3D structures of ubiquitin

From Proteopedia

Revision as of 09:16, 22 February 2024

3D Structures of Ubiquitin

Updated on 22-February-2024 - For a general description of the protein see Ubiquitin {{#tree:id=OrganizedByTopic|openlevels=0|

• Ubiquitin

• • 2ojr, 2nr2, 2fcq, 1ubi, 1ubq, 1xqq, 3ons, 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, 4pigת ]]7םםח[[ - 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, 5j8pת ]]7ד6ם[[ – hDiUBB
    
  • 5emz, 5khy, 8ic9 – hDiUBB (mutant)
    
  • 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
    
  • 7m4m, 7m4n, 7m4o – hDiUBB + E3 UBB protein ligase RNF216
    
  • 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
    
  • 7keo – hDiUBB + antigen binding fragment
    
  • 7eal – hDiUBB + ABIN-1
    
  • 7uyh – hDiUBB + LOTA
    
  • [7uv5]] – hDiUBB+ papain-like protease
    
  • 3ptf, 6if1 – hDiUBB + UBB conjugating enzyme E2
    
  • 3a1q – mDiUBB+UBB interaction motif-containing protein
    
  • 2znv – mDiUBB+hAMSH-like protease
    
  • 7e62 – mDiUBB (mutant) + TAB-2
    
  • 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
    
  • 8f1f – hTriUBB + non-proteinogenic cyclic peptide
    
  • 7nbb, 8a67 – hTriUBB + nanobody
    
  • 7eao – hTriUBB + ABIN-1
    

• Ubiquitin tetramer

• • 1f9j, 1tbe 2o6v, 3alb, 3hm3, 5go8, 5xdp – hTetraUBB
    
  • 8e7o – hTetraUBB (mutant)
    
  • 3tmp – hTetraUBB + deubiquitinase
    
  • 3zni – hTetraUBB + E3 UBB protein ligase + tyrosine protein kinase + UBB conjugating enzyme E2
    
  • 5b83 – hTetraUBB + optineurin
    
  • 3vuy – hTetraUBB + TNF α-induced proitein
    
  • 7eb9 – hTetraUBB + ABIN-1
    
  • 7yui – hTetraUBB + HOIL-1
    

• 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
    
  • 8c07 – hUBB + E3 UBB protein ligase UBR5 – Cryo EM
    
  • 7ojx – hUBB + E3 + E2
    
  • 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
    
  • 7ay2 – hUBB + WD repeat-containing protein 48 + USP1
    
  • 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
    
  • 7w3u – hUBB + UBB carboxy terminal hydrolase 34
    
  • 8bs9 – hUBB + UBB carboxy terminal hydrolase 36
    
  • [[7ne8i], 8h1t, 8sn0, 8sn3, 8sn4, 8sn5, 8sn6, 8sn7, 8sn8, 8sn9, 8sna, 8txv, 8txw, 8txx, 8wg5 – hUBB in nucleosome – Cryo EM
    
  • 7f7x – hUBB + ubiquitin-2 - NMR
    
  • 8cmr – hUBB + OUT domain--containing protein
    
  • 7oje – hUBB + deubiquitinase
    
  • 6xz1 – hUBB + HUWE1
    

• 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
    
  • 7b5n – hUBC + Cul1 + Nedd8 + RBX1 + ARITH1 + Ube2L3 – Cryo EM
    
  • 7b5l, 7b5m – hUBC in SCF-RBR E3-E2 complex – Cryo EM
    
  • 8b3i – hUBC in CRl4CSA E2 complex – Cryo EM
    
  • 6z7v – hUBC + Mindy-2
    
  • 7npi – hPentaUBC + Mindy-2
    
  • 7tv4 – hUBC + NEMO + RNF31 peptide
    
  • 7lmz, 7ln0, 7ln1 – hHexaUBC + p97 – Cryo EM
    
  • 7owd – hUBC in UBC8/UBE2H-GID/CTLH complex – Cryo EM
    

• Ubiquitin monomer bound to a single 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, 7f0u, 7mc9, 7rbr, 8cx9, 8eho – 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
    
  • 2nbv – hUBB + proteasomal UBB receptor - NMR
    
  • 5jg6 – hUBB + anaphase promoting complex subunit 11
    
  • 5ohv – hUBB + K33-specific affimer
    
  • 4un2 – hUBB + Dsk2 peptide
    
  • 4msq, 4msm – hUBB + AMSH-like protease
    
  • 6upu – hUBB + otDUB
    
  • 6pgv – hUBB + Josephine 2
    
  • 8dmq, 8dms – hUBB + MAVL
    
  • 8efx – hUBB + OtDUB
    
  • 7jxv – hUBB + CALM
    
  • 7mic – hUBB + RNA replication protein
    
  • 8ivb – hUBB + Bcl2-L-7 - NMR
    
  • 8htd, 8hte, 8htf – hUBB + ADP-ribosyltransferase
    
  • 8efw – hUBB (mutant) + SDEA
    
  • 7rma – hUBB (mutant) + ANKRD13D
    
  • 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 bound to multi proteins

• • 5l8w, 5cvn, 5cvo – hUBB + UBB carboxy terminal hydrolase 12 + WD repeat containing protein 48
    
  • 1yx5, 1yx6 - hUBB+26S proteasome non-ATPase regulatory subunit – NMR
    
  • 4dhj, 4dhz – hUBB (mutant) + UBB thiolesterase + UBB aldehyde
    
  • 5v1z, 5v1y – hUBB + RPN13 + RPN2
    
  • 5kgf, 7bwd, 7k6q, 7lyc, 7xcr, 8grm, 8svf – hUBB in nucleosome – Cryo EM
    
  • 7k6p – hUBB (mutant) in nucleosome – Cryo EM
    
  • 6eqi – hUBB + NB696 + PINK1
    
  • 7dni, 7dnj – hUBB + MAVS + CARDS – Cryo EM
    
  • 8dar, 8das, 8dat, 8dau, 8dav, 8daw – yUBB in UFD1/NPL4/CDC48 complex– Cryo EM
    
  • 8c83 – yUBB + OTU2 + 40S ribosome– Cryo EM
    

• Ubiquitin complex with ubiquitination enzymes

• • 1fxt, 3oj4, 3ugb, 5dfl, 3k9p, 3a33, 5ulf, 5tut, 6nyo, 6jb6, 6jb7, 7m2k – hUBB + UBB conjugating enzyme E2
    
  • 5bnb, 2kjh, 1zgu, 6d4p, 6d6i, 7myf, 7myh – hUBB (mutant) + UBB conjugating enzyme E2
    
  • 8st7, 8st8, 8st9 – hUBB + E3 UBB-protein ligase SOPA
    
  • 7m3q – hUBB (mutant) + E3 UBB-protein ligase Smurf2
    
  • 7us1 – hUBB (mutant) + E3 UBB-protein ligase Parkin
    
  • 5edv, 4whv, 5ait, 5aiu, 3jvz, 3jw0, 5udh, 5tte, 6w9d, 6w9d, 7bbd, 7bbf, 7r71 – hUBB + UBB conjugating enzyme E2 + E3 UBB-protein ligase
    
  • 8eb0 – hUBB + E3 UBB protein ligase RNF216 + UBB conjugating enzyme E2
    
  • 8ams, 8pjn – hPolyUBB-C + UBB conjugating enzyme E2 + E3 UBB-protein ligase
    
  • 8pql – hPolyUBB-C + UBB conjugating enzyme E2 R2 + E3 UBB-protein ligase RBX1 + cullin-2 + elongin –B + elongin-C + FEM1C – Cryo EM
    
  • 6ulh, 6ump, [[6ums], 7bxg] – hUBB (mutant) + UBB conjugating enzyme E2 + MavC
    
  • 7mex, 7mey – hUBB + UBB conjugating enzyme E2 + E3 UBB-protein ligase + degron – Cryo EM
    
  • [7k5jl]] – UBB (mutant) + yUBB activating enzyme E1 + yUBB conjugating enzyme E2 - wheat
    
  • 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
    

}}