3D structures of ubiquitin

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(New page: == 3D Structures of Ubiquitin == Updated on {{REVISIONDAY2}}-{{MONTHNAME|{{REVISIONMONTH}}}}-{{REVISIONYEAR}} - For a general description of the protein see Ubiquitin {{#tree:id=Organ...)
Current revision (09:23, 22 February 2024) (edit) (undo)
 
(5 intermediate revisions not shown.)
Line 7: Line 7:
**[[2ojr]], [[2nr2]], [[2fcq]], [[1ubi]], [[1ubq]], [[1xqq]], [[3ons]], [[4wzp]], [[5k9p]], [[4zqs]], [[5dk8]], [[4xof]], [[4xok]], [[4xol]], [[4zpz]] - hUBB - human<br />
**[[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 />
+
**[[2zcb]], [[2gbj]], [[2gbk]], [[2gbm]], [[2gbn]], [[2gbr]], [[2fcm]], [[2fcn]], [[2fcs]], [[1yiw]], [[1yj1]], [[1sif]], [[1ogw]], [[4hk2]], [[4hjk]], [[4pij]], [[4pih]], [[4pig]], [[7ooj]] - hUBB (mutant)<br />
**[[2kn5]], [[2klg]], [[2jzz]], [[2pe9]], [[2pea]], [[1g6j]], [[1d3z]], [[2kox]], [[2ld9]], [[2k25]], [[5ujl]], [[6v5d]] – hUBB – NMR<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 />
**[[1c3t]], [[1ud7]], [[2mi8]], [[2rsu]], [[2ru6]], [[6k4i]], [[5zd0]] - hUBB (mutant) - NMR<br />
Line 29: Line 29:
* Ubiquitin dimer
* Ubiquitin dimer
-
**[[2xk5]], [[3nob]], [[2xew]], [[3h7p]], [[3h7s]], [[2w9n]], [[2jf5]], [[3ns8]], [[3aul]], [[3axc]], [[5gob]], [[5goc]], [[5god]], [[5gog]], [[5goh]], [[5goi]], [[5goj]], [[5j8p]] – hDiUBB<br />
+
**[[2xk5]], [[3nob]], [[2xew]], [[3h7p]], [[3h7s]], [[2w9n]], [[2jf5]], [[3ns8]], [[3aul]], [[3axc]], [[5gob]], [[5goc]], [[5god]], [[5gog]], [[5goh]], [[5goi]], [[5goj]], [[5j8p]], [[7s6o]] – hDiUBB<br />
 +
**[[5emz]], [[5khy]], [[8ic9]] – hDiUBB (mutant)<br />
**[[2mbo]], [[2mbq]] – hDiUBB – NMR<br />
**[[2mbo]], [[2mbq]] – hDiUBB – NMR<br />
**[[2bgf]] – hDiUBB – chemical relaxation<br />
**[[2bgf]] – hDiUBB – chemical relaxation<br />
Line 43: Line 44:
**[[4hxd]] – hDiUBB + RNA polymerase <br />
**[[4hxd]] – hDiUBB + RNA polymerase <br />
**[[5o6t]] – hDiUBB + E3 UBB protein ligase XIAP<br />
**[[5o6t]] – hDiUBB + E3 UBB protein ligase XIAP<br />
 +
**[[7m4m]], [[7m4n]], [[7m4o]] – hDiUBB + E3 UBB protein ligase RNF216<br />
**[[2lvp]], [[2lvq]] – hDiUBB + E3 UBB protein ligase - NMR<br />
**[[2lvp]], [[2lvq]] – hDiUBB + E3 UBB protein ligase - NMR<br />
**[[4ksk]], [[4ksl]] – hDiUBB + Fam105B<br />
**[[4ksk]], [[4ksl]] – hDiUBB + Fam105B<br />
Line 54: Line 56:
**[[3wwq]] – hDiUBB + FAAP20 peptide <br />
**[[3wwq]] – hDiUBB + FAAP20 peptide <br />
**[[5ohp]], [[5ohn]], [[5ohk]] – hDiUBB + USP30<br />
**[[5ohp]], [[5ohn]], [[5ohk]] – hDiUBB + USP30<br />
 +
**[[7keo]] – hDiUBB + antigen binding fragment <br />
 +
**[[7eal]] – hDiUBB + ABIN-1 <br />
 +
**[[7uyh]] – hDiUBB + LOTA <br />
 +
**[[7uv5]] – hDiUBB+ papain-like protease<br />
**[[3ptf]], [[6if1]] – hDiUBB + UBB conjugating enzyme E2<br />
**[[3ptf]], [[6if1]] – hDiUBB + UBB conjugating enzyme E2<br />
**[[3a1q]] – mDiUBB+UBB interaction motif-containing protein <br />
**[[3a1q]] – mDiUBB+UBB interaction motif-containing protein <br />
**[[2znv]] – mDiUBB+hAMSH-like protease<br />
**[[2znv]] – mDiUBB+hAMSH-like protease<br />
 +
**[[7e62]] – mDiUBB (mutant) + TAB-2 <br />
**[[2kde]], [[2kdf]] – fDiUBB+26S proteasome non-ATPase regulatory subunit - NMR<br />
**[[2kde]], [[2kdf]] – fDiUBB+26S proteasome non-ATPase regulatory subunit - NMR<br />
**[[6jwi]] – yDiUBB + Npl4<br />
**[[6jwi]] – yDiUBB + Npl4<br />
Line 67: Line 74:
**[[4boz]] – hTriUBB + UBB thiolesterase <br />
**[[4boz]] – hTriUBB + UBB thiolesterase <br />
**[[3vuw]], [[3vux]] – hTriUBB + TNF α-induced proitein <br />
**[[3vuw]], [[3vux]] – hTriUBB + TNF α-induced proitein <br />
 +
**[[8f1f]] – hTriUBB + non-proteinogenic cyclic peptide<br />
 +
**[[7nbb]], [[8a67]] – hTriUBB + nanobody<br />
 +
**[[7eao]] – hTriUBB + ABIN-1<br />
* Ubiquitin tetramer
* Ubiquitin tetramer
-
**[[5go8]], [[5xdp]] – hTetraUBB <br />
+
**[[1f9j]], [[1tbe]] [[2o6v]], [[3alb]], [[3hm3]], [[5go8]], [[5xdp]] – hTetraUBB <br />
 +
**[[8e7o]] – hTetraUBB (mutant) <br />
**[[3tmp]] – hTetraUBB + deubiquitinase<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 />
**[[3zni]] – hTetraUBB + E3 UBB protein ligase + tyrosine protein kinase + UBB conjugating enzyme E2<br />
**[[5b83]] – hTetraUBB + optineurin<br />
**[[5b83]] – hTetraUBB + optineurin<br />
**[[3vuy]] – hTetraUBB + TNF α-induced proitein <br />
**[[3vuy]] – hTetraUBB + TNF α-induced proitein <br />
 +
**[[7eb9]] – hTetraUBB + ABIN-1<br />
 +
**[[7yui]] – hTetraUBB + HOIL-1<br />
* Polyubiquitin-B
* Polyubiquitin-B
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**[[5vey]] – hUBB + RNF169 + Histone H2A-H2B - NMR<br />
**[[5vey]] – hUBB + RNF169 + Histone H2A-H2B - NMR<br />
**[[5n38]] , [[5n2w]], [[6glc]] – hUBB + E3 UBB protein ligase PARKIN<br />
**[[5n38]] , [[5n2w]], [[6glc]] – hUBB + E3 UBB protein ligase PARKIN<br />
 +
**[[8c07]] – hUBB + E3 UBB protein ligase UBR5 – Cryo EM<br />
 +
**[[7ojx]] – hUBB + E3 + E2<br />
**[[6fyh]] – hUBB + E3 UBB protein ligase HUWE1<br />
**[[6fyh]] – hUBB + E3 UBB protein ligase HUWE1<br />
**[[6fx4]] – hUBB (mutant) + E3 UBB protein ligase SMURF2<br />
**[[6fx4]] – hUBB (mutant) + E3 UBB protein ligase SMURF2<br />
**[[6hek]] – hUBB + USP<br />
**[[6hek]] – hUBB + USP<br />
**[[5mnj]] – hUBB + E3 UBB protein ligase MDM2 + UbcH5B<br />
**[[5mnj]] – hUBB + E3 UBB protein ligase MDM2 + UbcH5B<br />
 +
**[[7ay2]] – hUBB + WD repeat-containing protein 48 + USP1<br />
**[[6hpr]] – hUBB + IAP1 + UbcH5B<br />
**[[6hpr]] – hUBB + IAP1 + UbcH5B<br />
**[[6njg]] – hUBB + vacuolar protein sorting-associated protein 27<br />
**[[6njg]] – hUBB + vacuolar protein sorting-associated protein 27<br />
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**[[6a6i]] – hUBB + Cockayne syndrome group B protein <br />
**[[6a6i]] – hUBB + Cockayne syndrome group B protein <br />
**[[5wvo]] – hUBB + hUBC + UCLH3<br />
**[[5wvo]] – hUBB + hUBC + UCLH3<br />
 +
**[[7w3u]] – hUBB + UBB carboxy terminal hydrolase 34<br />
 +
**[[8bs9]] – hUBB + UBB carboxy terminal hydrolase 36<br />
 +
**[[7ne8]], [[8h1t]], [[8sn0]], [[8sn3]], [[8sn4]], [[8sn5]], [[8sn6]], [[8sn7]], [[8sn8]], [[8sn9]], [[8sna]], [[8txv]], [[8txw]], [[8txx]], [[8wg5]] – hUBB in nucleosome – Cryo EM<br />
 +
**[[7f7x]] – hUBB + ubiquitin-2 - NMR<br />
 +
**[[8cmr]] – hUBB + OUT domain--containing protein<br />
 +
**[[7oje]] – hUBB + deubiquitinase<br />
 +
**[[6xz1]] – hUBB + HUWE1<br />
* Polyubiquitin-C
* Polyubiquitin-C
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**[[6ypt]] – hUBC + RNA replicase<br />
**[[6ypt]] – hUBC + RNA replicase<br />
**[[6tnf]] – hUBC + FANCI + FANCD2 + DNA - Cryo EM<br />
**[[6tnf]] – hUBC + FANCI + FANCD2 + DNA - Cryo EM<br />
 +
**[[7b5n]] – hUBC + Cul1 + Nedd8 + RBX1 + ARITH1 + Ube2L3 – Cryo EM<br />
 +
**[[7b5l]], [[7b5m]] – hUBC in SCF-RBR E3-E2 complex – Cryo EM<br />
 +
**[[8b3i]] – hUBC in CRl4CSA E2 complex – Cryo EM<br />
 +
**[[6z7v]] – hUBC + Mindy-2<br />
 +
**[[7npi]] – hPentaUBC + Mindy-2<br />
 +
**[[7tv4]] – hUBC + NEMO + RNF31 peptide<br />
 +
**[[7lmz]], [[7ln0]], [[7ln1]] – hHexaUBC + p97 – Cryo EM<br />
 +
**[[7owd]] – hUBC in UBC8/UBE2H-GID/CTLH complex – Cryo EM<br />
-
* Ubiquitin monomer bound to protein
+
* Ubiquitin monomer bound to a single protein
**[[3ofi]] – hUBB+insulin protease
**[[3ofi]] – hUBB+insulin protease
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**[[3rul]] – hUBB + dalvancin<br />
**[[3rul]] – hUBB + dalvancin<br />
**[[3vfk]] – hUBB + monodechloro-teicoplanin <br />
**[[3vfk]] – hUBB + monodechloro-teicoplanin <br />
-
**[[4ium]], [[4wur]], [[4mm3]] – hUBB+ papain-like protease<br />
+
**[[4ium]], [[4wur]], [[4mm3]], [[7f0u]], [[7mc9]], [[7rbr]], [[8cx9]], [[8eho]] – hUBB+ papain-like protease<br />
**[[2lz6]], [[2mcn]] – hUBB + CD2-associated protein<br />
**[[2lz6]], [[2mcn]] – hUBB + CD2-associated protein<br />
**[[2mbh]] – hUBB + Kreuppel-like factor<br />
**[[2mbh]] – hUBB + Kreuppel-like factor<br />
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**[[5lrw]] – hUBB (mutant)+ OTU domain containing protein 7B<br />
**[[5lrw]] – hUBB (mutant)+ OTU domain containing protein 7B<br />
**[[5lrx]] – hUBB (mutant)+ OTU domain containing protein 7C<br />
**[[5lrx]] – hUBB (mutant)+ OTU domain containing protein 7C<br />
-
**[[5kgf]] – hUBB + nucleosome - Cryo EM<br />
 
**[[2nbv]] – hUBB + proteasomal UBB receptor - NMR<br />
**[[2nbv]] – hUBB + proteasomal UBB receptor - NMR<br />
**[[5jg6]] – hUBB + anaphase promoting complex subunit 11<br />
**[[5jg6]] – hUBB + anaphase promoting complex subunit 11<br />
-
**[[6eqi]] – hUBB + NB696 + PINK1<br />
 
**[[5ohv]] – hUBB + K33-specific affimer<br />
**[[5ohv]] – hUBB + K33-specific affimer<br />
**[[4un2]] – hUBB + Dsk2 peptide<br />
**[[4un2]] – hUBB + Dsk2 peptide<br />
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**[[6upu]] – hUBB + otDUB<br />
**[[6upu]] – hUBB + otDUB<br />
**[[6pgv]] – hUBB + Josephine 2<br />
**[[6pgv]] – hUBB + Josephine 2<br />
 +
**[[8dmq]], [[8dms]] – hUBB + MAVL<br />
 +
**[[8efx]] – hUBB + OtDUB<br />
 +
**[[7jxv]] – hUBB + CALM<br />
 +
**[[7mic]] – hUBB + RNA replication protein<br />
 +
**[[8ivb]] – hUBB + Bcl2-L-7 - NMR<br />
 +
**[[8htd]], [[8hte]], [[8htf]] – hUBB + ADP-ribosyltransferase<br />
 +
**[[8efw]] – hUBB (mutant) + SDEA<br />
 +
**[[7rma]] – hUBB (mutant) + ANKRD13D<br />
**[[4m0w]] – bUBB + replicase polyprotein<br />
**[[4m0w]] – bUBB + replicase polyprotein<br />
**[[1uzx]] – bUBB+VPS23 UEV<br />
**[[1uzx]] – bUBB+VPS23 UEV<br />
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**[[2l00]] – yUBB + Zfand5<br />
**[[2l00]] – yUBB + Zfand5<br />
-
* Ubiquitin binary complex with protein
+
*Ubiquitin bound to multi proteins
-
**[[5l8w]], [[5cvn]], [[5cvo]] – hUBB + USP12 + WD repeat containing protein 48<br />
+
**[[5l8w]], [[5cvn]], [[5cvo]] – hUBB + UBB carboxy terminal hydrolase 12 + WD repeat containing protein 48<br />
 +
**[[1yx5]], [[1yx6]] - hUBB+26S proteasome non-ATPase regulatory subunit – NMR<br />
**[[4dhj]], [[4dhz]] – hUBB (mutant) + UBB thiolesterase + UBB aldehyde <br />
**[[4dhj]], [[4dhz]] – hUBB (mutant) + UBB thiolesterase + UBB aldehyde <br />
-
**[[5zq4]], [[5zq6]], [[5zq7]] – hUBB + SidE + nucleotide<br />
+
**[[5v1z]], [[5v1y]] – hUBB + RPN13 + RPN2<br />
-
**[[5v1z]], [[5v1y]], [[6oi4]] – hUBB + RPN13 + RPN2<br />
+
**[[5kgf]], [[7bwd]], [[7k6q]], [[7lyc]], [[7xcr]], [[8grm]], [[8svf]] – hUBB in nucleosome – Cryo EM<br />
-
**[[6eqi]] – hUBB + Nb696 + PINK1<br />
+
**[[7k6p]] – hUBB (mutant) in nucleosome – Cryo EM<br />
-
**[[5wvo]], [[6pzv]] – hUBB + DNMT1 + histone<br />
+
**[[6eqi]] – hUBB + NB696 + PINK1<br />
-
**[[6oaa]], [[6oa9]] – yUBB + Npl4 + cdc48 - Cryo EM<br />
+
**[[7dni]], [[7dnj]] – hUBB + MAVS + CARDS – Cryo EM<br />
-
**[[6t9l]] – hUBB in SAGA DUB module - Cryo EM<br />
+
**[[8dar]], [[8das]], [[8dat]], [[8dau]], [[8dav]], [[8daw]] – yUBB in UFD1/NPL4/CDC48 complex– Cryo EM<br />
-
**[[6wjd]], [[6wjn]], [[6ef0]], [[6ef1]], [[6ef2]] – hUBB in 26S proteasome - Cryo EM<br />
+
**[[8c83]] – yUBB + OTU2 + 40S ribosome– 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
* Ubiquitin complex with ubiquitination enzymes
-
**[[1fxt]], [[3oj4]], [[3ugb]], [[5dfl]], [[3k9p]], [[3a33]], [[5ulf]], [[5tut]], [[6nyo]], [[6jb6]], [[6jb7]] – hUBB + UBB conjugating enzyme E2<br />
+
**[[1fxt]], [[3oj4]], [[3ugb]], [[5dfl]], [[3k9p]], [[3a33]], [[5ulf]], [[5tut]], [[6nyo]], [[6jb6]], [[6jb7]], [[7m2k]] – hUBB + UBB conjugating enzyme E2<br />
-
**[[5bnb]], [[2kjh]], [[1zgu]], [[6d4p]], [[6d6i]] – hUBB (mutant) + UBB conjugating enzyme E2<br />
+
**[[5bnb]], [[2kjh]], [[1zgu]], [[6d4p]], [[6d6i]], [[7myf]], [[7myh]] – 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 />
+
**[[8st7]], [[8st8]], [[8st9]] – hUBB + E3 UBB-protein ligase SOPA<br />
 +
**[[7m3q]] – hUBB (mutant) + E3 UBB-protein ligase Smurf2<br />
 +
**[[7us1]] – hUBB (mutant) + E3 UBB-protein ligase Parkin<br />
 +
**[[5edv]], [[4whv]], [[5ait]], [[5aiu]], [[3jvz]], [[3jw0]], [[5udh]], [[5tte]], [[6w9d]], [[6w9d]], [[7bbd]], [[7bbf]], [[7r71]] – hUBB + UBB conjugating enzyme E2 + E3 UBB-protein ligase<br />
 +
**[[8eb0]] – hUBB + E3 UBB protein ligase RNF216 + UBB conjugating enzyme E2<br />
 +
**[[8ams]], [[8pjn]] – hPolyUBB-C + UBB conjugating enzyme E2 + E3 UBB-protein ligase<br />
 +
**[[8pql]] – hPolyUBB-C + UBB conjugating enzyme E2 R2 + E3 UBB-protein ligase RBX1 + cullin-2 + elongin –B + elongin-C + FEM1C – Cryo EM<br />
 +
**[[6ulh]], [[6ump]], [[6ums], [[7bxg]]] – hUBB (mutant) + UBB conjugating enzyme E2 + MavC<br />
 +
**[[7mex]], [[7mey]] – hUBB + UBB conjugating enzyme E2 + E3 UBB-protein ligase + degron – Cryo EM<br />
 +
**[7k5jl]] – UBB (mutant) + yUBB activating enzyme E1 + yUBB conjugating enzyme E2 - wheat<br />
**[[2gmi]] – hUBB + UBB conjugating enzyme E2<br />
**[[2gmi]] – hUBB + UBB conjugating enzyme E2<br />
**[[2fuh]] – hUBB + UBB conjugating enzyme E2 - NMR<br />
**[[2fuh]] – hUBB + UBB conjugating enzyme E2 - NMR<br />

Current revision

3D Structures of Ubiquitin

Updated on 22-February-2024 - For a general description of the protein see Ubiquitin

Proteopedia Page Contributors and Editors (what is this?)

Michal Harel

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