Ubiquitin

spinqualitylabelsall models Human ubiquitin (green) complex with ubiquitin-conjugating enzyme E2 (deep sky blue), 3k9p Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Function Ubiquitin (UBB) is found in almost all cells. It binds to proteins tagging them for destruction in the proteasome. UBB is activated by the UBB-activating enzymes E1, E2 and E3. UBB+1 is a frameshifted mutant of UBB observed in several diseases. A dimer of UBB (DiUBB) is formed by linkage of K48 to the C-terminus of a second UBB molecule. At least 4 UBB molecules are needed to tag a protein for the proteasome. Human ubiquitin interactions with ubiquitin-conjugating enzyme E2 (3k9p). For details see Ubiquitin Structure & Function Ubiquitin salt bridge discussion Ubiquitin chains. Additional Resources See also: Tumor susceptibility gene 101 SUMO Disease The UBB-proteasome system deregulation has been implicated in the pathogenesis of many neurodegenerative disorders like Alzheimer's disease, Parkinson disease, Huntington disease, Prion-like lethal disorders and in genetic diseases like cystic fibrosis, angelman's syndrome, Liddle syndrome and many cancers.

3D Structures of Ubiquitin

Updated on 03-February-2021

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

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