9RWZ | pdb_00009rwz

ZSWIM8-CUL3 complex bound to AGO2-miR-7-CYRANO

External Resource: Annotation


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
CSCOP2B SuperfamilyUbiquitin-like 8038575 3000157 SCOP2B (2022-06-29)
BSCOP2B SuperfamilyUbiquitin-like 8038575 3000157 SCOP2B (2022-06-29)
ASCOP2B SuperfamilyMid domain of argonaute 8053594 3002210 SCOP2B (2022-06-29)
ASCOP2B SuperfamilyRibonuclease H-like 8053661 3000143 SCOP2B (2022-06-29)
ASCOP2B SuperfamilyRNA-binding domain, RBD 8053657 3000110 SCOP2B (2022-06-29)
ASCOP2B SuperfamilyPAZ domain 8053659 3001750 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
ERVPe9rwzE1 A: beta barrelsX: cradle loop barrelH: RIFT-relatedT: acid proteaseF: RVPECOD (v294.2)
DRVPe9rwzD1 A: beta barrelsX: cradle loop barrelH: RIFT-relatedT: acid proteaseF: RVPECOD (v294.2)
CRVPe9rwzC1 A: beta barrelsX: cradle loop barrelH: RIFT-relatedT: acid proteaseF: RVPECOD (v294.2)
BRVPe9rwzB1 A: beta barrelsX: cradle loop barrelH: RIFT-relatedT: acid proteaseF: RVPECOD (v294.2)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
J [auth N],
K [auth M]		PF21055ZSWIM4-8, C-terminal (ZSWIM4-8_C)ZSWIM4-8, C-terminal- Repeat
J [auth N],
K [auth M]		PF25572ZSWIM8, TPR repeats (TPR_ZSWIM8)ZSWIM8, TPR repeats- Repeat
G [auth H],
H [auth I]		PF00888Cullin alpha solenoid domain (Cullin)Cullin alpha solenoid domain- Repeat
D, E
PF03931Skp1 family, tetramerisation domain (Skp1_POZ)Skp1 family, tetramerisation domainDomain
B, C
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
PF02171Piwi domain (Piwi)Piwi domainThis domain is found in the protein Piwi and its relatives. The function of this domain is the dsRNA guided hydrolysis of ssRNA. Determination of the crystal structure of Argonaute reveals that PIWI is an RNase H domain, and identifies Argonaute as S ...This domain is found in the protein Piwi and its relatives. The function of this domain is the dsRNA guided hydrolysis of ssRNA. Determination of the crystal structure of Argonaute reveals that PIWI is an RNase H domain, and identifies Argonaute as Slicer, the enzyme that cleaves mRNA in the RNAi RISC complex [2]. In addition, Mg+2 dependence and production of 3'-OH and 5' phosphate products are shared characteristics of RNaseH and RISC. The PIWI domain core has a tertiary structure belonging to the RNase H family of enzymes. RNase H fold proteins all have a five-stranded mixed beta-sheet surrounded by helices. By analogy to RNase H enzymes which cleave single-stranded RNA guided by the DNA strand in an RNA/DNA hybrid, the PIWI domain can be inferred to cleave single-stranded RNA, for example mRNA, guided by double stranded siRNA.
Domain
PF02170PAZ domain (PAZ)PAZ domainThis domain is named PAZ after the proteins Piwi Argonaut and Zwille. This domain is found in two families of proteins that are involved in post-transcriptional gene silencing. These are the Piwi family and the Dicer family, that includes the Carpel ...This domain is named PAZ after the proteins Piwi Argonaut and Zwille. This domain is found in two families of proteins that are involved in post-transcriptional gene silencing. These are the Piwi family and the Dicer family, that includes the Carpel factory protein. The function of the domains is unknown but has been suggested to mediate complex formation between proteins of the Piwi and Dicer families by hetero-dimerisation. The three-dimensional structure of this domain has been solved [2-4]. The PAZ domain is composed of two subdomains. One subdomain is similar to the OB fold, albeit with a different topology. The OB-fold is well known as a single-stranded nucleic acid binding fold. The second subdomain is composed of a beta-hairpin followed by an alpha-helix. The PAZ domains shows low-affinity nucleic acid binding and appears to interact with the 3' ends of single-stranded regions of RNA in the cleft between the two subdomains. PAZ can bind the characteristic two-base 3' overhangs of siRNAs, indicating that although PAZ may not be a primary nucleic acid binding site in Dicer or RISC, it may contribute to the specific and productive incorporation of siRNAs and miRNAs into the RNAi pathway.
Domain
PF16486N-terminal domain of argonaute (ArgoN)N-terminal domain of argonauteArgoN is the N-terminal domain of argonaute proteins in eukaryotes. ArgoN is composed of an antiparallel four-stranded beta sheet core that has two alpha helices positioned along one face of the sheet and an extended beta strand towards its N-terminu ...ArgoN is the N-terminal domain of argonaute proteins in eukaryotes. ArgoN is composed of an antiparallel four-stranded beta sheet core that has two alpha helices positioned along one face of the sheet and an extended beta strand towards its N-terminus. The core fold of the N domain most closely resembles the catalytic domain of replication-initiator protein Rep. The N domain is linked to the PAZ domain via linker 1 region, and together these three regions are designated the PAZ-containing lobe of argonaute.
Domain
PF16488Argonaute linker 2 domain (ArgoL2)Argonaute linker 2 domain- Family
PF16487Mid domain of argonaute (ArgoMid)Mid domain of argonauteThe ArgoMid domain is found to be part of the Piwi-lobe of the argonaute proteins. It is composed of a parallel four-stranded beta-sheet core surrounded by four alpha-helices and two additional short alpha-helices. It most closely resembles the amino ...The ArgoMid domain is found to be part of the Piwi-lobe of the argonaute proteins. It is composed of a parallel four-stranded beta-sheet core surrounded by four alpha-helices and two additional short alpha-helices. It most closely resembles the amino terminal tryptic core of the E.coli lactose repressor. There is an extensive interface between the Mid and the Piwi domains. The conserved C-terminal half or the Mid has extensive interactions with Piwi, with a deep basic pocket on the surface of the `Mid adjacent to the interface with Piwi. The Mid carries a binding pocket for the 5' phosphate overhang of the guide strand of DNA [1]. The N, Mid, and Piwi domains form a base upon which the PAZ domain sits, resembling a duck. The 5' phosphate and the U1 base are held in place by a conserved network of interactions from protein residues of the Mid and Piwi domains in order to place the guide uniquely in the proper position observed in all Argonaute-RNA complexes [2].
Domain
PF08699Argonaute linker 1 domain (ArgoL1)Argonaute linker 1 domainArgoL1 is a region found in argonaute [1] proteins. It normally co-occurs with Pfam:PF02179 and Pfam:PF02171. It is a linker region between the N-terminal and the PAZ domains. It contains an alpha-helix packed against a three-stranded antiparallel be ...ArgoL1 is a region found in argonaute [1] proteins. It normally co-occurs with Pfam:PF02179 and Pfam:PF02171. It is a linker region between the N-terminal and the PAZ domains. It contains an alpha-helix packed against a three-stranded antiparallel beta-sheet with two long beta-strands (beta8 and beta9) of the sheet spanning one face of the adjacent N and PAZ domains. L1 together with linker 2, L2, PAZ and ArgoN forms a compact global fold [2].
Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
J [auth N],
K [auth M]		Zinc finger SWIM domain-containing protein 8
I [auth T]CYRANO trigger RNA---
G [auth H],
H [auth I]		Cullin-3
F [auth G]miR-7---
D, E
Elongin-C
B, C
Elongin-B
Protein argonaute-2

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
J [auth N],
K [auth M]		IPR007527Zinc finger, SWIM-typeDomain
J [auth N],
K [auth M]		IPR048370ZSWIM4-8, C-terminalDomain
J [auth N],
K [auth M]		IPR057945ZSWIM8, TPR repeatsDomain
G [auth H],
H [auth I]		IPR045093CullinFamily
G [auth H],
H [auth I]		IPR016158Cullin homology domainDomain
G [auth H],
H [auth I]		IPR001373Cullin, N-terminalDomain
G [auth H],
H [auth I]		IPR036388Winged helix-like DNA-binding domain superfamilyHomologous Superfamily
G [auth H],
H [auth I]		IPR036390Winged helix DNA-binding domain superfamilyHomologous Superfamily
G [auth H],
H [auth I]		IPR016157Cullin, conserved siteConserved Site
G [auth H],
H [auth I]		IPR059120Cullin-like, alpha+beta domainDomain
G [auth H],
H [auth I]		IPR019559Cullin, neddylation domainDomain
G [auth H],
H [auth I]		IPR036317Cullin homology domain superfamilyHomologous Superfamily
G [auth H],
H [auth I]		IPR016159Cullin repeat-like-containing domain superfamilyHomologous Superfamily
D, E
IPR016073SKP1 component, POZ domainDomain
D, E
IPR001232S-phase kinase-associated protein 1-likeFamily
D, E
IPR039948Elongin-CFamily
D, E
IPR011333SKP1/BTB/POZ domain superfamilyHomologous Superfamily
B, C
IPR000626Ubiquitin-like domainDomain
B, C
IPR039049Elongin BFamily
B, C
IPR029071Ubiquitin-like domain superfamilyHomologous Superfamily
IPR036397Ribonuclease H superfamilyHomologous Superfamily
IPR014811Argonaute, linker 1 domainDomain
IPR032472Argonaute linker 2 domainDomain
IPR045246Argonaute-like, PIWI domainDomain
IPR003165Piwi domainDomain
IPR012337Ribonuclease H-like superfamilyHomologous Superfamily
IPR003100PAZ domainDomain
IPR028602Protein argonaute-2Family
IPR032473Protein argonaute, Mid domainDomain
IPR036085PAZ domain superfamilyHomologous Superfamily
IPR032474Protein argonaute, N-terminalDomain

Pharos: Disease Associations Pharos Homepage Annotation

ChainsDrug Target  Associated Disease
J [auth N],
K [auth M]		:  A7E2V4
G [auth H],
H [auth I]		:  Q13618
D, E
:  Q15369
B, C
:  Q15370
:  Q9UKV8