This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


Endonuclease 3D structures

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (08:30, 19 February 2023) (edit) (undo)
 
(3 intermediate revisions not shown.)
Line 25: Line 25:
**[[2abk]], [[1ako]] - EcENN – ''Escherichia coli''<br />
**[[2abk]], [[1ako]] - EcENN – ''Escherichia coli''<br />
**[[1orn]], [[1orp]], [[1p59]] - GsENN + DNA – ''Geobacillus stearothermophilus''<br />
**[[1orn]], [[1orp]], [[1p59]] - GsENN + DNA – ''Geobacillus stearothermophilus''<br />
-
**[[4unf]] – DrENN-1 – ''Deinococcus radiodurans'' <br />
+
**[[4l0k]], [[4unf]] – DrENN-1 – ''Deinococcus radiodurans'' <br />
 +
**[[8a5c]], [[8a5f]] – DrENN-1 (mutant)<br />
**[[4uob]] – DrENN-3 <br />
**[[4uob]] – DrENN-3 <br />
 +
**[[8a5g]] – DrENN-3 (mutant)<br />
*ENN-IV
*ENN-IV
Line 36: Line 38:
**[[1xp3]] - ENN – ''Bacillus anthracis''<br />
**[[1xp3]] - ENN – ''Bacillus anthracis''<br />
**[[3aal]] - GkENN – ''Geobacillus kaustophilus''<br />
**[[3aal]] - GkENN – ''Geobacillus kaustophilus''<br />
-
**[[3aam]] - TtENN – ''Thermus thermophilus''
+
**[[3aam]] - TtENN – ''Thermus thermophilus''<br />
 +
**[[2x7v]], [[2x7w]] - TmENN - ''Thermotoga maritima'' <br />
*ENN-V
*ENN-V
Line 72: Line 75:
**[[2opf]], [[2oq4]], [[6fbu]] - EcENN (mutant) + DNA
**[[2opf]], [[2oq4]], [[6fbu]] - EcENN (mutant) + DNA
-
*ENN-VIII-like
+
*ENN-VIII-like or NEIL1
-
**[[6lwa]], [[6lwb]], [[6lwc]], [[6lwd]], [[6lwf]], [[6lwf]], [[6lwg]], [[6lwh]], [[6lwi]], [[6lwj]], [[6lwl]], [[6lwk]], [[6lwm]], [[6lwn]], [[6lwo]], [[6lwp]], [[6lwq]], [[6lwr]] – hENN + DNA<br />
+
**[[1tdh]], [[4nrv]], [[5itq]] – hENN<br />
 +
**[[5itr]], [[5itt]], [[5itu]], [[5itx]], [[5ity]], [[6lwa]], [[6lwb]], [[6lwc]], [[6lwd]], [[6lwf]], [[6lwf]], [[6lwg]], [[6lwh]], [[6lwi]], [[6lwj]], [[6lwl]], [[6lwk]], [[6lwm]], [[6lwn]], [[6lwo]], [[6lwp]], [[6lwq]], [[6lwr]] – hENN + DNA<br />
*AP ENN
*AP ENN
Line 83: Line 87:
*Cas ENN
*Cas ENN
-
**[[1wj9]], [[4ej3]] – TtCas<br />
+
**[[1wj9]], [[4ej3]], [[6ke1]] – TtCas<br />
**[[4n06]] – AfCas1 - ''Archaeoglobus fulgidus'' <br />
**[[4n06]] – AfCas1 - ''Archaeoglobus fulgidus'' <br />
**[[3god]] – PaCas1 – ''Pseudomonas aeruginosa''<br />
**[[3god]] – PaCas1 – ''Pseudomonas aeruginosa''<br />
Line 96: Line 100:
**[[4p6i]], [[4qdl]] – EcCas1 + EcCas2<br />
**[[4p6i]], [[4qdl]] – EcCas1 + EcCas2<br />
**[[6qy3]] – GsCas1 + EcCas2 + Csn2 – Cryo EM<br />
**[[6qy3]] – GsCas1 + EcCas2 + Csn2 – Cryo EM<br />
 +
**[[7cr6]], [[7cr8]] – Cas1 + Cas2 + DNA – ''Synechocystis''<br />
 +
**[[7ei1]] – PfCas1 + Cas2 - ''Pyrococcus furiosus''<br />
**[[3s4l]] – MjCas3 – ''Methanocaldococcus jannaschii''<br />
**[[3s4l]] – MjCas3 – ''Methanocaldococcus jannaschii''<br />
**[[4qqw]] – TfCas3 – ''Thermobifida fusca''<br />
**[[4qqw]] – TfCas3 – ''Thermobifida fusca''<br />
Line 106: Line 112:
**[[6njy]] – Cas6 - ''Mahella australiensis''<br />
**[[6njy]] – Cas6 - ''Mahella australiensis''<br />
**[[4qr0]], [[4qr1]], [[6o56]] - SpCas9 (Csn1) – ''Streptococcus pyogenes''<br />
**[[4qr0]], [[4qr1]], [[6o56]] - SpCas9 (Csn1) – ''Streptococcus pyogenes''<br />
 +
**[[7vk9]] - SpCas9 (mutant)<br />
 +
**[[7mpz]] - GsCas9 HNH nuclease domain<br />
 +
**[[8f43]] - GsCas9 HNH nuclease domain (mutant)<br />
**[[4ilr]], [[3zfv]] – SsCas6 <br />
**[[4ilr]], [[3zfv]] – SsCas6 <br />
**[[3i4h]] – PfCas6 - ''Pyrococcus furiosus''<br />
**[[3i4h]] – PfCas6 - ''Pyrococcus furiosus''<br />
**[[4dzd]] – EcCas6e<br />
**[[4dzd]] – EcCas6e<br />
**[[7jzx]] – PaCas6f in crispr-Cas surveillance complex – Cryo EM<br />
**[[7jzx]] – PaCas6f in crispr-Cas surveillance complex – Cryo EM<br />
-
**[[4qr0]], [[4qr1]] - SpCas9 (Csn1) – ''Streptococcus pyogenes''<br />
 
**[[4qr0]], [[4qr1]], [[4cmp]], [[4cmq]] - SpCas9 <br />
**[[4qr0]], [[4qr1]], [[4cmp]], [[4cmq]] - SpCas9 <br />
**[[4ogc]], [[4oge]] – Cas9 II-C – ''Actinomyces naeslundii''<br />
**[[4ogc]], [[4oge]] – Cas9 II-C – ''Actinomyces naeslundii''<br />
Line 138: Line 146:
**[[6kdv]] – TtCas1 + DNA <br />
**[[6kdv]] – TtCas1 + DNA <br />
**[[6opm]] – Cas1 + DNA – ''Methanosarcina mazei''<br />
**[[6opm]] – Cas1 + DNA – ''Methanosarcina mazei''<br />
 +
**[[7mi9]] – GsuCas1 + Cas2 + DNA – ''Geobacter sulfurreducens''<br />
 +
**[[7mi5]], [[7mid]] – GsuCas1 + Cas2 + Cas4 + DNA <br />
 +
**[[7mi4]], [[7mib]] – GsuCas1 + Cas2 + Cas4 + DNA – Cryo EM<br />
 +
**[[8d3l]], [[8d3m]], [[8d3p]], [[8d3q]] – Cas1 + Cas2 + Cas4 + DNA – ''Alkalihalobacillus halodurans'' – Cryo EM<br />
**[[4ill]], [[4ilm]] – SsCas6 + RNA - ''Sulfolobus solfataricus''<br />
**[[4ill]], [[4ilm]] – SsCas6 + RNA - ''Sulfolobus solfataricus''<br />
**[[5uz9]] – PaCsa5f + Cas7f + Cas8f + anti-crispr protein + RNA - Cryo EM<br />
**[[5uz9]] – PaCsa5f + Cas7f + Cas8f + anti-crispr protein + RNA - Cryo EM<br />
Line 151: Line 163:
**[[6vqx]] – PaCas6f (Csy4) + ACRF6 + Cys1 + Csy2 + Csy3 + RNA – Cryo EM<br />
**[[6vqx]] – PaCas6f (Csy4) + ACRF6 + Cys1 + Csy2 + Csy3 + RNA – Cryo EM<br />
**[[4al5]], [[4al6]] - PaCas6f (Csy4) (mutant) + RNA <br />
**[[4al5]], [[4al6]] - PaCas6f (Csy4) (mutant) + RNA <br />
-
**[[4zt0]] - SpCas9 + RNA <br />
+
**[[4zt0]], [[7ox8]], [[7ox9]] - SpCas9 + RNA <br />
**[[4zt9]] - SpCas9 (mutant) + RNA <br />
**[[4zt9]] - SpCas9 (mutant) + RNA <br />
-
**[[5f9r]], [[6k4p]], [[6k4q]], [[6o0x]], [[6o0y]], [[6o0z]] - SpCas9 + RNA + DNA<br />
+
**[[7qqo]], [[7qqp]], [[7qqq]], [[7qqr]], [[7qqs]], [[7qqt]], [[7qqu]], [[7qqv]], [[7qqw]], [[7qqx]], [[7qqz]], [[7qr0]], [[7qr1]], [[7qr5]], [[7qr7]], [[7qr8]], [[7s4u]], [[7s4v]],[[7z4c]], [[7z4d]], [[7z4e]], [[7z4g]], [[7z4h]], [[7z4i]], [[7z4j]],[[7z4k]], [[7z4l]]] - SpCas9 + DNA <br />
-
**[[4oo8]], [[4un3]], [[4un4]], [[4un5]], [[5fw1]], [[5fw2]], [[5fw3]], [[5fq5]], [[5b2r]], [[5b2s]], [[5b2t]], [[5y36]], [[6ia6]], [[6k3z]], [[6k4s]], [[6k4u]], [[6k57]] - SpCas9 (Csn1) (mutant) + RNA + DNA<br />
+
**[[5f9r]], [[6k4p]], [[6k4q]], [[6o0x]], [[6o0y]], [[6o0z]], [[7ox7]], [[7oxa]], [[7s36]], [[7s37]], [[7s38]], [[7s3h]], [[7s4x]], [[7zo1]] - SpCas9 + RNA + DNA<br />
 +
**[[7v59]] - SpCas9 + RNA + DNA – Cryo EM<br />
 +
**[[4oo8]], [[4un3]], [[4un4]], [[4un5]], [[5fw1]], [[5fw2]], [[5fw3]], [[5fq5]], [[5b2r]], [[5b2s]], [[5b2t]], [[5y36]], [[6ai6]], [[6k3z]], [[6k4s]], [[6k4u]], [[6k57]] - SpCas9 (Csn1) (mutant) + RNA + DNA<br />
**[[5xbl]] - SpCas9 + associated protein + RNA <br />
**[[5xbl]] - SpCas9 + associated protein + RNA <br />
**[[6ifo]] - SpCas9 + AcriiA2 + RNA <br />
**[[6ifo]] - SpCas9 + AcriiA2 + RNA <br />
**[[5vw1]] - SpCas9 + AcriiA4 + RNA <br />
**[[5vw1]] - SpCas9 + AcriiA4 + RNA <br />
**[[6mcc]], [[5vzl]], [[6mcb]] - SpCas9 + AcriiA4 + RNA – Cryo EM<br />
**[[6mcc]], [[5vzl]], [[6mcb]] - SpCas9 + AcriiA4 + RNA – Cryo EM<br />
 +
**[[6vpc]] - SpCas9 + TADA-8E + RNA + DNA<br />
**[[5vgb]] - NmCas9 + AcriiC1 – ''Neisseria meningitidis'' <br />
**[[5vgb]] - NmCas9 + AcriiC1 – ''Neisseria meningitidis'' <br />
**[[6jdx]], [[6jdj]], [[6j9m]] - NmCas9 + AcriiC2 <br />
**[[6jdx]], [[6jdj]], [[6j9m]] - NmCas9 + AcriiC2 <br />
Line 166: Line 181:
**[[6kc7]] - NmCas9 (mutant) + RNA + DNA<br />
**[[6kc7]] - NmCas9 (mutant) + RNA + DNA<br />
**[[6je9]] - NmCas9 + RNA + AcriiC3<br />
**[[6je9]] - NmCas9 + RNA + AcriiC3<br />
 +
**[[8hj4]] - NmCas9 + RNA + AcriiC5 – Cryo EM<br />
**[[6je4]] - NmCas9 + RNA + DNA + AcriiC3<br />
**[[6je4]] - NmCas9 + RNA + DNA + AcriiC3<br />
**[[6rj9]], [[6rja]], [[6rjg]] - StCas9 + RNA + DNA + AcriiA6 – ''Streptococcus thermophilus''<br />
**[[6rj9]], [[6rja]], [[6rjg]] - StCas9 + RNA + DNA + AcriiA6 – ''Streptococcus thermophilus''<br />
Line 172: Line 188:
**[[5czz]] - SaCas9 (Csn1) + RNA + DNA - ''Staphylococcus aureus''<br />
**[[5czz]] - SaCas9 (Csn1) + RNA + DNA - ''Staphylococcus aureus''<br />
**[[5axw]] - SaCas9 (Csn1) (mutant) + RNA + DNA <br />
**[[5axw]] - SaCas9 (Csn1) (mutant) + RNA + DNA <br />
 +
**[[7enh]], [[7eni]], [[7enr]] - SaCas9 + RNA + ACRIIA <br />
**[[6joo]] - Cas9 + RNA + DNA – ''Corynebacterium diphtheriae''<br />
**[[6joo]] - Cas9 + RNA + DNA – ''Corynebacterium diphtheriae''<br />
**[[5b2o]], [[5b2p]], [[5b2q]] - FtCas9 (mutant) + RNA + DNA – ''Francisella tularensis''<br />
**[[5b2o]], [[5b2p]], [[5b2q]] - FtCas9 (mutant) + RNA + DNA – ''Francisella tularensis''<br />
-
**[[6wc0]] - Cas9 + RNA + DNA – ''Acidothermus cellulolyticus''<br />
+
**[[6wbr]], [[6wc0]] - Cas9 + RNA + DNA – ''Acidothermus cellulolyticus''<br />
**[[6i1l]], [[6i1k]], [[6gtg]], [[6gtf]], [[6gte]], [[6gtd]], [[6gtc]] – FtCas12a (mutant) + RNA + DNA <br />
**[[6i1l]], [[6i1k]], [[6gtg]], [[6gtf]], [[6gte]], [[6gtd]], [[6gtc]] – FtCas12a (mutant) + RNA + DNA <br />
**[[6w62]] – Cas12i + RNA – ''Lachnospiraceae bacterium'' – Cryo EM<br />
**[[6w62]] – Cas12i + RNA – ''Lachnospiraceae bacterium'' – Cryo EM<br />
Line 252: Line 269:
**[[2gw6]] – hENN subunit sen15 – NMR<br />
**[[2gw6]] – hENN subunit sen15 – NMR<br />
**[[6z9u]] – hENN subunits sen15+sen34<br />
**[[6z9u]] – hENN subunits sen15+sen34<br />
 +
**[[7uxa]] – hENN + tRNA-Arg – Cryo EM<br />
**[[1a79]], [[1a76]], [[1a77]] - MjENN – ''Methanocaldococcus jannaschii''<br />
**[[1a79]], [[1a76]], [[1a77]] - MjENN – ''Methanocaldococcus jannaschii''<br />
**[[2cv8]] - ENN – ''Sulfolobus tokodaii''<br />
**[[2cv8]] - ENN – ''Sulfolobus tokodaii''<br />
Line 258: Line 276:
**[[2ohc]], [[2ohe]] - TaENN – ''Thermoplasma acidophilum''<br />
**[[2ohc]], [[2ohe]] - TaENN – ''Thermoplasma acidophilum''<br />
**[[2zyz]] – ENN – ''Pyrobaculum aerophilum''<br />
**[[2zyz]] – ENN – ''Pyrobaculum aerophilum''<br />
-
**[[3iey]] - ENN + NEQ261 – ''Nanoarchaeum equitans''<br />
+
**[[3if0]] - ENN + NEQ261 – ''Nanoarchaeum equitans''<br />
**[[3ajv]] - ApENN (mutant) – ''Aeropyrum pernix''<br />
**[[3ajv]] - ApENN (mutant) – ''Aeropyrum pernix''<br />
**[[3p1y]] - ApENN /AfENN<br />
**[[3p1y]] - ApENN /AfENN<br />
Line 283: Line 301:
*Sm ENN
*Sm ENN
-
**[[1smn]], [[1qae]], [[1ql0]], [[1g8t]] – ENN – ''Serratia marcescens''
+
**[[1smn]], [[1qae]], [[1ql0]], [[1g8t]], [[4e3y]] – ENN – ''Serratia marcescens''
*NaeI ENN
*NaeI ENN
Line 316: Line 334:
*HinDIII ENN
*HinDIII ENN
-
**[[2e52]], [[3a4k]] - HiENN + DNA
+
**[[2e52]], [[3a4k]], [[3wvg]], [[3wvh]], [[3wvi]], [[3wvk]], [[3wvp]] - HiENN + DNA
*HinP1I ENN
*HinP1I ENN
Line 331: Line 349:
**[[1ul1]] - hENN + PCNA <br />
**[[1ul1]] - hENN + PCNA <br />
**[[6tnz]] - hENN in processive polymerase – Cryo EM <br />
**[[6tnz]] - hENN in processive polymerase – Cryo EM <br />
 +
**[[7qo1]] - hENN + DNA ligase + PCNA + DNA – Cryo EM <br />
**[[1mc8]] - PhENN (mutant) <br />
**[[1mc8]] - PhENN (mutant) <br />
**[[3ory]]– ENN – ''Desulfurococcus amylolyticus''<br />
**[[3ory]]– ENN – ''Desulfurococcus amylolyticus''<br />
Line 339: Line 358:
**[[1rxz]] - AfENN + PCNA <br />
**[[1rxz]] - AfENN + PCNA <br />
**[[4wa8]] – ENN – ''Methanopyrus kandleri''<br />
**[[4wa8]] – ENN – ''Methanopyrus kandleri''<br />
 +
**[[6c33]] - MsENN – ''Mycobacterium smegmatis''<br />
 +
**[[6c34]], [[6c35]], [[6c36]] - MsENN (mutant) <br />
-
*DNA mismatch ENN
+
*DNA mismatch ENN or Pms2
-
**[[1h7u]] – hENN<br />
+
**[[1h7u]], [[7rck]] – hENN + ATP<br />
-
**[[6mfq]] – hENN Pms2<br />
+
**[[7rci]] - hENN (mutant) + ATP<br />
 +
**[[6mfq]], [[7rcb]] – hENN Pms2<br />
**[[5u5r]] – hENN + importin<br />
**[[5u5r]] – hENN + importin<br />
**[[1odg]] - EcENN + DNA<br />
**[[1odg]] - EcENN + DNA<br />
 +
**[[5x9y]] – ENN MutL – ''Aquifex aeolicus''<br />
*Vvn ENN
*Vvn ENN
Line 351: Line 374:
**[[1ouo]] – VvENN – ''Vibrio vulnificus''<br />
**[[1ouo]] – VvENN – ''Vibrio vulnificus''<br />
**[[1oup]], [[2ivk]] - VvENN + DNA
**[[1oup]], [[2ivk]] - VvENN + DNA
 +
 +
*Splicing ENN
 +
 +
**[[1r0v]], [[1r11]], [[1rlv]] – AfENN
*Structure-specific ENN
*Structure-specific ENN
Line 365: Line 392:
*BfiI ENN
*BfiI ENN
-
**[[2c1l]] – ENN – ''Bacillus firmus''
+
**[[2c1l]] – BfENN – ''Bacillus firmus''<br />
 +
**[[3zi5]] – BfENN + DNA<br />
*SfiI ENN
*SfiI ENN
Line 432: Line 460:
**[[2ziv]] – hENN EME1 (mutant) + Mus81<br />
**[[2ziv]] – hENN EME1 (mutant) + Mus81<br />
**[[6vwb]] – hENN Mus81 N-terminal - NMR<br />
**[[6vwb]] – hENN Mus81 N-terminal - NMR<br />
 +
**[[2mc3]] – hENN Mus81 winged-helix domain - NMR<br />
**[[4p0p]], [[4p0q]], [[4p0r]], [[4p0s]] – hENN EME1 + Mus81 + DNA<br />
**[[4p0p]], [[4p0q]], [[4p0r]], [[4p0s]] – hENN EME1 + Mus81 + DNA<br />
**[[2kpf]] - mENN – mouse<br />
**[[2kpf]] - mENN – mouse<br />
Line 472: Line 501:
**[[4och]], [[4od6]] - DrENN SMR domain<br />
**[[4och]], [[4od6]] - DrENN SMR domain<br />
 +
**[[7vuf]] - TtENN core<br />
 +
**[[7vuk]] - TtENN core + ADP<br />
*Endoms ENN
*Endoms ENN
Line 498: Line 529:
**[[5dff]], [[5dfh]], [[5dfi]], [[5dfj]], [[5dg0]], [[5wn5]], [[5wn4]], [[5wn3]], [[5wn2]], [[5wn1]], [[5wn0]], [[6bos]], [[6w3l]], [[6w3n]], [[6w3q]], [[6w3u]] – hAPE1 + DNA<br />
**[[5dff]], [[5dfh]], [[5dfi]], [[5dfj]], [[5dg0]], [[5wn5]], [[5wn4]], [[5wn3]], [[5wn2]], [[5wn1]], [[5wn0]], [[6bos]], [[6w3l]], [[6w3n]], [[6w3q]], [[6w3u]] – hAPE1 + DNA<br />
**[[6bot]], [[6boq]], [[6bor]], [[6bou]], [[6bov]], [[6bow]], [[6p93]], [[6p94]], [[6w0q]], [[6w43]], [[6w4i]], [[6w4t]] – hAPE1 (mutant) + DNA<br />
**[[6bot]], [[6boq]], [[6bor]], [[6bou]], [[6bov]], [[6bow]], [[6p93]], [[6p94]], [[6w0q]], [[6w43]], [[6w4i]], [[6w4t]] – hAPE1 (mutant) + DNA<br />
 +
**[[7n3z]] – hAPE2 <br />
**[[7cd5]], [[7cd6]] – mAPE1 + DNA<br />
**[[7cd5]], [[7cd6]] – mAPE1 + DNA<br />
**[[6wcd]] – fAPE2 catalytic domain - frog<br />
**[[6wcd]] – fAPE2 catalytic domain - frog<br />
Line 509: Line 541:
**[[6uke]], [[6ukf]], [[6ukg]], [[6ukh]], [[6uki]] – ENN + DNA – ''Haemophilus parahaemolyticus'' <br />
**[[6uke]], [[6ukf]], [[6ukg]], [[6ukh]], [[6uki]] – ENN + DNA – ''Haemophilus parahaemolyticus'' <br />
 +
 +
*Cap-snatching ENN see [[RNA polymerase]]
 +
 +
*PA ENN see polymerase acidic protein in [[RNA polymerase]]
*'''Intron-encoded endonuclease'''
*'''Intron-encoded endonuclease'''

Current revision

3D structures of endonuclease

Updated on 19-February-2023

Proteopedia Page Contributors and Editors (what is this?)

Michal Harel

Retrieved from "http://52.214.119.220/wiki/index.php/Endonuclease_3D_structures"
Personal tools