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Conserved domains on  [gi|79315331|ref|NP_001030873|]
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RNA-binding (RRM/RBD/RNP motifs) family protein [Arabidopsis thaliana]

Protein Classification

RNA-binding protein( domain architecture ID 10188096)

RNA-binding protein recognizes RNA via an RNA recognition motif (RRM)

Gene Ontology:  GO:0003723
PubMed:  15853797|22278943|18515081
SCOP:  3000110

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RRM_ABT1_like cd12263
RNA recognition motif (RRM) found in activator of basal transcription 1 (ABT1) and similar ...
 50-146 1.83e-54

RNA recognition motif (RRM) found in activator of basal transcription 1 (ABT1) and similar proteins; This subfamily corresponds to the RRM of novel nuclear proteins termed ABT1 and its homologous counterpart, pre-rRNA-processing protein ESF2 (eighteen S factor 2), from yeast. ABT1 associates with the TATA-binding protein (TBP) and enhances basal transcription activity of class II promoters. Meanwhile, ABT1 could be a transcription cofactor that can bind to DNA in a sequence-independent manner. The yeast ABT1 homolog, ESF2, is a component of 90S preribosomes and 5' ETS-based RNPs. It is previously identified as a putative partner of the TATA-element binding protein. However, it is primarily localized to the nucleolus and physically associates with pre-rRNA processing factors. ESF2 may play a role in ribosome biogenesis. It is required for normal pre-rRNA processing, as well as for SSU processome assembly and function. Both ABT1 and ESF2 contain an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


:

Pssm-ID: 409707 [Multi-domain]  Cd Length: 98  Bit Score: 170.46  E-value: 1.83e-54
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79315331  50 GVCYLSRIPPHMDHVRLRHILAQYGELGRIYLAPEDSEAQVHRKRAGGFRGQRFSEGWVEFAKKSVAKRVADMLNGEQIG 129
Cdd:cd12263   1 GIVYLSRIPPGMNPAKLRQLLSQYGEVGRIYLQPEDPSKRKKRKKKGGNKKKKFTEGWVEFEDKKVAKRVAESLNNTPIG 80

                        90
                ....*....|....*..
gi 79315331 130 GKKKSSVYYDIWNIKYL 146
Cdd:cd12263  81 GKKRSRFRDDLWNIKYL 97
 
Name Accession Description Interval E-value
RRM_ABT1_like cd12263
RNA recognition motif (RRM) found in activator of basal transcription 1 (ABT1) and similar ...
 50-146 1.83e-54

RNA recognition motif (RRM) found in activator of basal transcription 1 (ABT1) and similar proteins; This subfamily corresponds to the RRM of novel nuclear proteins termed ABT1 and its homologous counterpart, pre-rRNA-processing protein ESF2 (eighteen S factor 2), from yeast. ABT1 associates with the TATA-binding protein (TBP) and enhances basal transcription activity of class II promoters. Meanwhile, ABT1 could be a transcription cofactor that can bind to DNA in a sequence-independent manner. The yeast ABT1 homolog, ESF2, is a component of 90S preribosomes and 5' ETS-based RNPs. It is previously identified as a putative partner of the TATA-element binding protein. However, it is primarily localized to the nucleolus and physically associates with pre-rRNA processing factors. ESF2 may play a role in ribosome biogenesis. It is required for normal pre-rRNA processing, as well as for SSU processome assembly and function. Both ABT1 and ESF2 contain an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 409707 [Multi-domain]  Cd Length: 98  Bit Score: 170.46  E-value: 1.83e-54
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79315331  50 GVCYLSRIPPHMDHVRLRHILAQYGELGRIYLAPEDSEAQVHRKRAGGFRGQRFSEGWVEFAKKSVAKRVADMLNGEQIG 129
Cdd:cd12263   1 GIVYLSRIPPGMNPAKLRQLLSQYGEVGRIYLQPEDPSKRKKRKKKGGNKKKKFTEGWVEFEDKKVAKRVAESLNNTPIG 80

                        90
                ....*....|....*..
gi 79315331 130 GKKKSSVYYDIWNIKYL 146
Cdd:cd12263  81 GKKRSRFRDDLWNIKYL 97
RRM smart00360
RNA recognition motif;
53-132 2.16e-05

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 41.43  E-value: 2.16e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79315331     53 YLSRIPPHMDHVRLRHILAQYGELGRIYLAPEdseaqvhrKRAGGFRGQRFsegwVEFAKKSVAKRVADMLNGEQIGGKK 132
Cdd:smart00360   3 FVGNLPPDTTEEELRELFSKFGKVESVRLVRD--------KETGKSKGFAF----VEFESEEDAEKALEALNGKELDGRP 70
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
 53-132 3.95e-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: 35.29  E-value: 3.95e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79315331    53 YLSRIPPHMDHVRLRHILAQYGELgriylapedSEAQVHRKRAGGFRGQRFsegwVEFAKKSVAKRVADMLNGEQIGGKK 132
Cdd:pfam00076   2 FVGNLPPDTTEEDLKDLFSKFGPI---------KSIRLVRDETGRSKGFAF----VEFEDEEDAEKAIEALNGKELGGRE 68
 
Name Accession Description Interval E-value
RRM_ABT1_like cd12263
RNA recognition motif (RRM) found in activator of basal transcription 1 (ABT1) and similar ...
 50-146 1.83e-54

RNA recognition motif (RRM) found in activator of basal transcription 1 (ABT1) and similar proteins; This subfamily corresponds to the RRM of novel nuclear proteins termed ABT1 and its homologous counterpart, pre-rRNA-processing protein ESF2 (eighteen S factor 2), from yeast. ABT1 associates with the TATA-binding protein (TBP) and enhances basal transcription activity of class II promoters. Meanwhile, ABT1 could be a transcription cofactor that can bind to DNA in a sequence-independent manner. The yeast ABT1 homolog, ESF2, is a component of 90S preribosomes and 5' ETS-based RNPs. It is previously identified as a putative partner of the TATA-element binding protein. However, it is primarily localized to the nucleolus and physically associates with pre-rRNA processing factors. ESF2 may play a role in ribosome biogenesis. It is required for normal pre-rRNA processing, as well as for SSU processome assembly and function. Both ABT1 and ESF2 contain an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 409707 [Multi-domain]  Cd Length: 98  Bit Score: 170.46  E-value: 1.83e-54
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79315331  50 GVCYLSRIPPHMDHVRLRHILAQYGELGRIYLAPEDSEAQVHRKRAGGFRGQRFSEGWVEFAKKSVAKRVADMLNGEQIG 129
Cdd:cd12263   1 GIVYLSRIPPGMNPAKLRQLLSQYGEVGRIYLQPEDPSKRKKRKKKGGNKKKKFTEGWVEFEDKKVAKRVAESLNNTPIG 80

                        90
                ....*....|....*..
gi 79315331 130 GKKKSSVYYDIWNIKYL 146
Cdd:cd12263  81 GKKRSRFRDDLWNIKYL 97
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
 53-132 3.10e-08

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: 49.59  E-value: 3.10e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79315331  53 YLSRIPPHMDHVRLRHILAQYGELGRIylapedseaQVHRKRAGGFRGQrfseGWVEFAKKSVAKRVADMLNGEQIGGKK 132
Cdd:cd00590   2 FVGNLPPDTTEEDLRELFSKFGEVVSV---------RIVRDRDGKSKGF----AFVEFESPEDAEKALEALNGTELGGRP 68
RRM smart00360
RNA recognition motif;
53-132 2.16e-05

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 41.43  E-value: 2.16e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79315331     53 YLSRIPPHMDHVRLRHILAQYGELGRIYLAPEdseaqvhrKRAGGFRGQRFsegwVEFAKKSVAKRVADMLNGEQIGGKK 132
Cdd:smart00360   3 FVGNLPPDTTEEELRELFSKFGKVESVRLVRD--------KETGKSKGFAF----VEFESEEDAEKALEALNGKELDGRP 70
RRM_NIFK_like cd12307
RNA recognition motif in nucleolar protein interacting with the FHA domain of pKI-67 (NIFK) ...
 51-125 5.00e-04

RNA recognition motif in nucleolar protein interacting with the FHA domain of pKI-67 (NIFK) and similar proteins; This subgroup corresponds to the RRM of NIFK and Nop15p. NIFK, also termed MKI67 FHA domain-interacting nucleolar phosphoprotein, or nucleolar phosphoprotein Nopp34, is a putative RNA-binding protein interacting with the forkhead associated (FHA) domain of pKi-67 antigen in a mitosis-specific and phosphorylation-dependent manner. It is nucleolar in interphase but associates with condensed mitotic chromosomes. This family also includes Saccharomyces cerevisiae YNL110C gene encoding ribosome biogenesis protein 15 (Nop15p), also termed nucleolar protein 15. Both, NIFK and Nop15p, contain an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 409748 [Multi-domain]  Cd Length: 74  Bit Score: 37.94  E-value: 5.00e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 79315331  51 VCYLSRIPPHMDHVRLRHILAQYGELGRIYLApedseaqvHRKRAGGFRGQRFsegwVEFAKKSVAKRVADMLNG 125
Cdd:cd12307   1 VVYIGHLPHGFYEPELRKYFSQFGTVTRLRLS--------RSKKTGKSKGYAF----VEFEDPEVAKIVAETMNN 63
RRM_Nop15p cd12552
RNA recognition motif in yeast ribosome biogenesis protein 15 (Nop15p) and similar proteins; ...
 51-132 1.55e-03

RNA recognition motif in yeast ribosome biogenesis protein 15 (Nop15p) and similar proteins; This subgroup corresponds to the RRM of Nop15p, also termed nucleolar protein 15, which is encoded by YNL110C from Saccharomyces cerevisiae, and localizes to the nucleoplasm and nucleolus. Nop15p has been identified as a component of a pre-60S particle. It interacts with RNA components of the early pre-60S particles. Furthermore, Nop15p binds directly to a pre-rRNA transcript in vitro and is required for pre-rRNA processing. It functions as a ribosome synthesis factor required for the 5' to 3' exonuclease digestion that generates the 5' end of the major, short form of the 5.8S rRNA as well as for processing of 27SB to 7S pre-rRNA. Nop15p also play a specific role in cell cycle progression. Nop15p contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 409968 [Multi-domain]  Cd Length: 77  Bit Score: 36.38  E-value: 1.55e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79315331  51 VCYLSRIPPHMDHVRLRHILAQYGELGRIYLApedseaqvHRKRAGGFRGQrfseGWVEFAKKSVAKRVADMLNGEQIGG 130
Cdd:cd12552   1 IIYVSHLPHGFHEKELKKYFAQFGDLKNVRLA--------RSKKTGNSKHY----GFLEFVNPEDAMIAQKSMNNYLLMG 68


                ..
gi 79315331 131 KK 132
Cdd:cd12552  69 KL 70
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
 53-132 3.95e-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: 35.29  E-value: 3.95e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79315331    53 YLSRIPPHMDHVRLRHILAQYGELgriylapedSEAQVHRKRAGGFRGQRFsegwVEFAKKSVAKRVADMLNGEQIGGKK 132
Cdd:pfam00076   2 FVGNLPPDTTEEDLKDLFSKFGPI---------KSIRLVRDETGRSKGFAF----VEFEDEEDAEKAIEALNGKELGGRE 68
RRM2_RAVER cd12389
RNA recognition motif 2 (RRM2) found in ribonucleoprotein PTB-binding raver-1, raver-2 and ...
 55-130 5.14e-03

RNA recognition motif 2 (RRM2) found in ribonucleoprotein PTB-binding raver-1, raver-2 and similar proteins; This subfamily corresponds to the RRM2 of raver-1 and raver-2. Raver-1 is a ubiquitously expressed heterogeneous nuclear ribonucleoprotein (hnRNP) that serves as a co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. It shuttles between the cytoplasm and the nucleus and can accumulate in the perinucleolar compartment, a dynamic nuclear substructure that harbors PTB. Raver-1 also modulates focal adhesion assembly by binding to the cytoskeletal proteins, including alpha-actinin, vinculin, and metavinculin (an alternatively spliced isoform of vinculin) at adhesion complexes, particularly in differentiated muscle tissue. Raver-2 is a novel member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family. It shows high sequence homology to raver-1. Raver-2 exerts a spatio-temporal expression pattern during embryogenesis and is mainly limited to differentiated neurons and glia cells. Although it displays nucleo-cytoplasmic shuttling in heterokaryons, raver2 localizes to the nucleus in glia cells and neurons. Raver-2 can interact with PTB and may participate in PTB-mediated RNA-processing. However, there is no evidence indicating that raver-2 can bind to cytoplasmic proteins. Both, raver-1 and raver-2, contain three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two [SG][IL]LGxxP motifs. They binds to RNA through the RRMs. In addition, the two [SG][IL]LGxxP motifs serve as the PTB-binding motifs in raver1. However, raver-2 interacts with PTB through the SLLGEPP motif only.


Pssm-ID: 409823 [Multi-domain]  Cd Length: 77  Bit Score: 34.98  E-value: 5.14e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 79315331  55 SRIPPHMDHVRLRHILAQYGELGRIYLapedseaqVHRKRAGGFRGQrfseGWVEFAKKSVAKRVADMLNGEQIGG 130
Cdd:cd12389   5 TNLPLSFTEEQFEELVRPYGNVERCFL--------VYSEVTGESKGY----GFVEYTSKESAIRAKNQLHGRQIGG 68
RRM2_NsCP33_like cd21608
RNA recognition motif 2 (RRM2) found in Nicotiana sylvestris chloroplastic 33 kDa ...
 52-131 8.01e-03

RNA recognition motif 2 (RRM2) found in Nicotiana sylvestris chloroplastic 33 kDa ribonucleoprotein (NsCP33) and similar proteins; The family includes NsCP33, Arabidopsis thaliana chloroplastic 31 kDa ribonucleoprotein (CP31A) and mitochondrial glycine-rich RNA-binding protein 2 (AtGR-RBP2). NsCP33 may be involved in splicing and/or processing of chloroplast RNA's. AtCP31A, also called RNA-binding protein 1/2/3 (AtRBP33), or RNA-binding protein CP31A, or RNA-binding protein RNP-T, or RNA-binding protein cp31, is required for specific RNA editing events in chloroplasts and stabilizes specific chloroplast mRNAs, as well as for normal chloroplast development under cold stress conditions by stabilizing transcripts of numerous mRNAs under these conditions. CP31A may modulate telomere replication through RNA binding domains. AtGR-RBP2, also called AtRBG2, or glycine-rich protein 2 (AtGRP2), or mitochondrial RNA-binding protein 1a (At-mRBP1a), plays a role in RNA transcription or processing during stress. It binds RNAs and DNAs sequence with a preference to single-stranded nucleic acids. AtGR-RBP2 displays strong affinity to poly(U) sequence. It exerts cold and freezing tolerance, probably by exhibiting an RNA chaperone activity during the cold and freezing adaptation process. Some members in this family contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the second RRM motif.


Pssm-ID: 410187 [Multi-domain]  Cd Length: 76  Bit Score: 34.45  E-value: 8.01e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79315331  52 CYLSRIPPHMDHVRLRHILAQYGELgriylapedSEAQVHRKRAGGfRGQRFseGWVEFAKKSVAKRVADMLNGEQIGGK 131
Cdd:cd21608   2 LYVGNLSWDTTEDDLRDLFSEFGEV---------ESAKVITDRETG-RSRGF--GFVTFSTAEAAEAAIDALNGKELDGR 69
 
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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