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Conserved domains on  [gi|469474345|pdb|4DKK|A]
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Chain A, Double-stranded RNA-binding protein Staufen homolog 1

Protein Classification

DSRM_STAU1_rpt5 domain-containing protein( domain architecture ID 11243092)

DSRM_STAU1_rpt5 domain-containing protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Staufen_C pfam16482
Staufen C-terminal domain; This is the C-terminal domain of Staufen proteins. It consists of ...
 5-115 6.96e-69

Staufen C-terminal domain; This is the C-terminal domain of Staufen proteins. It consists of an N-terminal Staufen-swapping motif (SSM) comprising two alpha helices, connected by a linker region to a dsRNA-binding-like domain ('RBD'). The 'RBD' has the fold of a functional dsRNA-binding domain, but lacks the residues required to bind RNA. This domain is responsible for dimerization, the SSM from one molecule interacts with the 'RBD' of another.


:

Pssm-ID: 465131  Cd Length: 110  Bit Score: 202.06  E-value: 6.96e-69
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
4DKK_A          5 SKATVTAMIARELLYGGTSPTAETILKNNISSGHVPHGPlTRPSEQLDYLSRVQGFQVEYKDFPKNNKNEFVSLINCSSQ 84
Cdd:pfam16482   1 SKATVTAAIARELLYGGTSPTAEAILKNNGKTGAVPCGL-VQPSQQLEYLARVQGFQVEYSDFPRQNKNEFLSLLTLSSQ 79

                          90       100       110
                  ....*....|....*....|....*....|.
4DKK_A         85 PPLISHGIGKDVESCHDMAALNILKLLSELD 115
Cdd:pfam16482  80 PVQMTHGIGSSLEASHDQAALSALKQLSEQG 110
 
Name Accession Description Interval E-value
Staufen_C pfam16482
Staufen C-terminal domain; This is the C-terminal domain of Staufen proteins. It consists of ...
 5-115 6.96e-69

Staufen C-terminal domain; This is the C-terminal domain of Staufen proteins. It consists of an N-terminal Staufen-swapping motif (SSM) comprising two alpha helices, connected by a linker region to a dsRNA-binding-like domain ('RBD'). The 'RBD' has the fold of a functional dsRNA-binding domain, but lacks the residues required to bind RNA. This domain is responsible for dimerization, the SSM from one molecule interacts with the 'RBD' of another.


Pssm-ID: 465131  Cd Length: 110  Bit Score: 202.06  E-value: 6.96e-69
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
4DKK_A          5 SKATVTAMIARELLYGGTSPTAETILKNNISSGHVPHGPlTRPSEQLDYLSRVQGFQVEYKDFPKNNKNEFVSLINCSSQ 84
Cdd:pfam16482   1 SKATVTAAIARELLYGGTSPTAEAILKNNGKTGAVPCGL-VQPSQQLEYLARVQGFQVEYSDFPRQNKNEFLSLLTLSSQ 79

                          90       100       110
                  ....*....|....*....|....*....|.
4DKK_A         85 PPLISHGIGKDVESCHDMAALNILKLLSELD 115
Cdd:pfam16482  80 PVQMTHGIGSSLEASHDQAALSALKQLSEQG 110
DSRM_STAU1_rpt5 cd19887
fifth double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen homolog ...
 46-115 1.46e-45

fifth double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen homolog 1 (Staufen 1) and similar proteins; Staufen 1 may play a role in specific positioning of mRNAs at given sites in the cell by cross-linking cytoskeletal and RNA components, and in stimulating their translation at the site. It binds double-stranded RNA (regardless of the sequence) and tubulin. Staufen 1 contains five double-stranded RNA binding motifs (DSRMs). This model describes the fifth motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380716  Cd Length: 70  Bit Score: 141.73  E-value: 1.46e-45
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
4DKK_A       46 RPSEQLDYLSRVQGFQVEYKDFPKNNKNEFVSLINCSSQPPLISHGIGKDVESCHDMAALNILKLLSELD 115
Cdd:cd19887   1 RPSEQLDYLSRVQGLQVEYKDFPKNNKNEFVSLINCSSQPPLISHGIGKDVESCHDMAALNILKLLSELD 70
 
Name Accession Description Interval E-value
Staufen_C pfam16482
Staufen C-terminal domain; This is the C-terminal domain of Staufen proteins. It consists of ...
 5-115 6.96e-69

Staufen C-terminal domain; This is the C-terminal domain of Staufen proteins. It consists of an N-terminal Staufen-swapping motif (SSM) comprising two alpha helices, connected by a linker region to a dsRNA-binding-like domain ('RBD'). The 'RBD' has the fold of a functional dsRNA-binding domain, but lacks the residues required to bind RNA. This domain is responsible for dimerization, the SSM from one molecule interacts with the 'RBD' of another.


Pssm-ID: 465131  Cd Length: 110  Bit Score: 202.06  E-value: 6.96e-69
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
4DKK_A          5 SKATVTAMIARELLYGGTSPTAETILKNNISSGHVPHGPlTRPSEQLDYLSRVQGFQVEYKDFPKNNKNEFVSLINCSSQ 84
Cdd:pfam16482   1 SKATVTAAIARELLYGGTSPTAEAILKNNGKTGAVPCGL-VQPSQQLEYLARVQGFQVEYSDFPRQNKNEFLSLLTLSSQ 79

                          90       100       110
                  ....*....|....*....|....*....|.
4DKK_A         85 PPLISHGIGKDVESCHDMAALNILKLLSELD 115
Cdd:pfam16482  80 PVQMTHGIGSSLEASHDQAALSALKQLSEQG 110
DSRM_STAU1_rpt5 cd19887
fifth double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen homolog ...
 46-115 1.46e-45

fifth double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen homolog 1 (Staufen 1) and similar proteins; Staufen 1 may play a role in specific positioning of mRNAs at given sites in the cell by cross-linking cytoskeletal and RNA components, and in stimulating their translation at the site. It binds double-stranded RNA (regardless of the sequence) and tubulin. Staufen 1 contains five double-stranded RNA binding motifs (DSRMs). This model describes the fifth motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380716  Cd Length: 70  Bit Score: 141.73  E-value: 1.46e-45
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
4DKK_A       46 RPSEQLDYLSRVQGFQVEYKDFPKNNKNEFVSLINCSSQPPLISHGIGKDVESCHDMAALNILKLLSELD 115
Cdd:cd19887   1 RPSEQLDYLSRVQGLQVEYKDFPKNNKNEFVSLINCSSQPPLISHGIGKDVESCHDMAALNILKLLSELD 70
DSRM_STAU_rpt5 cd19861
fifth double-stranded RNA binding motif of Drosophila melanogaster maternal effect protein ...
 47-114 6.80e-32

fifth double-stranded RNA binding motif of Drosophila melanogaster maternal effect protein Staufen and similar proteins; Staufen is a double-stranded RNA binding protein required both for the localization of maternal determinants to the posterior pole of the egg, oskar (osk) RNA, and for correct localization to the anterior pole, anchoring bicoid (bcd) RNA. The family also includes two Staufen homologs from vertebrates, Staufen 1 and Staufen 2. They are present in distinct ribonucleoprotein complexes and associate with different mRNAs. Staufen 1 may play a role in specific positioning of mRNAs at given sites in the cell by cross-linking cytoskeletal and RNA components, and in stimulating their translation at the site. It binds double-stranded RNA (regardless of the sequence) and tubulin. Staufen 2 is an RNA-binding protein required for the microtubule-dependent transport of neuronal RNA from the cell body to the dendrite. Staufen proteins contain five double-stranded RNA binding motifs (DSRMs). This model describes the fifth motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380690  Cd Length: 68  Bit Score: 106.92  E-value: 6.80e-32
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
4DKK_A       47 PSEQLDYLSRVQGFQVEYKDFPKNNKNEFVSLINCSSQPPLISHGIGKDVESCHDMAALNILKLLSEL 114
Cdd:cd19861   1 PKEQLEYLAKVLGFSVEFTDFPKGNKSEYLSLVSLGTEPPQVCHGSGSSVEESRDAAALNALKLLKEL 68
DSRM_STAU2_rpt5 cd19888
fifth double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen homolog ...
 46-113 4.94e-16

fifth double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen homolog 2 (Staufen 2) and similar proteins; Staufen 2 is an RNA-binding protein required for the microtubule-dependent transport of neuronal RNA from the cell body to the dendrite. Staufen 2 contains five double-stranded RNA binding motifs (DSRMs). This model describes the fifth motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380717  Cd Length: 68  Bit Score: 66.90  E-value: 4.94e-16
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
4DKK_A       46 RPSEQLDYLSRVQGFQVEYKDfpKNNKNEFVSLINCSSQpPLISHGIGKDVESCHDMAALNILKLLSE 113
Cdd:cd19888   2 QPSKQLEYLARIQGFQVQYSD--RQNGKECMTCLTLSPV-QMTFHGIGSSIEASHDQAALSALKQLSE 66
DSRM_PRKRA-like_rpt3 cd19864
third double-stranded RNA binding motif of PRKRA, TARBP2 and similar proteins; The family ...
 47-111 4.94e-11

third double-stranded RNA binding motif of PRKRA, TARBP2 and similar proteins; The family includes protein activator of the interferon-induced protein kinase (PRKRA) and the RISC-loading complex subunit TARBP2. PRKRA (also known as interferon-inducible double-stranded RNA-dependent protein kinase activator A, PKR-associated protein X (RAX), PKR-associating protein X, protein kinase, interferon-inducible double-stranded RNA-dependent activator, PACT, or HSD14) is a cellular activator for double-stranded RNA-dependent protein kinase during stress signaling. TARBP2 (also called TAR RNA-binding protein 2, or trans-activation-responsive RNA-binding protein (TRBP)) participates in the formation of the RNA-induced silencing complex (RISC). It is part of the RISC-loading complex (RLC), together with dicer1 and eif2c2/ago2, and is required to process precursor miRNAs. The family also includes Drosophila melanogaster Loquacious and similar proteins. Loquacious (Loqs) is a double-stranded RNA-binding domain (dsRBD) protein, a homolog of human TAR RNA binding protein (TRBP) that is a protein first identified as binding the HIV trans-activator RNA (TAR). Loqs interacts with Dicer1 (dmDcr1) to facilitate miRNA processing. PRKRA family proteins contain three double-stranded RNA binding motifs (DSRMs). This model describes the third motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure.


Pssm-ID: 380693  Cd Length: 72  Bit Score: 54.15  E-value: 4.94e-11
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
4DKK_A       47 PSEQLDYLSRVQGFQVEYKDFPKNNKN-EFVSLINCSSQPPLISHGIGKDVESCHDMAALNILKLL 111
Cdd:cd19864   3 YCELLQELAEEQKFKVTYVDIEELSSSgKYQCLVQLSTLPPTVCHGSGASLEEAKEEAARNALEYL 68
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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