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Conserved domains on  [gi|26983840|gb|AAN86172|]
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unknown protein [Arabidopsis thaliana]

Protein Classification

nucleoporin Nup35 family protein( domain architecture ID 11155686)

nucleoporin Nup35 family RNA-binding protein similar to nucleoporin 35 (also known as Nup53) is part of the nuclear pore complex (NPC), which has an eight-fold symmetrical structure comprising a central transport channel and two rings, the cytoplasmic and nuclear rings, to which eight filaments are attached

CATH:  3.30.70.330
Gene Ontology:  GO:0003676|GO:0005543|GO:0051028|GO:0006999|GO:0017056|GO:0031965|GO:0006913
PubMed:  18515081|15853797|22278943
SCOP:  3000110

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Nup35_RRM pfam05172
Nup53/35/40-type RNA recognition motif; Members of this family belong to the nucleor pore ...
 186-266 2.26e-41

Nup53/35/40-type RNA recognition motif; Members of this family belong to the nucleor pore complex, NPC, the only gateway between the nucleus and the cytoplasm. The NPC consists of several subcomplexes each one of which is made up of multiple copies of several individual Nup, Nic or Sec protein subunits. In yeast, this Nup or nucleoporin subunit is numbered Nup53, Nup40 in Schizo. pombe and in vertebrates as Nup35. This subunit forms part of the inner ring within the membrane and interacts directly with Nup-Ndc1, considered to be an anchor for the NPC in the pore membrane. This region of the Nup is the RNA-recognition region.


:

Pssm-ID: 398713 [Multi-domain]  Cd Length: 81  Bit Score: 138.68  E-value: 2.26e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 26983840   186 EEWVTVYGFSPGDTNLVLREFEKCGMVLKHVPGPRNANWMHILYQNRSDAHKALNKAGMMINGVVIVGVKPVDPIQKQAL 265
Cdd:pfam05172   1 DTWVTVFGFPPSITNIVLLHFSRFGEIVSHVPGPTNGNWMHLTYSSRSSAQKALSENGTIINGSVIVGVSYCPATDKQVI 80


                  .
gi 26983840   266 N 266
Cdd:pfam05172  81 N 81
 
Name Accession Description Interval E-value
Nup35_RRM pfam05172
Nup53/35/40-type RNA recognition motif; Members of this family belong to the nucleor pore ...
 186-266 2.26e-41

Nup53/35/40-type RNA recognition motif; Members of this family belong to the nucleor pore complex, NPC, the only gateway between the nucleus and the cytoplasm. The NPC consists of several subcomplexes each one of which is made up of multiple copies of several individual Nup, Nic or Sec protein subunits. In yeast, this Nup or nucleoporin subunit is numbered Nup53, Nup40 in Schizo. pombe and in vertebrates as Nup35. This subunit forms part of the inner ring within the membrane and interacts directly with Nup-Ndc1, considered to be an anchor for the NPC in the pore membrane. This region of the Nup is the RNA-recognition region.


Pssm-ID: 398713 [Multi-domain]  Cd Length: 81  Bit Score: 138.68  E-value: 2.26e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 26983840   186 EEWVTVYGFSPGDTNLVLREFEKCGMVLKHVPGPRNANWMHILYQNRSDAHKALNKAGMMINGVVIVGVKPVDPIQKQAL 265
Cdd:pfam05172   1 DTWVTVFGFPPSITNIVLLHFSRFGEIVSHVPGPTNGNWMHLTYSSRSSAQKALSENGTIINGSVIVGVSYCPATDKQVI 80


                  .
gi 26983840   266 N 266
Cdd:pfam05172  81 N 81
RRM_Nup53_like cd12441
RNA recognition motif (RRM) found in nucleoporin Nup53 and similar proteins; This subfamily ...
 186-259 3.15e-37

RNA recognition motif (RRM) found in nucleoporin Nup53 and similar proteins; This subfamily corresponds to the RRM domain of nucleoporin Nup53, also termed mitotic phosphoprotein 44 (MP-44), or nuclear pore complex protein Nup53, required for normal cell growth and nuclear morphology in vertebrate. It tightly associates with the nuclear envelope membrane and the nuclear lamina where it interacts with lamin B. It may also interact with a group of nucleoporins including Nup93, Nup155, and Nup205 and play a role in the association of the mitotic checkpoint protein Mad1 with the nuclear pore complex (NPC). The family also includes Saccharomyces cerevisiae Nup53p, an ortholog of vertebrate nucleoporin Nup53. A unique property of yeast Nup53p is that it contains an additional Kap121p-binding domain and interacts specifically with the karyopherin Kap121p, which is involved in the assembly of Nup53p into NPCs. Both, vertebrate Nup35 and yeast Nup53p, contain an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a C-terminal amphipathic alpha-helix and several FG repeats. This family corresponds to the RRM domain which lacks the conserved residues that typically bind RNA in canonical RRM domains.


Pssm-ID: 409875 [Multi-domain]  Cd Length: 73  Bit Score: 127.73  E-value: 3.15e-37
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 26983840 186 EEWVTVYGFSPGDTNLVLREFEKCGMVLKHVPGPrNANWMHILYQNRSDAHKALNKAGMMINGVVIVGVKPVDP 259
Cdd:cd12441   1 DTWVTVFGFPPSNASLVLREFSKCGDIVEHEYPP-GGNWIHIRYENRLQAERALSKNGRVLNGNVMIGVKPCTD 73
 
Name Accession Description Interval E-value
Nup35_RRM pfam05172
Nup53/35/40-type RNA recognition motif; Members of this family belong to the nucleor pore ...
 186-266 2.26e-41

Nup53/35/40-type RNA recognition motif; Members of this family belong to the nucleor pore complex, NPC, the only gateway between the nucleus and the cytoplasm. The NPC consists of several subcomplexes each one of which is made up of multiple copies of several individual Nup, Nic or Sec protein subunits. In yeast, this Nup or nucleoporin subunit is numbered Nup53, Nup40 in Schizo. pombe and in vertebrates as Nup35. This subunit forms part of the inner ring within the membrane and interacts directly with Nup-Ndc1, considered to be an anchor for the NPC in the pore membrane. This region of the Nup is the RNA-recognition region.


Pssm-ID: 398713 [Multi-domain]  Cd Length: 81  Bit Score: 138.68  E-value: 2.26e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 26983840   186 EEWVTVYGFSPGDTNLVLREFEKCGMVLKHVPGPRNANWMHILYQNRSDAHKALNKAGMMINGVVIVGVKPVDPIQKQAL 265
Cdd:pfam05172   1 DTWVTVFGFPPSITNIVLLHFSRFGEIVSHVPGPTNGNWMHLTYSSRSSAQKALSENGTIINGSVIVGVSYCPATDKQVI 80


                  .
gi 26983840   266 N 266
Cdd:pfam05172  81 N 81
RRM_Nup53_like cd12441
RNA recognition motif (RRM) found in nucleoporin Nup53 and similar proteins; This subfamily ...
 186-259 3.15e-37

RNA recognition motif (RRM) found in nucleoporin Nup53 and similar proteins; This subfamily corresponds to the RRM domain of nucleoporin Nup53, also termed mitotic phosphoprotein 44 (MP-44), or nuclear pore complex protein Nup53, required for normal cell growth and nuclear morphology in vertebrate. It tightly associates with the nuclear envelope membrane and the nuclear lamina where it interacts with lamin B. It may also interact with a group of nucleoporins including Nup93, Nup155, and Nup205 and play a role in the association of the mitotic checkpoint protein Mad1 with the nuclear pore complex (NPC). The family also includes Saccharomyces cerevisiae Nup53p, an ortholog of vertebrate nucleoporin Nup53. A unique property of yeast Nup53p is that it contains an additional Kap121p-binding domain and interacts specifically with the karyopherin Kap121p, which is involved in the assembly of Nup53p into NPCs. Both, vertebrate Nup35 and yeast Nup53p, contain an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a C-terminal amphipathic alpha-helix and several FG repeats. This family corresponds to the RRM domain which lacks the conserved residues that typically bind RNA in canonical RRM domains.


Pssm-ID: 409875 [Multi-domain]  Cd Length: 73  Bit Score: 127.73  E-value: 3.15e-37
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 26983840 186 EEWVTVYGFSPGDTNLVLREFEKCGMVLKHVPGPrNANWMHILYQNRSDAHKALNKAGMMINGVVIVGVKPVDP 259
Cdd:cd12441   1 DTWVTVFGFPPSNASLVLREFSKCGDIVEHEYPP-GGNWIHIRYENRLQAERALSKNGRVLNGNVMIGVKPCTD 73
RRM_Nup53 cd12722
RNA recognition motif (RRM) found in nucleoporin Nup53; This subgroup corresponds to the RRM ...
 185-256 6.31e-19

RNA recognition motif (RRM) found in nucleoporin Nup53; This subgroup corresponds to the RRM of nucleoporin Nup53, also termed mitotic phosphoprotein 44 (MP-44), or nuclear pore complex protein Nup53, required for normal cell growth and nuclear morphology in vertebrate. It tightly associates with the nuclear envelope membrane and the nuclear lamina where it interacts with lamin B. It may also interact with a group of nucleoporins including Nup93, Nup155, and Nup205 and play a role in the association of the mitotic checkpoint protein Mad1 with the nuclear pore complex (NPC). Nup35 contains an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a C-terminal amphipathic alpha-helix and several FG repeats. This RRM lacks the conserved residues that typically bind RNA in canonical RRM domains.


Pssm-ID: 410121  Cd Length: 74  Bit Score: 79.43  E-value: 6.31e-19
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 26983840 185 EEEWVTVYGFSPGDTNLVLREFEKCGMVLKHVPGPrNANWMHILYQNRSDAHKALNKAGMMINGVVIVGVKP 256
Cdd:cd12722   1 DDTWVTVFGFPPAAASYILQQFSQYGNILKHVMSN-NGNWMHIQYQSKLQAKKALSKNGKIFGENIMIGVKP 71
RRM_Nup53p_fungi cd12721
RNA recognition motif (RRM) found in yeast nucleoporin Nup53p and similar proteins; This ...
 189-259 1.42e-08

RNA recognition motif (RRM) found in yeast nucleoporin Nup53p and similar proteins; This subgroup corresponds to the RRM of Saccharomyces cerevisiae Nup53p, the ortholog of vertebrate nucleoporin Nup53. A unique property of yeast Nup53p is that it contains an additional Kap121p-binding domain and interacts specifically with the karyopherin Kap121p, which is involved in the assembly of Nup53p into NPCs. Like vertebrate Nup35, yeast Nup53p contains an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a C-terminal amphipathic alpha-helix and several FG repeats. The RRM domain lacks the conserved residues that typically bind RNA in canonical RRM domains.


Pssm-ID: 410120 [Multi-domain]  Cd Length: 86  Bit Score: 51.25  E-value: 1.42e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 26983840 189 VTVYGFSPGDTNLVLREFEKCGMVLKHVPGPRN------------ANWMHILYQNRSDAHKALNKAGMMINGVVIVGVKP 256
Cdd:cd12721   4 VIVFGFPETITSQVIEHFSGFGEILEDFSVPRSgkalqkypiptgSNWLKLTYAEPSSALRALRENGEILNGQCMIGCIW 83


                ...
gi 26983840 257 VDP 259
Cdd:cd12721  84 YDD 86
Nup35_RRM_2 pfam14605
Nup53/35/40-type RNA recognition motif;
188-239 1.50e-07

Nup53/35/40-type RNA recognition motif;


Pssm-ID: 373156  Cd Length: 53  Bit Score: 47.24  E-value: 1.50e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 26983840   188 WVTVYGFSPGDTNLVLREFEKCGMVLKHVPGPRnANWMHILYQNRSDAHKAL 239
Cdd:pfam14605   3 WIVVSGYPAELAYLVRRHFADFGEIVKHYFPPE-TNSMYLKYASRKDAEQAL 53
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
 189-251 5.19e-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: 35.34  E-value: 5.19e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 26983840 189 VTVYGFSPGDTNLVLRE-FEKCGMV----LKHVPGPRNANWMHILYQNRSDAHKALNKA-GMMINGVVI 251
Cdd:cd00590   1 LFVGNLPPDTTEEDLRElFSKFGEVvsvrIVRDRDGKSKGFAFVEFESPEDAEKALEALnGTELGGRPL 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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