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Conserved domains on  [gi|307133514|dbj|BAJ19019|]
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RNA-binding protein 5 variant [Homo sapiens]

Protein Classification

RNA-binding protein( domain architecture ID 106745)

RNA-binding protein containing an RNA recognition motif (RRM)

CATH:  3.30.70.330
Gene Ontology:  GO:0003723
PubMed:  15853797
SCOP:  3000110

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RRM_SF super family cl17169
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
 93-139 3.86e-25

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).


The actual alignment was detected with superfamily member cd12752:

Pssm-ID: 473069 [Multi-domain]  Cd Length: 87  Bit Score: 91.54  E-value: 3.86e-25
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 307133514  93 DERESKTIMLRGLPITITESDIREMMESFEGPQPADVRLMKRKTGES 139
Cdd:cd12752    1 DEKESKTIMLRGLPINITENDIRELIESFEGPQPADVRLMKRKTGVS 47
 
Name Accession Description Interval E-value
RRM1_RBM5 cd12752
RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 5 (RBM5); This subgroup ...
 93-139 3.86e-25

RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 5 (RBM5); This subgroup corresponds to the RRM1 of RBM5, also termed protein G15, or putative tumor suppressor LUCA15, or renal carcinoma antigen NY-REN-9, a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor. RBM5 shows high sequence similarity to RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). Both, RBM5 and RBM6, specifically bind poly(G) RNA. They contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, a nuclear localization signal, and a G-patch/D111 domain.


Pssm-ID: 410146 [Multi-domain]  Cd Length: 87  Bit Score: 91.54  E-value: 3.86e-25
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 307133514  93 DERESKTIMLRGLPITITESDIREMMESFEGPQPADVRLMKRKTGES 139
Cdd:cd12752    1 DEKESKTIMLRGLPINITENDIRELIESFEGPQPADVRLMKRKTGVS 47
RRM smart00360
RNA recognition motif;
99-139 9.54e-03

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 32.95  E-value: 9.54e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 307133514    99 TIMLRGLPITITESDIREMMESFeGPqPADVRLMK-RKTGES 139
Cdd:smart00360   1 TLFVGNLPPDTTEEELRELFSKF-GK-VESVRLVRdKETGKS 40
 
Name Accession Description Interval E-value
RRM1_RBM5 cd12752
RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 5 (RBM5); This subgroup ...
 93-139 3.86e-25

RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 5 (RBM5); This subgroup corresponds to the RRM1 of RBM5, also termed protein G15, or putative tumor suppressor LUCA15, or renal carcinoma antigen NY-REN-9, a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor. RBM5 shows high sequence similarity to RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). Both, RBM5 and RBM6, specifically bind poly(G) RNA. They contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, a nuclear localization signal, and a G-patch/D111 domain.


Pssm-ID: 410146 [Multi-domain]  Cd Length: 87  Bit Score: 91.54  E-value: 3.86e-25
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 307133514  93 DERESKTIMLRGLPITITESDIREMMESFEGPQPADVRLMKRKTGES 139
Cdd:cd12752    1 DEKESKTIMLRGLPINITENDIRELIESFEGPQPADVRLMKRKTGVS 47
RRM1_RBM5_like cd12561
RNA recognition motif 1 (RRM1) found in RNA-binding protein 5 (RBM5) and similar proteins; ...
 96-139 2.32e-12

RNA recognition motif 1 (RRM1) found in RNA-binding protein 5 (RBM5) and similar proteins; This subgroup corresponds to the RRM1 of RNA-binding protein 5 (RBM5 or LUCA15 or H37), RNA-binding protein 10 (RBM10 or S1-1) and similar proteins. RBM5 is a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor; it specifically binds poly(G) RNA. RBM10, a paralog of RBM5, may play an important role in mRNA generation, processing and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. Both, RBM5 and RBM10, contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, and a G-patch/D111 domain.


Pssm-ID: 409977 [Multi-domain]  Cd Length: 81  Bit Score: 58.53  E-value: 2.32e-12
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 307133514  96 ESKTIMLRGLPITITESDIREMMESFeGPQPADVRLMKRK-TGES 139
Cdd:cd12561    1 PNNTIMLRGLPLSVTEEDIRNALVSH-GVQPKDVRLMRRKtTGAS 44
RRM1_RBM10 cd12753
RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 10 (RBM10); This ...
 97-139 5.22e-07

RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 10 (RBM10); This subgroup corresponds to the RRM1 of RBM10, also termed G patch domain-containing protein 9, or RNA-binding protein S1-1 (S1-1), a paralog of putative tumor suppressor RNA-binding protein 5 (RBM5 or LUCA15 or H37). It may play an important role in mRNA generation, processing and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. RBM10 is structurally related to RBM5 and RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). It contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, and a G-patch/D111 domain.


Pssm-ID: 410147 [Multi-domain]  Cd Length: 84  Bit Score: 44.93  E-value: 5.22e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 307133514  97 SKTIMLRGLPITITESDIREMMESfEGPQPADVRLMKRK-TGES 139
Cdd:cd12753    1 SNIIMLRMLPQSATENDIRGQLQA-HGVQPREVRLMRNKsSGQS 43
RRM1_RRM2_RBM5_like cd12313
RNA recognition motif 1 (RRM1) and 2 (RRM2) found in RNA-binding protein 5 (RBM5) and similar ...
 96-139 1.86e-06

RNA recognition motif 1 (RRM1) and 2 (RRM2) found in RNA-binding protein 5 (RBM5) and similar proteins; This subfamily includes the RRM1 and RRM2 of RNA-binding protein 5 (RBM5 or LUCA15 or H37) and RNA-binding protein 10 (RBM10 or S1-1), and the RRM2 of RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). These RBMs share high sequence homology and may play an important role in regulating apoptosis. RBM5 is a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor. RBM6 has been predicted to be a nuclear factor based on its nuclear localization signal. Both, RBM6 and RBM5, specifically bind poly(G) RNA. RBM10 is a paralog of RBM5. It may play an important role in mRNA generation, processing and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. All family members contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, and a G-patch/D111 domain.


Pssm-ID: 409752 [Multi-domain]  Cd Length: 85  Bit Score: 43.41  E-value: 1.86e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 307133514  96 ESKTIMLRGLPITITESDIREMMESFEGPQPADVRLMKRK-TGES 139
Cdd:cd12313    1 PTNVLILRGLDVLTTEEDILSALQAHADLPIKDVRLIRDKlTGTS 45
RRM1_MRD1 cd12565
RNA recognition motif 1 (RRM1) found in yeast multiple RNA-binding domain-containing protein 1 ...
 100-139 2.46e-03

RNA recognition motif 1 (RRM1) found in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins; This subgroup corresponds to the RRM1 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events.


Pssm-ID: 409981 [Multi-domain]  Cd Length: 76  Bit Score: 34.84  E-value: 2.46e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 307133514 100 IMLRGLPITITESDIREMMESFEgpQPADVRLMKRKTGES 139
Cdd:cd12565    3 IIVKNLPKYVTEKRLKEHFSKKG--EITDVKVMRTKDGKS 40
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
 100-139 6.27e-03

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: 33.41  E-value: 6.27e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 307133514 100 IMLRGLPITITESDIREMMESFEGPQpaDVRLMKRKTGES 139
Cdd:cd00590    1 LFVGNLPPDTTEEDLRELFSKFGEVV--SVRIVRDRDGKS 38
RRM smart00360
RNA recognition motif;
99-139 9.54e-03

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 32.95  E-value: 9.54e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 307133514    99 TIMLRGLPITITESDIREMMESFeGPqPADVRLMK-RKTGES 139
Cdd:smart00360   1 TLFVGNLPPDTTEEELRELFSKF-GK-VESVRLVRdKETGKS 40
 
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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