9KHT | pdb_00009kht

cryo-EM structure of Ufd2/Ubc4-Ub in complex with K29-linked triUb (dimeric conformation)


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
L [auth b]SCOP2B SuperfamilyUBC-like 8034822 3000570 SCOP2B (2022-06-29)
J [auth B]SCOP2B SuperfamilyUBC-like 8034822 3000570 SCOP2B (2022-06-29)
K [auth a]SCOP2B SuperfamilyRING/U-box like 8052866 3000160 SCOP2B (2022-06-29)
K [auth a]SCOP2B SuperfamilyUfd2 core-like 8052864 3002149 SCOP2B (2022-06-29)
I [auth A]SCOP2B SuperfamilyUfd2 core-like 8052864 3002149 SCOP2B (2022-06-29)
I [auth A]SCOP2B SuperfamilyRING/U-box like 8052866 3000160 SCOP2B (2022-06-29)
D [auth d]SCOP2B SuperfamilyUbiquitin-like 8043829 3000157 SCOP2B (2022-06-29)
A [auth D]SCOP2B SuperfamilyUbiquitin-like 8043829 3000157 SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
J [auth B],
L [auth b]
PF00179Ubiquitin-conjugating enzyme (UQ_con)Ubiquitin-conjugating enzymeProteins destined for proteasome-mediated degradation may be ubiquitinated. Ubiquitination follows conjugation of ubiquitin to a conserved cysteine residue of UBC homologues. TSG101 is one of several UBC homologues that lacks this active site cystein ...Proteins destined for proteasome-mediated degradation may be ubiquitinated. Ubiquitination follows conjugation of ubiquitin to a conserved cysteine residue of UBC homologues. TSG101 is one of several UBC homologues that lacks this active site cysteine [4, 5].
Domain
I [auth A],
K [auth a]
PF10408Ubiquitin elongating factor core (Ufd2P_core)Ubiquitin elongating factor core- Family
I [auth A],
K [auth a]
PF04564U-box domain (U-box)U-box domainThe U-box is a domain of ~70 amino acids that is present in proteins from yeast to human. It consists of the beta-beta-alpha-beta-alpha- fold typical of U-box and RING domains. The central alpha helix is flanked by two prominent surface-exposed loop ...The U-box is a domain of ~70 amino acids that is present in proteins from yeast to human. It consists of the beta-beta-alpha-beta-alpha- fold typical of U-box and RING domains. The central alpha helix is flanked by two prominent surface-exposed loop regions. This domain is one class of E3 ligases, involved in the ubiquitination process [1-3]. This domain is related to the Ring finger Pfam:PF00097 but lacks the zinc binding residues [4].
Domain
PF00240Ubiquitin family (ubiquitin)Ubiquitin familyThis family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue) (see Swiss:Q02724), Nedd8 (see Swiss:P29595), Elongin B (see Swiss:Q15370), Rub1 (see Swiss:Q9SHE7), and Parkin (see Swiss:O60260). A number of them are thought to carry ...This family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue) (see Swiss:Q02724), Nedd8 (see Swiss:P29595), Elongin B (see Swiss:Q15370), Rub1 (see Swiss:Q9SHE7), and Parkin (see Swiss:O60260). A number of them are thought to carry a distinctive five-residue motif termed the proteasome-interacting motif (PIM), which may have a biologically significant role in protein delivery to proteasomes and recruitment of proteasomes to transcription sites [5].
Domain
A [auth D],
D [auth d]
PF00240Ubiquitin family (ubiquitin)Ubiquitin familyThis family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue) (see Swiss:Q02724), Nedd8 (see Swiss:P29595), Elongin B (see Swiss:Q15370), Rub1 (see Swiss:Q9SHE7), and Parkin (see Swiss:O60260). A number of them are thought to carry ...This family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue) (see Swiss:Q02724), Nedd8 (see Swiss:P29595), Elongin B (see Swiss:Q15370), Rub1 (see Swiss:Q9SHE7), and Parkin (see Swiss:O60260). A number of them are thought to carry a distinctive five-residue motif termed the proteasome-interacting motif (PIM), which may have a biologically significant role in protein delivery to proteasomes and recruitment of proteasomes to transcription sites [5].
Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
J [auth B],
L [auth b]
Ubiquitin-conjugating enzyme E2 4
I [auth A],
K [auth a]
E4 ubiquitin-protein ligase UFD2
Ubiquitin
A [auth D],
D [auth d]
Polyubiquitin-C

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
J [auth B],
L [auth b]
IPR016135Ubiquitin-conjugating enzyme/RWD-likeHomologous Superfamily
J [auth B],
L [auth b]
IPR000608Ubiquitin-conjugating (UBC), catalytic core domainDomain
J [auth B],
L [auth b]
IPR023313Ubiquitin-conjugating enzyme, active siteActive Site
I [auth A],
K [auth a]
IPR003613U-box domainDomain
I [auth A],
K [auth a]
IPR013083Zinc finger, RING/FYVE/PHD-typeHomologous Superfamily
I [auth A],
K [auth a]
IPR045132Ubiquitin conjugation factor E4Family
I [auth A],
K [auth a]
IPR019474Ubiquitin conjugation factor E4, coreDomain
IPR019954Ubiquitin conserved siteConserved Site
IPR050158Ubiquitin and ubiquitin-likeFamily
IPR011332Zinc-binding ribosomal proteinHomologous Superfamily
IPR000626Ubiquitin-like domainDomain
IPR038582Small ribosomal subunit protein eS31 eukaryotic-type superfamilyHomologous Superfamily
IPR002906Small ribosomal subunit protein eS31Domain
IPR019956Ubiquitin domainDomain
IPR029071Ubiquitin-like domain superfamilyHomologous Superfamily
A [auth D],
D [auth d]
IPR019954Ubiquitin conserved siteConserved Site
A [auth D],
D [auth d]
IPR000626Ubiquitin-like domainDomain
A [auth D],
D [auth d]
IPR019956Ubiquitin domainDomain
A [auth D],
D [auth d]
IPR050158Ubiquitin and ubiquitin-likeFamily
A [auth D],
D [auth d]
IPR029071Ubiquitin-like domain superfamilyHomologous Superfamily