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Ribonuclease 3D structures: Difference between revisions

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{{#tree:id=OrganizedByTopic|openlevels=0|
{{#tree:id=OrganizedByTopic|openlevels=0|


*RNase I or RNase A
*RNase I or RNase A or RNase pancreatic


**[[4kxh]] - hRNase I - human<br />
**[[4kxh]] - hRNase I - human<br />
**[[3f8g]], [[2e0j]], [[2e0l]], [[2e0m]], [[2e0o]], [[1h8x]], [[1e21]], [[1dza]] - hRNase I pancreatic (mutant) <br />
**[[3f8g]], [[2e0j]], [[2e0l]], [[2e0m]], [[2e0o]], [[1h8x]], [[1e21]], [[1dza]] - hRNase I pancreatic (mutant) <br />
**[[2k11]] - hRNase I pancreatic - NMR<br />
**[[2k11]] - hRNase I pancreatic - NMR<br />
**[[3mwq]], [[3mx8]], [[3i67]], [[3i6f]], [[3i6h]], [[3i6j]], [[3i7w]], [[3eux]], [[3euy]], [[3euz]], [[3ev0]], [[3ev1]], [[3ev2]], [[3ev3]], [[3ev4]], [[3ev5]], [[3ev6]], [[3dh5]], [[2e3w]], [[2g4w]], [[2g4x]], [[2gbq]], [[2blp]], [[2blz]], [[2jvt]], [[1jvv]], [[1jvt]], [1js0]], [[1fs3]], [[1kf2]], [[1kf3]], [[1kf4]], [[1kf5]], [[1kf7]], [[1kf8]], [[1aqp]], [[1a2w]], [[1rnw]], [[1rnz]], [[1rno]], [[1rnq]], [[1rbx]], [[1ssc]], [[3srn]], [[4srn]], [[1srn]], [[5rsa]], [[1afu]], [[1bel]], [[1c0b]], [[1c0c]], [[1lsq]], [[1rat]], [[1rbn]], [[1rha]], [[1rhb]], [[1rnx]], [[1rny]], [[1rsm]], [[1xps]], [[1xpt]], [[2g8q]], [[2rat]], [[3mzq]], [[3mzr]], [[3rat]], [[3rn3]], [[4rat]], [[5rat]], [[6rat]], [[7rat]], [[7rsa]], [[8rat]], [[8rsa]], [[9rat]], [[9rsa]], [[3mwr]], [[4ao1]], [[4j5z]], [[4j60]], [[4j61]], [[4j62]], [[4j63]], [[4j64]], [[4j65]], [[4j66]], [[4j67]], [[4j68]], [[4j69]], [[4j6a]], [[4mxf]], [[4ooh]], [[4ot4]], [[4qh3]], [[4rte]], [[4s0q]], [[4s18]], [[5d6u]], [[5jmg]], [[5jml]], [[5na9]], [[5obc]], [[5obd]], [[5obe]], [[4srn]], [[6etr]], [[6etq]], [[6etp]], [[6eto]], [[6etn]], [[6etm]], [[6etl]], [[6etk]] - bRNase I pancreatic - bovine<br />
**[[3mwq]], [[3mx8]], [[3i67]], [[3i6f]], [[3i6h]], [[3i6j]], [[3i7w]], [[3eux]], [[3euy]], [[3euz]], [[3ev0]], [[3ev1]], [[3ev2]], [[3ev3]], [[3ev4]], [[3ev5]], [[3ev6]], [[3dh5]], [[2e3w]], [[2g4w]], [[2g4x]], [[2gbq]], [[2blp]], [[2blz]], [[2jvt]], [[1jvv]], [[1jvt]], [1js0]], [[1fs3]], [[1kf2]], [[1kf3]], [[1kf4]], [[1kf5]], [[1kf7]], [[1kf8]], [[1aqp]], [[1a2w]], [[1rnw]], [[1rnz]], [[1rno]], [[1rnq]], [[1rbx]], [[1ssc]], [[3srn]], [[4srn]], [[1srn]], [[5rsa]], [[1afu]], [[1bel]], [[1c0b]], [[1c0c]], [[1lsq]], [[1rat]], [[1rbn]], [[1rha]], [[1rhb]], [[1rnx]], [[1rny]], [[1rsm]], [[1xps]], [[1xpt]], [[2g8q]], [[2rat]], [[3mzq]], [[3mzr]], [[3rat]], [[3rn3]], [[4rat]], [[5rat]], [[6rat]], [[7rat]], [[7rsa]], [[8rat]], [[8rsa]], [[9rat]], [[9rsa]], [[3mwr]], [[4ao1]], [[4j5z]], [[4j60]], [[4j61]], [[4j62]], [[4j63]], [[4j64]], [[4j65]], [[4j66]], [[4j67]], [[4j68]], [[4j69]], [[4j6a]], [[4mxf]], [[4ooh]], [[4ot4]], [[4qh3]], [[4rte]], [[4s0q]], [[4s18]], [[5d6u]], [[5jmg]], [[5jml]], [[5na9]], [[5obc]], [[5obd]], [[5obe]], [[4srn]], [[6etr]], [[6etq]], [[6etp]], [[6eto]], [[6etn]], [[6etm]], [[6etl]], [[6etk]], [[6xvx]], [6xw0]], [[6yo1]], [[7p8r]], [[7pni]] - bRNase I pancreatic - bovine<br />
**[[3a1r]], [[4zz4]], [[5d97]], [[5rsa]], [[6rsa]] - bRNase I pancreatic - neutron<br />
**[[3a1r]], [[4zz4]], [[5d97]], [[5rsa]], [[6rsa]] - bRNase I pancreatic - neutron<br />
**[[2aas]] - bRNase I pancreatic - NMR<br />
**[[2aas]] - bRNase I pancreatic - NMR<br />
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**[[6bu9]] – DmDicer2 + RNA <br />
**[[6bu9]] – DmDicer2 + RNA <br />
**[[2l6m]] - Dicer residues 1259-1358 - fission yeast - NMR<br />
**[[2l6m]] - Dicer residues 1259-1358 - fission yeast - NMR<br />
**[[2ff1]] - Dicer - ''Giardia intestinalis''<br />  
**[[2ff1]] - Dicer - ''Giardia intestinalis''<br />
**[[7dey]] - Dicer - ''Pichia stipitis''<br />  


*RNase 4
*RNase 4
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**[[1kvz]] - BuRNase 4 - NMR<br />
**[[1kvz]] - BuRNase 4 - NMR<br />


*RNase 5 or angiogenin
*RNase 5 or angiogenin (Ang)


**[[4aoh]] - hRNase 5 <br />
**[[1ang]], [[1b1i]], [[1h52]], [[4aoh]], [[5eop]], [[5epz]], [[5eqo]] - hRNase 5 <br />
**[[1un3]], [[1un4]], [[1un5]], [[1gv7]], [[4ahd]], [[4ahe]], [[4ahf]], [[4ahg]], [[4ahh]], [[4ahi]], [[4ahj]], [[4ahk]], [[4ahl]], [[4ahm]], [[4ahn]], [[5m9v]], [[5m9t]],  [[5m9s]], [[5m9r]], [[5m9q]], [[5m9p]], [[5m9m]], [[5m9j]], [[5m9g]], [[5m9c]], [[5m9a]] - hRNase 5 (mutant)<br />
**[[1awz]] – hAng - NMR<br />
**[[1b1e]], [[1b1j]], [[1h53]], [[1hby]], [[1k58]], [1k59]], [[1k5a]], [[1k5b]], [[1un3]], [[1un4]], [[1un5]], [[1gv7]], [[2ang]], [[4ahd]], [[4ahe]], [[4ahf]], [[4ahg]], [[4ahh]], [[4ahi]], [[4ahj]], [[4ahk]], [[4ahl]], [[4ahm]], [[4ahn]], [[4b36]], [[5m9v]], [[5m9t]],  [[5m9s]], [[5m9r]], [[5m9q]], [[5m9p]], [[5m9m]], [[5m9j]], [[5m9g]], [[5m9c]], [[5m9a]], [[7pnj]], [[7pnr]] - hRNase 5 (mutant)<br />
**[[1h0d]] - hRNase 5 + antibody<br />
**[[1h0d]] - hRNase 5 + antibody<br />
**[[1a4y]] - hRNase 5 + RNae inhibitor<br />
**[[1agi]] – bAng <br />
**[[1gio]] – bAng - NMR<br />
**[[4qfi]], [[4qfj]] – rAng<br />
**[[2bwk]], [[2bwl]] – mAng<br />
**[[3zbv]] – mAng-2<br />
**[[3zbw]] – mAng-3<br />
**[[2j4t]] – mAng-4<br />
**[[3lje]] - ZeRNase 5<br />
**[[3lje]] - ZeRNase 5<br />
**[[7bfk]], [[7bfl]] – saAng-1 (mutant) - salmon<br />


*RNase 6
*RNase 6
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**[[1rbj]] - bRNase B + tetranucleotide <br />
**[[1rbj]] - bRNase B + tetranucleotide <br />


*RNase BA
*RNase BA or barnase


**[[1yvs]], [[1b2x]], [[1a2p]], [[1bni]], [[1bnj]] - BaRNase BA - ''Bacillus amyloliquefaciens''<br />
**[[1yvs]], [[1b2x]], [[1a2p]], [[1bni]], [[1bnj]] - BaRNase BA - ''Bacillus amyloliquefaciens''<br />
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**[[5ohg]] - EcRNase E residues 813-850 + enolase<br />
**[[5ohg]] - EcRNase E residues 813-850 + enolase<br />
**[[4oxp]] - CcRNase E S1+ sensor domains – ''Caulobacter crescentus'' <br />
**[[4oxp]] - CcRNase E S1+ sensor domains – ''Caulobacter crescentus'' <br />
**[[6x2d]] - RNase E DNAse I  domain – ''Vibrio cholerae''<br />
**[[6x2d]] - VcRNase E DNAse I  domain – ''Vibrio cholerae''<br />


*RNase F1
*RNase F1
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**[[3bk2]] - TtRNase J + nucleotide<br />
**[[3bk2]] - TtRNase J + nucleotide<br />
**[[3zq4]] - BsRNase J1 - ''Bacillus subtilis'' <br />
**[[3zq4]] - BsRNase J1 - ''Bacillus subtilis'' <br />
**[[6k6s]] - SeRNase J1 - ''Staphylococcus epidermidis'' <br />
**[[6k6w]] - SeRNase J2 <br />
**[[5haa]] - MpRNase - ''Methanolobus psychrophilus''<br />
**[[5haa]] - MpRNase - ''Methanolobus psychrophilus''<br />
**[[5hab]], [[5ws2]] - MpRNase (mutant) + RNA<br />
**[[5hab]], [[5ws2]] - MpRNase (mutant) + RNA<br />
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**[[6vq6]], [[6vq7]], [[6vq8]], [[6vqc]], [[6vqg]], [[6vqh]] - rRNase K in v-ATPase – Cryo EM <br />
**[[6vq6]], [[6vq7]], [[6vq8]], [[6vqc]], [[6vqg]], [[6vqh]] - rRNase K in v-ATPase – Cryo EM <br />


*RNase L
*RNase L or 2-5A-dependent RNase


**[[4g8k]] - hRNase L <br />
**[[1wdy]], [[4g8l]] - hRNase L + 2-5A<br />
**[[4oau]] - hRNase L + ADP  + RNA<br />
**[[4o1o]] - pRNase L + oligoadenylate + CMP - pig <br />
**[[4o1o]] - pRNase L + oligoadenylate + CMP - pig <br />
**[[4o1p]] - pRNase L + oligoadenylate + AMPPNP  <br />
**[[4o1p]] - pRNase L + oligoadenylate + AMPPNP  <br />
**[[4oav]] - pRNase L + oligoadenylate + AMPPCP  + RNA<br />
**[[4oav]] - pRNase L + oligoadenylate + AMPPCP  + RNA<br />
**[[7dsy]], [[7dts]], [[7elw]] - pRNase L + inhibitor<br />
**[[6m11]], [[6m12]], [[6m13]] - pRNase L + drug<br />


*RNase LE
*RNase LE
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**[[6w6v]], [[7c79]], [[7c7a]] - yRNase MRP – Cryo EM<br />
**[[6w6v]], [[7c79]], [[7c7a]] - yRNase MRP – Cryo EM<br />
**[[7c7a]] - yRNase MRP + RNA – Cryo EM<br />


*RNase MS
*RNase MS
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**[[6tg6]] - GsRNase M5 toprim domain <br />
**[[6tg6]] - GsRNase M5 toprim domain <br />
**[[6tgj]] - GsRNase M5 RBD <br />
**[[6tgj]], [[6z2b]] - GsRNase M5 RBD <br />
**[[6tpq]] - BsRNase M5 in 50S ribosome – Cryo EM<br />
**[[6tpq]] - BsRNase M5 in 50S ribosome – Cryo EM<br />


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**[[6ahr]] - hRNase P – cryo EM<br />
**[[6ahr]] - hRNase P – cryo EM<br />
**[[6ahu]] - hRNase P + tRNA – cryo EM<br />
**[[6ahu]] - hRNase P + tRNA – cryo EM<br />
**[[7onu]] - hRNase P catalytic subunit + tRNA-Tyr + CoA dehydrogenase – cryo EM<br />
**[[5nfj]] - hRNase P protein 1 + SAM<br />
**[[5nfj]] - hRNase P protein 1 + SAM<br />
**[[6cwx]] - hRNase P subunits P20+P25 <br />
**[[6cwx]] - hRNase P subunits P20+P25 <br />
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**[[3q1q]], [[3q1r]] - TmRNase P + TmRNase P RNA + tRNAPhe <br />
**[[3q1q]], [[3q1r]] - TmRNase P + TmRNase P RNA + tRNAPhe <br />
**[[1d6t]], [[6d1r]] - SaRNase P <br />
**[[1d6t]], [[6d1r]] - SaRNase P <br />
**[[6ov1]] - SaRNase P (mutant)<br />
**[[2a64]] - GsRNase P (mutant) <br />
**[[2a64]] - GsRNase P (mutant) <br />
**[[1a6f]], [[1nbs]], [[2jg4]] - BsRNase P (mutant) <br />
**[[1a6f]], [[1nbs]], [[2jg4]] - BsRNase P (mutant) <br />
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**[[6k0b]] - MjRNase P components 1-4 + L7AE + tRNA + RPR – Cryo EM<br />
**[[6k0b]] - MjRNase P components 1-4 + L7AE + tRNA + RPR – Cryo EM<br />
**[[5diz]], [[5ft9]] - RNase P2 - ''Arabidopsis thaliana''<br />
**[[5diz]], [[5ft9]] - RNase P2 - ''Arabidopsis thaliana''<br />
**[[7og5]] - RNase P – Cryo EM – ''Halorhodospira halophila''<br />
**[[7f3e]] - AaRNase P – cryo EM<br />


*RNase PH
*RNase PH
Line 306: Line 329:


**[[5xgu]] - EcRNase R (mutant) <br />
**[[5xgu]] - EcRNase R (mutant) <br />
**[[7dcy]] - MgRNase R – ''Mycoplasma genitalium''<br />
**[[7dic]], [[7did]], [[7dol]] - MgRNase R (mutant) + RNA<br />


*RNase RH
*RNase RH
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**[[1iqq]] - RNase S3 - Japanese pear <br />
**[[1iqq]] - RNase S3 - Japanese pear <br />


*RNase SA
*RNase SA or guanyl-specific RNase SA


**[[3a5e]], [[1zgx]], [[1ynv]], [[1t2h]], [[1t2i]], [[1uci]], [[1ucj]], [[1uck]], [[1ucl]], [[1i70]], [[1i8v]], [[1box]], [[4gho]], [[4j5g]], [[4j5k]] - SaRNase SA guanyl-specific (mutant) - ''Streptomyces aureofaciens'' <br />
**[[3a5e]], [[1zgx]], [[1ynv]], [[1t2h]], [[1t2i]], [[1uci]], [[1ucj]], [[1uck]], [[1ucl]], [[1i70]], [[1i8v]], [[1box]], [[4gho]], [[4j5g]], [[4j5k]] - SaRNase SA guanyl-specific (mutant) - ''Streptomyces aureofaciens'' <br />
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**[[1lov]], [[1low]], [[1loy]], [[1i0v]],  [[1i0x]],  [[1b2m]], [[1rhl]], [[1bir]], [[1rgk]], [[1rgl]], [[5hoh]] - AoRNase T1 (mutant) + nucleotide<br />
**[[1lov]], [[1low]], [[1loy]], [[1i0v]],  [[1i0x]],  [[1b2m]], [[1rhl]], [[1bir]], [[1rgk]], [[1rgl]], [[5hoh]] - AoRNase T1 (mutant) + nucleotide<br />
**[[3rnt]] - AoRNase T1 + V<br />
**[[3rnt]] - AoRNase T1 + V<br />
**[[5gy6]] - RNase T1 - ''Hericium erinaceus''<br />
**[[5gy6]] - HeRNase T1 - ''Hericium erinaceus''<br />
**[[6ls1]] - HeRNase T1 + nucleotide<br />


*RNase T2
*RNase T2
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*Oligoribonuclease
*Oligoribonuclease


**[[6rci]] - hORNase <br />
**[[6j7y]], [[6j7z]], [[6j80]], [[6rcn]] - hORNase + DNA<br />
**[[6rcl]], [[6sty]] - hORNase + RNA<br />
**[[2igi]], [[1yta]] - EcORNase<br />
**[[2igi]], [[1yta]] - EcORNase<br />
**[[2gbz]] - ORNase - ''Xanthomonas campestris''<br />
**[[2gbz]] - ORNase - ''Xanthomonas campestris''<br />
Line 402: Line 431:
**[[6nkl]] - HiORNase + VAPB1<br />
**[[6nkl]] - HiORNase + VAPB1<br />
**[[3tr8]] - CbORNase - ''Coxiella burnetii''<br />
**[[3tr8]] - CbORNase - ''Coxiella burnetii''<br />
**[[5cy4]] - ORNase - ''Acinetobacter baumannii''<br />
**[[5cy4]] - AbORNase - ''Acinetobacter baumannii''<br />
**[[7v5h]] - VcORNase <br />
**[[6n6a]], [[6n6c]], [[6n6d]], [[6n6e]], [[6n6f]], [[6n6g]], [[6n6h]], [[6n6i]], [[6n6j]], [[6n6k]] - VcORNase + RNA<br />
**[[6a4a]] - CpORNase – ''Colwella psychreythraea''<br />
**[[6a4e]] - CpORNase (mutant) + RNA <br />
**[[6a4d]] - CpORNase (mutant) + PNP-TMP<br />
**[[6a4f]] - CpORNase + UMP<br />
**[[6rk6]] - ORNase - metagenome<br />


*NanoRNase or bifunctional oligoribonuclease and PAP phosphatase nRNA
*NanoRNase or bifunctional oligoribonuclease and PAP phosphatase nRNA
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**[[5izo]] - BsNNase (mutant) <br />
**[[5izo]] - BsNNase (mutant) <br />
**[[5cet]] - MtNNase <br />
**[[5cet]] - MtNNase <br />
**[[7mpr]], [[7mps]], [[7mpt]] - BmNNase C – ''Brucella melitensis''<br />
**[[7mpu]] - BmNNase C + GG<br />
**[[7mpl]], [[7mpm]], [[7mpn]], [[7mpo]], [[7mpp]], [[7mpq]], [[7mqb]], [[7mqc]], [[7mqd]], [[7mqe]] [[7mqf]], [[7mqg]], [[7mqh]], [[7mqi]] - NNase C + RNA – ''Bartonella henselae''<br />


*Polynucleotide phosphorylase
*Polynucleotide phosphorylase or Polyribonucleotide nucleotidyltransferase


**[[3cdi]] - EcPNPase<br />
**[[3cdi]], [[7ogl]] - EcPNPase<br />
**[[3gll]] - EcPNPase core<br />
**[[3gll]] - EcPNPase core<br />
**[[3cdj]] - EcPNPase C terminal truncated<br />
**[[3cdj]] - EcPNPase C terminal truncated<br />
**[[1sro]] - EcPNPase RNA-binding domain - NMR<br />
**[[1sro]], [[6qh2]] - EcPNPase RNA-binding domain - NMR<br />
**[[3gcm]], [[3gme]], [[3h1c]] - EcPNPase + RNase E recognition domain<br />
**[[3gcm]], [[3gme]], [[3h1c]] - EcPNPase + RNase E recognition domain<br />
**[[7ogk]] - EcPNPase + RNA - CryoEM<br />
**[[7ogm]] - EcPNPase + Hfq + RNA - CryoEM<br />
**[[1e3h]], [[1e3p]] - PNPase - ''Streptomyces antibioticus''<br />
**[[1e3h]], [[1e3p]] - PNPase - ''Streptomyces antibioticus''<br />
**[[3h36]] - PNPase fragment - ''Streptomyces mutans''<br />
**[[3h36]] - PNPase fragment - ''Streptomyces mutans''<br />
**[[4nbq]] - CbPNPase<br />
**[[4nbq]] - CbPNPase<br />
**[[4am3]] - PNPase + RNA - ''Caulobacter vibrioides''<br />
**[[4am3]] - PNPase + RNA - ''Caulobacter vibrioides''<br />
**[[7ld5]] - PNPase + RNA - ''Mycobcterium smegmatis''<br />
**[[6d6k]] - AbPNPase<br />


*Binase
*Binase
Line 453: Line 496:


**[[6tnn]] - BsMRNase in 50S ribosome – Cryo EM<br />
**[[6tnn]] - BsMRNase in 50S ribosome – Cryo EM<br />
**[[4oun]] - BsMRNase 3<br />


*Other RNases
*Other RNases


**[[6ttc]], [[6tcd]] – Rnase - salmon<br />
**[[6ttc]], [[6tcd]] – saRnase<br />
**[[2zpo]] - RNase - ''Chelonia mydas''<br />
**[[2zpo]] - RNase - ''Chelonia mydas''<br />
**[[3iek]] - TtRNase  - ''Thermus thermophilus''<br />
**[[3iek]] - TtRNase  - ''Thermus thermophilus''<br />

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

Michal Harel
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