Ubiquitin: Difference between revisions

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==[[3D structures of ubiquitin]]==
==[[3D structures of ubiquitin]]==
</StructureSection>
</StructureSection>
== 3D Structures of Ubiquitin ==


Updated on {{REVISIONDAY2}}-{{MONTHNAME|{{REVISIONMONTH}}}}-{{REVISIONYEAR}}
{{#tree:id=OrganizedByTopic|openlevels=0|
* Ubiquitin
**[[2ojr]], [[2nr2]], [[2fcq]], [[1ubi]], [[1ubq]], [[1xqq]], [[3ons]], [[4wzp]], [[5k9p]], [[4zqs]], [[5dk8]], [[4xof]], [[4xok]], [[4xol]], [[4zpz]] - hUBB - human<br />
**[[2zcb]], [[2gbj]], [[2gbk]], [[2gbm]], [[2gbn]], [[2gbr]], [[2fcm]], [[2fcn]], [[2fcs]], [[1yiw]], [[1yj1]], [[1sif]], [[1ogw]], [[4hk2]], [[4hjk]], [[4pij]], [[4pih]], [[4pig]] - hUBB (mutant)<br />
**[[2kn5]], [[2klg]], [[2jzz]], [[2pe9]], [[2pea]], [[1g6j]], [[1d3z]], [[2kox]], [[2ld9]], [[2k25]], [[5ujl]], [[6v5d]] – hUBB – NMR<br />
**[[1c3t]], [[1ud7]], [[2mi8]], [[2rsu]], [[2ru6]], [[6k4i]], [[5zd0]] - hUBB (mutant) - NMR<br />
**[[2m0x]] - hUBB - engineered – NMR<br />
**[[6gf1]] - hUBB D<br />
**[[6gf2]] - hUBB D - NMR<br />
**[[1gjz]], [[2l3z]] – hUBB N-terminal – NMR<br />
**[[1e0q]] - hUBB N-terminal  (mutant) – NMR<br />
**[[3q3f]] – hUBB/ribonuclease<br />
**[[2zcc]] – bUBB - bovine<br />
**[[2k39]] – fUBB – frog – NMR<br />
**[[2jwz]], [[1zw7]] – yUBB (mutant) – yeast<br />
**[[1cmx]] – yUBB (modified)<br />
**[[6kna]] – UBB - polyhedrosis virus - NMR<br />
* Ubiquitin+1 mutant
**[[2kx0]] – hUBB+1 – human – NMR<br />
**[[3k9o]] – hUBB+1+E2<br />
* Ubiquitin dimer
**[[2xk5]], [[3nob]], [[2xew]], [[3h7p]], [[3h7s]], [[2w9n]], [[2jf5]], [[3ns8]], [[3aul]], [[3axc]], [[5gob]], [[5goc]], [[5god]], [[5gog]], [[5goh]], [[5goi]], [[5goj]], [[5j8p]]  – hDiUBB<br />
**[[2mbo]], [[2mbq]] – hDiUBB – NMR<br />
**[[2bgf]] – hDiUBB – chemical relaxation<br />
**[[3m3j]], [[1aar]], [[3aui]], [[4s22]] – bDiUBB <br />
* Ubiquitin dimer bound to protein
**[[3a9j]], [[3a9k]], [[2wwz]], [[2wx0]], [[2wx1]] – hDiUBB+mitogen-activated protein kinase<br />
**[[3jsv]], [[2zvn]], [[2zvo]] – hDiUBB+NF-κ-b essential modulator<br />
**[[3dvg]], [[3dvn]] – hDiUBB+IGG1 fab light&heavy chains<br />
**[[3b08]], [[3b0a]] – hDiUBC + HOIL-1<br />
**[[3u30]] – hDiUBB + antibody<br />
**[[4hxd]] – hDiUBB + RNA polymerase <br />
**[[5o6t]] – hDiUBB + E3 UBB protein ligase XIAP<br />
**[[2lvp]], [[2lvq]] – hDiUBB + E3 UBB protein ligase - NMR<br />
**[[4ksk]], [[4ksl]] – hDiUBB + Fam105B<br />
**[[4fjv]] – hDiUBB + UBB thiolesterase <br />
**[[4bos]] – hDiUBB + UBB thiolesterase + OTUD2<br />
**[[4s1z]] – hDiUBB + ZranB1<br />
**[[6njd]] – hDiUBB + RavD<br />
**[[6isu]] – hDiUBB + UCHL3<br />
**[[5e6j]] – hDiUBB (mutant) + replicase polyprotein<br />
**[[2n13]] – hDiUBB + myosin peptide - NMR<br />
**[[3wwq]] – hDiUBB + FAAP20 peptide <br />
**[[5ohp]], [[5ohn]], [[5ohk]] – hDiUBB + USP30<br />
**[[3ptf]], [[6if1]] – hDiUBB + UBB conjugating enzyme E2<br />
**[[3a1q]] – mDiUBB+UBB interaction motif-containing protein <br />
**[[2znv]] – mDiUBB+hAMSH-like protease<br />
**[[2kde]], [[2kdf]] – fDiUBB+26S proteasome non-ATPase regulatory subunit - NMR<br />
**[[6jwi]] – yDiUBB + Npl4<br />
* Ubiquitin trimer
**[[5go7]], [[5gok]], [[5jby]], [[5jbv]], [[6oq1]], [[7cap]] – hTriUBB <br />
**[[3zlz]], [[5o44]] – hTriUBB (mutant) <br />
**[[6oq2]] – hTriUBB - NMR<br />
**[[4boz]] – hTriUBB + UBB thiolesterase <br />
**[[3vuw]], [[3vux]] – hTriUBB + TNF α-induced proitein <br />
* Ubiquitin tetramer
**[[5go8]], [[5xdp]] – hTetraUBB <br />
**[[3tmp]] – hTetraUBB + deubiquitinase<br />
**[[3alb]], [[3hm3]], [[2o6v]], [[1f9j]], [[1tbe]] – tetra-hUBB<br />
**[[3zni]] – hTetraUBB + E3 UBB protein ligase + tyrosine protein kinase + UBB conjugating enzyme E2<br />
**[[5b83]] – hTetraUBB  + optineurin<br />
**[[3vuy]] – hTetraUBB + TNF α-induced proitein <br />
* Polyubiquitin-B
**[[6nxl]], [[5x3n]] – hUBB<br />
**[[4zpz]], [[6qk9]], [[5w46]] – hUBB (mutant)<br />
**[[5xk5]], [[6kow]], [[6kox]], [[6qf8]] – hUBB - NMR<br />
**[[5x3m]], [[5x3o]], [[3x3m]] – hUBB + d-ubiquitin <br />
**[[3phd]] – hUBB + histone deacetylase 6
**[[3znh]] – hUBB + UBB thioesterase<br />
**[[7jms]] – hUBB + UBB replicase<br />
**[[5ydr]] – hUBB + DNMT1<br />
**[[6fdk]], [[6gzs]] – hUBB + Dub1<br />
**[[6ei1]], [[6fge]] – hUBB + ZUP1<br />
**[[6ei1]] – hUBB + ZUFSP<br />
**[[6cp2]] – hUBB + UbcH7 + SidC<br />
**[[6bva]], [[6byh]], [[6c16]] – hUBB + SKP1 + FBL10<br />
**[[4uf6]] – hUBB + UCHL5 + NF-κ-b-related protein<br />
**[[5vf0]] – hUBB + RAD18 - NMR<br />
**[[5vey]] – hUBB + RNF169 + Histone H2A-H2B - NMR<br />
**[[5n38]] , [[5n2w]], [[6glc]] – hUBB + E3 UBB protein ligase PARKIN<br />
**[[6fyh]] – hUBB + E3 UBB protein ligase HUWE1<br />
**[[6fx4]] – hUBB (mutant) + E3 UBB protein ligase SMURF2<br />
**[[6hek]] – hUBB + USP<br />
**[[5mnj]] – hUBB + E3 UBB protein ligase MDM2 + UbcH5B<br />
**[[6hpr]] – hUBB + IAP1 + UbcH5B<br />
**[[6njg]] – hUBB + vacuolar protein sorting-associated protein 27<br />
**[[5l8w]] – hUBB + WD repeat-containing protein 48 + USP12<br />
**[[5l8h]] – hUBB + WD repeat-containing protein 48 + USP46<br />
**[[6dgf]] – hUBB + USP2<br />
**[[5kyf]], [[5kye]], [[5kyd]], [[5kyc]]  – hUBB + USP7<br />
**[[6hei]] – hUBB + USP28<br />
**[[6ftx]] – hUBB + histones H4+H2A+H2B+H3.3C + DNA - Cryo EM<br />
**[[6byh]], [[6c16]] – hUBB + Skp1 + Fbl11<br />
**[[6bva]] – hUBB + Skp1 + Fbl10<br />
**[[6a6i]] – hUBB + Cockayne syndrome group B protein <br />
**[[5wvo]] – hUBB + hUBC + UCLH3<br />
* Polyubiquitin-C
**[[5af4]], [[4xyz]]. [[6k2u]] – hUBC <br />
**[[5af5]], [[5nl4]] – hUBC (mutant)<br />
**[[3znz]] – hUBC + otulin<br />
**[[4jqw]] – hUBC + NOD1 CARD<br />
**[[4k1r]] – hUBC + SST2<br />
**[[5oe7]] – hUBC + otulin<br />
**[[6kbe]] – hUBC + UBB thioesterase<br />
**[[6b7m]], [[6b70]] – hUBC + SDED<br />
**[[6aqr]] – hUBC + SAGA + UBP8 + SGF11 + SUS1 + SGF73<br />
**[[6s53]] – hUBC + TRIM1 + UB-conjugating enzyme E2<br />
**[[6t7f]] – hUBC + E3 UBB protein ligase + UB-conjugating enzyme E2<br />
**[[6nxk]] – hUBC + anaphase promoting complex subunit 2<br />
**[[6rya]] – hUBC + Dup1<br />
**[[6b7o]] – hUBC + SdeD<br />
**[[6ypt]] – hUBC + RNA replicase<br />
**[[6tnf]] – hUBC + FANCI + FANCD2 + DNA - Cryo EM<br />
* Ubiquitin monomer bound to protein
**[[3ofi]] – hUBB+insulin protease
**[[3i3t]], [[2ibi]], [[2ayo]], [[1nbf]], [[2wdt]], [[4i6l]], [[4i6n]], [[4ig7]], [[5l8h]], [[5jtj]], [[5cvm]], [[6crn]], [[6ml1]] - hUBB+ USP catalytic domain<br />
**[[3n3k]], [[3ifw]], [[3kvf]], [[3kw5]], [[3irt]], [[3mtn]], [[3ihp]], [[3v6c]], [[3v6e]]– hUBB (mutant)+hUBB carboxyl-terminal esterase catalytic domain<br />
**[[6cpm]] – hUBB (mutant) + USP15<br />
**[[2khw]] – hUBB+immunoglobulin G-binding protein G<br />
**[[1yx5]], [[1yx6]] - hUBB+26S proteasome non-ATPase regulatory subunit – NMR<br />
**[[2k6d]] – hUBB+SH3 domain-containing kinase-binding protein – NMR<br />
**[[2z59]] – hUBB+mProtein Adhesion-regulating molecule 1<br />
**[[2jy6]] – hUBB+hUbiquilin – NMR<br />
**[[3by4]], [[3c0r]], [[6k9p]] – hUBB+ UBB thioesterase<br />
**[[2hth]] – hUBB+vacuolar protein sorting protein<br />
**[[1s1q]] – hUBB+tumor susceptibility gene 101 protein<br />
**[[1q5w]] – hUBB+NPL4 zinc-fingers<br />
**[[2k8b]], [[2k8c]] – hUBB+phospholipase A2-activating protein fragment<br />
**[[2ktf]] – hUBB+hDNA polymerase IOTA<br />
**[[2l0f]] – hUBB (mutant)+hDNA polymerase IOTA<br />
**[[2kwu]], [[2kwv]] - hUBB+mDNA polymerase IOTA – mouse<br />
**[[2l0t]] – hUBB+signal transducing adapter molecule 2<br />
**[[3o65]] – hUBB+ataxin-3-like protein josephin domain<br />
**[[3oj3]] – hUBB+tumor necrosis factor α-induced protein 3<br />
**[[3prm]], [[3prp]] – hUBB+protein L<br />
**[[3pt2]] – hUBB+RNA polymerase OTU domain<br />
**[[5v5i]], [[5v5h]], [[5v5g]] - hUBB+RNA polymerase L<br />
**[[2rr9]] – hUBB + Uimc1<br />
**[[2g45]] – hUBB + isopeptidase T<br />
**[[2den]] – hUBB + immunoglobulin G binding protein/ubiquitin-like protein 7 - NMR<br />
**[[4xkl]] – hUBB + NDP52<br />
**[[4zfr]], [[4zft]] – hUBB + SST2<br />
**[[2j7q]] – hUBB + McmV tegument protein<br />
**[[3rul]] – hUBB + dalvancin<br />
**[[3vfk]] – hUBB + monodechloro-teicoplanin <br />
**[[4ium]], [[4wur]], [[4mm3]] – hUBB+ papain-like protease<br />
**[[2lz6]], [[2mcn]] – hUBB + CD2-associated protein<br />
**[[2mbh]] – hUBB + Kreuppel-like factor<br />
**[[3tbl]] – hUBB + PCNA<br />
**[[3vht]] – hUBB + GFP<br />
**[[4jio]] – hUBB + yBRO1<br />
**[[5af6]] – hUBB + TRABID<br />
**[[6q01]], [[6q00]] – hUBB + TDP2<br />
**[[6asr]] – hUBB + REV1<br />
**[[5vzm]] – hUBB + REV1 - NMR<br />
**[[5zq5]] – hUBB + SidE<br />
**[[6oam]] – hUBB + Dub2<br />
**[[5yij]] – hUBB + SdeA<br />
**[[6b7m]] – hUBB + SdeD<br />
**[[5ydr]] – hUBB + DNMT1<br />
**[[5xpk]] – hUBB + D-UBB<br />
**[[6ob1]] – hUBB + WHB - NMR<br />
**[[4un2]] – hUBB + Dsk2 peptide<br />
**[[4msq]], [[4msm]] – hUBB + AMSH-like protease<br />
**[[5yt6]] – hUBB + Tax1 binding protein<br />
**[[6q01]] – hUBB + RPN10<br />
**[[5jp3]] – hUBB + xanthomonas outer protein<br />
**[[6w9s]], [[6w9r]] – hUBB + OTU domain containing protein <br />
**[[5lrw]] – hUBB (mutant)+ OTU domain containing protein 7B<br />
**[[5lrx]] – hUBB (mutant)+ OTU domain containing protein 7C<br />
**[[5kgf]] – hUBB + nucleosome - Cryo EM<br />
**[[2nbv]] – hUBB + proteasomal UBB receptor - NMR<br />
**[[5jg6]] – hUBB + anaphase promoting complex subunit 11<br />
**[[6eqi]] – hUBB + NB696 + PINK1<br />
**[[5ohv]] – hUBB + K33-specific affimer<br />
**[[4un2]] – hUBB + Dsk2 peptide<br />
**[[4msq]], [[4msm]] – hUBB + AMSH-like protease<br />
**[[6upu]] – hUBB + otDUB<br />
**[[6pgv]] – hUBB + Josephine 2<br />
**[[4m0w]] – bUBB + replicase polyprotein<br />
**[[1uzx]] – bUBB+VPS23 UEV<br />
**[[2hd5]] - bUBB+hUSP catalytic domain<br />
**[[3ldz]] – bUBB+signal transducing adapter molecule<br />
**[[1v80]], [[1v81]] – bUBB/L40 ribosomal protein fusion - NMR<br />
**[[2dx5]], [[1p3q]] - bUBB+vacuolar protein sorting protein<br />
**[[2c7m]], [[2c7n]], [[2fid]], [[2fif]] – bUBB+RAB guanine nucleotide exchange factor<br />
**[[2d3g]] – bUBB+HRS-UIM<br />
**[[1wrd]] – bUBB+TOM1 GAT domain<br />
**[[1wr6]], [[1yd8]] - bUBB+GGA3 GAT domain<br />
**[[1uzx]] – bUBB+VPS23 UEV<br />
**[[4nql]] – mUBB + AMSH-like protease<br />
**[[2kdi]] – yUBB/UIM fusion <br />
**[[2jt4]] – yUBB fragment+cytoskeleton assembly control protein<br />
**[[1q0w]] - yUBB+vacuolar protein sorting protein<br />
**[[2g3q]] – yUBB+EDE1 UBA<br />
**[[1wr1]] – yUBB+DSK2P UBA<br />
**[[1otr]] – yUBB+CUE2<br />
**[[2l00]] – yUBB + Zfand5<br />
* Ubiquitin binary complex with protein
**[[5l8w]], [[5cvn]], [[5cvo]] – hUBB + USP12 + WD repeat containing protein 48<br />
**[[4dhj]], [[4dhz]] – hUBB (mutant) + UBB thiolesterase  + UBB aldehyde <br />
**[[5zq4]], [[5zq6]], [[5zq7]] – hUBB + SidE + nucleotide<br />
**[[5v1z]], [[5v1y]], [[6oi4]] – hUBB + RPN13 + RPN2<br />
**[[6eqi]] – hUBB + Nb696 + PINK1<br />
**[[5wvo]], [[6pzv]] – hUBB + DNMT1 + histone<br />
**[[6oaa]], [[6oa9]] – yUBB + Npl4 + cdc48 - Cryo EM<br />
**[[6t9l]] – hUBB in SAGA DUB module - Cryo EM<br />
**[[6wjd]], [[6wjn]], [[6ef0]], [[6ef1]], [[6ef2]] – hUBB in 26S proteasome - Cryo EM<br />
**[[6ttu]] – hUBB in cullin-ring-ube2d assembly - Cryo EM<br />
**[[6nj9]], [[6nog]], [[6nqa]], [[6jma]], [[6ven]], [[6j99]] – hUBB in nucleosome - Cryo EM<br />
**[[6xiq]] – hUBB (mutant) in ribosome - Cryo EM<br />
**[[6vae]], [[6vaf]] – hUBB + FANCI + FANCD2 + DNA<br />
* Ubiquitin complex with ubiquitination enzymes
**[[1fxt]], [[3oj4]], [[3ugb]], [[5dfl]], [[3k9p]], [[3a33]], [[5ulf]], [[5tut]], [[6nyo]], [[6jb6]], [[6jb7]]  – hUBB + UBB conjugating enzyme E2<br />
**[[5bnb]], [[2kjh]], [[1zgu]], [[6d4p]], [[6d6i]] – hUBB (mutant) + UBB conjugating enzyme E2<br />
**[[5edv]], [[4whv]], [[5ait]], [[5aiu]], [[3jvz]], [[3jw0]], [[5udh]], [[5tte]], [[6w9d]] – hUBB + UBB conjugating enzyme E2 + E3 UBB-protein ligase<br />
**[[2gmi]] – hUBB + UBB conjugating enzyme E2<br />
**[[2fuh]] – hUBB + UBB conjugating enzyme E2 - NMR<br />
**[[5d0k]], [[5d0m]], [[5ulk]], [[5ulh]] – hUBB + UBB conjugating enzyme E2 + RNF165<br />
**[[6jky]], [[6kl4]], [[6p5b]], [[6ulh]], [[6ump]], [[6ums]], [[7bxg]] – hUBB + UBB conjugating enzyme E2 + MvcA<br />
**[[6n13]] – hUBB + UBB conjugating enzyme E2 + parkin + phosphoUBB - NMR<br />
**[[2oob]], [[2qho]] – hUBB + E3 UBB protein ligase<br />
**[[2lvo]] – hUBB + E3 UBB protein ligase - NMR<br />
**[[5o76]] – hUBB + Zap70 peptide + E3-UBB-protein ligase CBL<br />
**[[4auq]] – hUBB + UBB conjugating enzyme E2 + livin<br />
**[[6dc6]] – hUBB + UBB activating enzyme E1<br />
**[[5tr4]] – bUBB + UBB activating enzyme E1<br />
**[[6djw]], [[6djx]] – bUBB + UBB activating enzyme E2 + parkin<br />
**[[6nya]] – UBB (mutant) + yUBB activating enzyme E1 + yUBB conjugating enzyme E2 - wheat <br />
**[[4q5h]], [[4q5e]] – yUBB + UBB conjugating enzyme E2 + OspG<br />
**[[3cmm]] – yUBB + UBB activating enzyme E1<br />
**[[5knl]] – yUBB (mutant) + UBB activating enzyme E1 + UBB conjugating enzyme E2 <br />
* Ubiquitin + ions
**[[3ehv]], [[3eec]], [[3efu]] – hUBB+ions<br />
**[[3n30]], [[4k7s]], [[4k7u]], [[4k7w]] – hUBB+Zn<br />
**[[3n32]] – hUBB+Pt<br />
**[[3h1u]] – bUBB+Cd<br />
* Ubiquitin + small molecule
**[[6e2b]] – bUBB+ pyridine derivative<br />
}}
==References==
==References==
<references />
<references />
[[Category:Topic Page]]
[[Category:Topic Page]]

Revision as of 07:22, 3 February 2021

Human ubiquitin (green) complex with ubiquitin-conjugating enzyme E2 (deep sky blue), 3k9p

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References

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