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.


3D structures of ubiquitin

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
(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
Line 96: Line 108:
**[[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 />
Line 112: Line 127:
**[[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
Line 131: Line 153:
**[[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
Line 165: Line 195:
**[[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 />
Line 190: Line 220:
**[[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 />
Line 199: Line 227:
**[[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 />
Line 219: Line 255:
**[[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

Retrieved from "http://52.214.119.220/wiki/index.php/3D_structures_of_ubiquitin"
Personal tools