum'' 
**[[6wlt]], [[6wlu]] – Gly RZ – ''Vibrio cholerae'' 
}}

[[Category: Topic Page]]

← Older revision		Revision as of 08:31, 2 November 2023
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	**[[2npy]], [[2npz]] - Hairpin RZ + RZ domain linking strand<BR />		**[[2npy]], [[2npz]] - Hairpin RZ + RZ domain linking strand<BR />
	**[[2p7d]], [[2p7e]], [[2p7f]], [[2oue]], [[1m5o]], [[1m5p]], [[1m5v]] - Hairpin RZ strands I, II, III +substrate strand – Tobacco ringspot virus<BR />		**[[2p7d]], [[2p7e]], [[2p7f]], [[2oue]], [[1m5o]], [[1m5p]], [[1m5v]] - Hairpin RZ strands I, II, III +substrate strand – Tobacco ringspot virus<BR />
	**[[1m5k]] - Hairpin RZ + RNA inhibitor substrate + U1 small nuclear ribonucleoprotein A		**[[1m5k]] - Hairpin RZ + RNA inhibitor substrate + U1 small nuclear ribonucleoprotein A<br />
			**[[1f9l]] – Hairpin RZ – STRV<br />

	*Hammerhead ribozyme		*Hammerhead ribozyme
Line 57:		Line 58:
	**[[1y0q]] – RZ group I + RNA – Staphylococcus phage twort<BR />		**[[1y0q]] – RZ group I + RNA – Staphylococcus phage twort<BR />
	**[[1x8w]] – TtRZ – ''Tetrahymena thermophilia''<BR />		**[[1x8w]] – TtRZ – ''Tetrahymena thermophilia''<BR />
	**[[6wls]], [[7ez0]], [[7ez2]] – TtRZ – Cryo EM<br />		**[[6wls]], [[7ez0]], [[7ez2]], [[7uvt]], [[7xsk]], [[7xsl]], [[7xsm]], [[7xsn]], [[7yc8]], [[7ycb]], [[7ycg]], [[7ych]], [[7yg8]], [[7yg9]], [[7yga]], [[7ygc]], [[7ygd]], [[8tju]], [[8tjv]], [[8tjx]] – TtRZ – Cryo EM<br />
	**[[1grz]], [[6bjx]], [[6d8l]], [[6d8m]], [[6d8n]], [[6d8o]] – TtRZ (mutant) <BR />		**[[1grz]], [[6bjx]], [[6d8l]], [[6d8m]], [[6d8n]], [[6d8o]] – TtRZ (mutant) <BR />
	**[[1l8v]], [[1gid]] – TtRZ P4-P6 domain<BR />		**[[1l8v]], [[1gid]] – TtRZ P4-P6 domain<BR />
Line 75:		Line 76:
	**[[1b36]] – RZ loop B - NMR<BR />		**[[1b36]] – RZ loop B - NMR<BR />
	**[[5v3i]] – VS RZ – ''Neurospora'' <BR />		**[[5v3i]] – VS RZ – ''Neurospora'' <BR />
	**[[2l5z]], [[1e4p]], [[2mis]] – 26-mer of VS RZ – NMR<BR />		**[[2l5z]], [[1e4p]], [[2mi0]], [[2mis]] – 26-mer of VS RZ – NMR<BR />
			**[[2mtj]], [[2mtk]] – 47-mer of VS RZ – NMR<br />
			**[[2n3q]], [[2n3r]] – 62-mer of VS RZ – NMR<br />
	**[[1yn1]], [[1yn2]], [[1tbk]], [[1tjz]], [[1hwq]] - VS RZ stem-loop V – NMR<BR />		**[[1yn1]], [[1yn2]], [[1tbk]], [[1tjz]], [[1hwq]] - VS RZ stem-loop V – NMR<BR />
	**[[5v3i]] - VS RZ <BR />		**[[5v3i]] - VS RZ <BR />
Line 90:		Line 93:
	**[[1ykq]] – Diels-Alder RZ<BR />		**[[1ykq]] – Diels-Alder RZ<BR />
	**[[1ykv]], [[1yls]] - Diels-Alder RZ + reaction products<br />		**[[1ykv]], [[1yls]] - Diels-Alder RZ + reaction products<br />
	**[[4qjh]], [[5dun]] – twister sRZ – synthetic<br />		**[[4oji]], [[4qjh]], [[5dun]] – twister sRZ – synthetic<br />
	**[[4rge]], [[4rgf]] – twister sRZ env22 <br />		**[[4rge]], [[4rgf]] – twister sRZ env22 <br />
	**[[5t5a]], [[5y85]], [[5y87]] – twister sister RZ – Metagenome<br />		**[[5t5a]], [[5y85]], [[5y87]] – twister sister RZ – Metagenome<br />
Line 96:		Line 99:
	**[[6uey]], [[6uf1]] – pistol EcRZ <br />		**[[6uey]], [[6uf1]] – pistol EcRZ <br />
	**[[6r47]] – pistol RZ – Alistipes putredinis <br />		**[[6r47]] – pistol RZ – Alistipes putredinis <br />
	**[[6g7z]], [[6gyv]] – lariat-capping RZ – ''Didymium iridis''<BR />		**[[4p9r]], [[6g7z]], [[6gyv]] – lariat-capping RZ – ''Didymium iridis''<BR />
	**[[6jq5]], [[6jq6]] – hatchet sRZ <br />		**[[6jq5]], [[6jq6]] – hatchet sRZ <br />
	**[[6xjq]], [[6xjw]], [[6xjy]], [[6xjz]] – self-alkylating RZ + antibody – ''Aeropyrum pernix'' <br />		**[[6xjq]], [[6xjw]], [[6xjy]], [[6xjz]] – self-alkylating RZ + antibody – ''Aeropyrum pernix'' <br />
			**[[7q7x]], [[7q7y]], [[7q7z]], [[7q80]], [[7q81]], [[7q82]] – methyltransferase sRZ <br />
			**[[7v9e]] – methyltransferase hRZ <br />
	**[[7dlz]], [[7dwh]] – SAM-dependent methyltransferase sRZ + U1A <br />		**[[7dlz]], [[7dwh]] – SAM-dependent methyltransferase sRZ + U1A <br />
	**[[6wll]], [[6wlm]] – Gly RZ – ''Fusobacterium nucleatum'' <br />		**[[6wll]], [[6wlm]] – Gly RZ – ''Fusobacterium nucleatum'' <br />

Ribozyme 3D structures - Revision history

Michal Harel at 08:31, 2 November 2023

Michal Harel: New page: == 3D Structures of Ribozymes == Updated on {{REVISIONDAY2}}-{{MONTHNAME|{{REVISIONMONTH}}}}-{{REVISIONYEAR}} {{#tree:id=OrganizedByTopic|openlevels=0| *Hepatitis delta virus ribozyme *...

Michal Harel: New page: == 3D Structures of Ribozymes == Updated on {{REVISIONDAY2}}-{{MONTHNAME|{{REVISIONMONTH}}}}-{{REVISIONYEAR}} {{#tree:id=OrganizedByTopic|openlevels=0| Hepatitis delta virus ribozyme ...