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Conserved domains on  [gi|557878616|ref|NP_001273608|]
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la-related protein 6 isoform 3 [Homo sapiens]

Protein Classification

RRM_LARP6 and SUZ-C domain-containing protein( domain architecture ID 10188295)

RRM_LARP6 and SUZ-C domain-containing protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RRM_LARP6 cd12289
RNA recognition motif (RRM) found in La-related protein 6 (LARP6) and similar proteins; This ...
 1-108 2.13e-44

RNA recognition motif (RRM) found in La-related protein 6 (LARP6) and similar proteins; This subfamily corresponds to the RRM of LARP6, also termed Acheron (Achn), a novel member of the lupus antigen (La) family. It is expressed predominantly in neurons and muscle in vertebrates. LARP6 functions as a key regulatory protein that may play a role in mediating a variety of developmental and homeostatic processes in animals, including myogenesis, neurogenesis and possibly metastasis. LARP6 binds to Ca2+/calmodulin-dependent serine protein kinase (CASK), and forms a complex with inhibitor of differentiation transcription factors. It is structurally related to the La autoantigen and contains a La motif (LAM), nuclear localization and export (NLS and NES) signals, and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


:

Pssm-ID: 409731 [Multi-domain]  Cd Length: 93  Bit Score: 146.29  E-value: 2.13e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557878616   1 MLLVYDLYLSPKlwalatpqkngrvqekVMEHLLKLFGTFGVISSVRILKPGRELPPDIRRISSRYSQVGTQECAIVEFE 80
Cdd:cd12289    2 TVVAYNLPLNPK----------------SIEHVSKLFSPCGEISLIRILRPGRTIPPDVKRHSNRHSQLGTKECAIVEFE 65

                         90       100
                 ....*....|....*....|....*...
gi 557878616  81 EVEAAIKAHEFMITESQGKENMKAVLIG 108
Cdd:cd12289   66 EVEAARKAHELLGAEDDGKGGIKVVLLG 93
SUZ-C pfam12901
SUZ-C motif; The SUZ-C domain is a conserved motif found in one or more copies in several ...
 268-298 1.31e-06

SUZ-C motif; The SUZ-C domain is a conserved motif found in one or more copies in several RNA-binding proteins. It is always found at the C-terminus of the protein and appear to be required for localization of the protein to specific subcellular structures. It was first characterized in the C.elegans protein Szy-20 which localizes to the centrosome. It is widely distributed in eukaryotes.


:

Pssm-ID: 463745  Cd Length: 33  Bit Score: 44.07  E-value: 1.31e-06
                          10        20        30
                  ....*....|....*....|....*....|.
gi 557878616  268 PLLSRKMQTADGLPVGVLRLPRGPDNTRGFH 298
Cdd:pfam12901   1 RLKSVSLDDANRPNNNVLRQPRGPDGSKGFR 31
 
Name Accession Description Interval E-value
RRM_LARP6 cd12289
RNA recognition motif (RRM) found in La-related protein 6 (LARP6) and similar proteins; This ...
 1-108 2.13e-44

RNA recognition motif (RRM) found in La-related protein 6 (LARP6) and similar proteins; This subfamily corresponds to the RRM of LARP6, also termed Acheron (Achn), a novel member of the lupus antigen (La) family. It is expressed predominantly in neurons and muscle in vertebrates. LARP6 functions as a key regulatory protein that may play a role in mediating a variety of developmental and homeostatic processes in animals, including myogenesis, neurogenesis and possibly metastasis. LARP6 binds to Ca2+/calmodulin-dependent serine protein kinase (CASK), and forms a complex with inhibitor of differentiation transcription factors. It is structurally related to the La autoantigen and contains a La motif (LAM), nuclear localization and export (NLS and NES) signals, and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 409731 [Multi-domain]  Cd Length: 93  Bit Score: 146.29  E-value: 2.13e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557878616   1 MLLVYDLYLSPKlwalatpqkngrvqekVMEHLLKLFGTFGVISSVRILKPGRELPPDIRRISSRYSQVGTQECAIVEFE 80
Cdd:cd12289    2 TVVAYNLPLNPK----------------SIEHVSKLFSPCGEISLIRILRPGRTIPPDVKRHSNRHSQLGTKECAIVEFE 65

                         90       100
                 ....*....|....*....|....*...
gi 557878616  81 EVEAAIKAHEFMITESQGKENMKAVLIG 108
Cdd:cd12289   66 EVEAARKAHELLGAEDDGKGGIKVVLLG 93
SUZ-C pfam12901
SUZ-C motif; The SUZ-C domain is a conserved motif found in one or more copies in several ...
 268-298 1.31e-06

SUZ-C motif; The SUZ-C domain is a conserved motif found in one or more copies in several RNA-binding proteins. It is always found at the C-terminus of the protein and appear to be required for localization of the protein to specific subcellular structures. It was first characterized in the C.elegans protein Szy-20 which localizes to the centrosome. It is widely distributed in eukaryotes.


Pssm-ID: 463745  Cd Length: 33  Bit Score: 44.07  E-value: 1.31e-06
                          10        20        30
                  ....*....|....*....|....*....|.
gi 557878616  268 PLLSRKMQTADGLPVGVLRLPRGPDNTRGFH 298
Cdd:pfam12901   1 RLKSVSLDDANRPNNNVLRQPRGPDGSKGFR 31
RRM smart00360
RNA recognition motif;
31-92 4.44e-04

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 37.96  E-value: 4.44e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 557878616    31 EHLLKLFGTFGVISSVRIlkpgrelPPDIRRISSRysqvGtqeCAIVEFEEVEAAIKAHEFM 92
Cdd:smart00360  14 EELRELFSKFGKVESVRL-------VRDKETGKSK----G---FAFVEFESEEDAEKALEAL 61
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
 33-88 6.15e-03

RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteriztic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease.


Pssm-ID: 425453 [Multi-domain]  Cd Length: 70  Bit Score: 34.90  E-value: 6.15e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 557878616   33 LLKLFGTFGVISSVRIlkpgrelPPDIRRISSRYsqvgtqecAIVEFEEVEAAIKA 88
Cdd:pfam00076  15 LKDLFSKFGPIKSIRL-------VRDETGRSKGF--------AFVEFEDEEDAEKA 55
 
Name Accession Description Interval E-value
RRM_LARP6 cd12289
RNA recognition motif (RRM) found in La-related protein 6 (LARP6) and similar proteins; This ...
 1-108 2.13e-44

RNA recognition motif (RRM) found in La-related protein 6 (LARP6) and similar proteins; This subfamily corresponds to the RRM of LARP6, also termed Acheron (Achn), a novel member of the lupus antigen (La) family. It is expressed predominantly in neurons and muscle in vertebrates. LARP6 functions as a key regulatory protein that may play a role in mediating a variety of developmental and homeostatic processes in animals, including myogenesis, neurogenesis and possibly metastasis. LARP6 binds to Ca2+/calmodulin-dependent serine protein kinase (CASK), and forms a complex with inhibitor of differentiation transcription factors. It is structurally related to the La autoantigen and contains a La motif (LAM), nuclear localization and export (NLS and NES) signals, and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 409731 [Multi-domain]  Cd Length: 93  Bit Score: 146.29  E-value: 2.13e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 557878616   1 MLLVYDLYLSPKlwalatpqkngrvqekVMEHLLKLFGTFGVISSVRILKPGRELPPDIRRISSRYSQVGTQECAIVEFE 80
Cdd:cd12289    2 TVVAYNLPLNPK----------------SIEHVSKLFSPCGEISLIRILRPGRTIPPDVKRHSNRHSQLGTKECAIVEFE 65

                         90       100
                 ....*....|....*....|....*...
gi 557878616  81 EVEAAIKAHEFMITESQGKENMKAVLIG 108
Cdd:cd12289   66 EVEAARKAHELLGAEDDGKGGIKVVLLG 93
SUZ-C pfam12901
SUZ-C motif; The SUZ-C domain is a conserved motif found in one or more copies in several ...
 268-298 1.31e-06

SUZ-C motif; The SUZ-C domain is a conserved motif found in one or more copies in several RNA-binding proteins. It is always found at the C-terminus of the protein and appear to be required for localization of the protein to specific subcellular structures. It was first characterized in the C.elegans protein Szy-20 which localizes to the centrosome. It is widely distributed in eukaryotes.


Pssm-ID: 463745  Cd Length: 33  Bit Score: 44.07  E-value: 1.31e-06
                          10        20        30
                  ....*....|....*....|....*....|.
gi 557878616  268 PLLSRKMQTADGLPVGVLRLPRGPDNTRGFH 298
Cdd:pfam12901   1 RLKSVSLDDANRPNNNVLRQPRGPDGSKGFR 31
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
 31-92 6.41e-06

RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).


Pssm-ID: 409669 [Multi-domain]  Cd Length: 72  Bit Score: 43.43  E-value: 6.41e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 557878616  31 EHLLKLFGTFGVISSVRILKpgrelppDIRRISSRYsqvgtqecAIVEFEEVEAAIKAHEFM 92
Cdd:cd00590   13 EDLRELFSKFGEVVSVRIVR-------DRDGKSKGF--------AFVEFESPEDAEKALEAL 59
RRM_La_like_plant cd12288
RNA recognition motif (RRM) found in plant proteins related to the La autoantigen; This ...
 30-88 1.46e-04

RNA recognition motif (RRM) found in plant proteins related to the La autoantigen; This subfamily corresponds to the RRM of plant La-like proteins related to the La autoantigen. A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes. Members in this family contain an LAM domain followed by an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 409730 [Multi-domain]  Cd Length: 90  Bit Score: 40.18  E-value: 1.46e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 557878616  30 MEHLLKLFGTFGVISSVRILKPGRElpPDIRRISSRYSQVGTQECAIVEFEEVEAAIKA 88
Cdd:cd12288   14 IQNLREIFGTVGSVKNVRVCDPGRV--GSGEKAKKPDTFVSNKLHALVEYETVEAAEKA 70
RRM smart00360
RNA recognition motif;
31-92 4.44e-04

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 37.96  E-value: 4.44e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 557878616    31 EHLLKLFGTFGVISSVRIlkpgrelPPDIRRISSRysqvGtqeCAIVEFEEVEAAIKAHEFM 92
Cdd:smart00360  14 EELRELFSKFGKVESVRL-------VRDKETGKSK----G---FAFVEFESEEDAEKALEAL 61
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
 33-88 6.15e-03

RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteriztic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease.


Pssm-ID: 425453 [Multi-domain]  Cd Length: 70  Bit Score: 34.90  E-value: 6.15e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 557878616   33 LLKLFGTFGVISSVRIlkpgrelPPDIRRISSRYsqvgtqecAIVEFEEVEAAIKA 88
Cdd:pfam00076  15 LKDLFSKFGPIKSIRL-------VRDETGRSKGF--------AFVEFEDEEDAEKA 55
 
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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