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Conserved domains on  [gi|215272334|ref|NP_001135821|]
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sodium channel subunit beta-4 isoform 3 [Homo sapiens]

Protein Classification

immunoglobulin domain-containing family protein( domain architecture ID 34076)

immunoglobulin (Ig) domain-containing family protein is a member of a large superfamily containing cell surface antigen receptors, co-receptors and co-stimulatory molecules of the immune system, molecules involved in antigen presentation to lymphocytes, cell adhesion molecules, certain cytokine receptors and intracellular muscle proteins; immunoglobulin domains are typically divided into 4 main classes based on their structures and sequences: the Variable (V), Constant 1 (C1), Constant 2 (C2), and Intermediate (I) sets

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Ig super family cl11960
Immunoglobulin domain; The members here are composed of the immunoglobulin (Ig) domain found ...
 2-41 1.11e-06

Immunoglobulin domain; The members here are composed of the immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, including T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, including butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond. Ig superfamily (IgSF) domains can be divided into 4 main classes based on their structures and sequences: the Variable (V), Constant 1 (C1), Constant 2 (C2), and Intermediate (I) sets. Typically, the V-set domains have A, B, E, and D strands in one sheet and A', G, F, C, C' and C" in the other. The structures in C1-set are smaller than those in the V-set; they have one beta sheet that is formed by strands A, B, E, and D and the other by strands G, F, C, and C'. Moreover, a C1-set Ig domain contains a short C' strand (three residues) and lacks A' and C" strand. Unlike other Ig domain sets, C2-set structures do not have a D strand. Like the V-set Ig domains, members of the I-set have a discontinuous A strand, but lack a C" strand.


The actual alignment was detected with superfamily member cd05715:

Pssm-ID: 472250  Cd Length: 117  Bit Score: 43.96  E-value: 1.11e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 215272334   2 NNISIVLRDLEFSDTGKYTCHVKNPKEnNLQHHATIFLQV 41
Cdd:cd05715   79 KDASIVISNLQFSDNGTYTCDVKNPPD-IVGGHGEIRLYV 117
 
Name Accession Description Interval E-value
IgV_P0-like cd05715
Immunoglobulin (Ig)-like domain of protein zero (P0) and similar proteins; The members here ...
 2-41 1.11e-06

Immunoglobulin (Ig)-like domain of protein zero (P0) and similar proteins; The members here are composed of the immunoglobulin (Ig) domain of protein zero (P0), a myelin membrane adhesion molecule. P0 accounts for over 50% of the total protein in peripheral nervous system (PNS) myelin. P0 is a single-pass transmembrane glycoprotein with a highly basic intracellular domain and an extracellular Ig domain. The extracellular domain of P0 (P0-ED) is similar to the Ig variable domain, carrying one acceptor sequence for N-linked glycosylation. P0 plays a role in membrane adhesion in the spiral wraps of the myelin sheath. The intracellular domain is thought to mediate membrane apposition of the cytoplasmic faces and may, through electrostatic interactions, interact directly with lipid headgroups. It is thought that homophilic interactions of the P0 extracellular domain mediate membrane juxtaposition in the extracellular space of PNS myelin. This group also contains the Ig domain of sodium channel subunit beta-2 (SCN2B), and of epithelial V-like antigen 1 (EVA). EVA, also known as myelin protein zero-like 2, is an adhesion molecule, which may play a role in structural organization of the thymus and early lymphocyte development. SCN2B subunits play a role in determining sodium channel density and function in neurons,and in control of electrical excitability in the brain.


Pssm-ID: 409380  Cd Length: 117  Bit Score: 43.96  E-value: 1.11e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 215272334   2 NNISIVLRDLEFSDTGKYTCHVKNPKEnNLQHHATIFLQV 41
Cdd:cd05715   79 KDASIVISNLQFSDNGTYTCDVKNPPD-IVGGHGEIRLYV 117
V-set pfam07686
Immunoglobulin V-set domain; This domain is found in antibodies as well as neural protein P0 ...
 2-34 1.08e-03

Immunoglobulin V-set domain; This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.


Pssm-ID: 462230  Cd Length: 109  Bit Score: 35.90  E-value: 1.08e-03
                          10        20        30
                  ....*....|....*....|....*....|...
gi 215272334    2 NNISIVLRDLEFSDTGKYTCHVKNPKENNLQHH 34
Cdd:pfam07686  71 GDGSLTIQNLTLSDSGTYTCAVIPSGEGVFGKG 103
IG_like smart00410
Immunoglobulin like; IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
 2-41 2.59e-03

Immunoglobulin like; IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.


Pssm-ID: 214653 [Multi-domain]  Cd Length: 85  Bit Score: 34.40  E-value: 2.59e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|
gi 215272334     2 NNISIVLRDLEFSDTGKYTCHVKNpkeNNLQHHATIFLQV 41
Cdd:smart00410  49 STSTLTISNVTPEDSGTYTCAATN---SSGSASSGTTLTV 85
 
Name Accession Description Interval E-value
IgV_P0-like cd05715
Immunoglobulin (Ig)-like domain of protein zero (P0) and similar proteins; The members here ...
 2-41 1.11e-06

Immunoglobulin (Ig)-like domain of protein zero (P0) and similar proteins; The members here are composed of the immunoglobulin (Ig) domain of protein zero (P0), a myelin membrane adhesion molecule. P0 accounts for over 50% of the total protein in peripheral nervous system (PNS) myelin. P0 is a single-pass transmembrane glycoprotein with a highly basic intracellular domain and an extracellular Ig domain. The extracellular domain of P0 (P0-ED) is similar to the Ig variable domain, carrying one acceptor sequence for N-linked glycosylation. P0 plays a role in membrane adhesion in the spiral wraps of the myelin sheath. The intracellular domain is thought to mediate membrane apposition of the cytoplasmic faces and may, through electrostatic interactions, interact directly with lipid headgroups. It is thought that homophilic interactions of the P0 extracellular domain mediate membrane juxtaposition in the extracellular space of PNS myelin. This group also contains the Ig domain of sodium channel subunit beta-2 (SCN2B), and of epithelial V-like antigen 1 (EVA). EVA, also known as myelin protein zero-like 2, is an adhesion molecule, which may play a role in structural organization of the thymus and early lymphocyte development. SCN2B subunits play a role in determining sodium channel density and function in neurons,and in control of electrical excitability in the brain.


Pssm-ID: 409380  Cd Length: 117  Bit Score: 43.96  E-value: 1.11e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 215272334   2 NNISIVLRDLEFSDTGKYTCHVKNPKEnNLQHHATIFLQV 41
Cdd:cd05715   79 KDASIVISNLQFSDNGTYTCDVKNPPD-IVGGHGEIRLYV 117
IgV_EVA1 cd05880
Immunoglobulin (Ig)-like domain of epithelial V-like antigen (EVA) 1; The members here are ...
 2-28 4.60e-06

Immunoglobulin (Ig)-like domain of epithelial V-like antigen (EVA) 1; The members here are composed of the immunoglobulin (Ig) domain of epithelial V-like antigen 1 (EVA 1). EVA is also known as myelin protein zero-like 2. EVA is an adhesion molecule and may play a role in the structural organization of the thymus and early lymphocyte development.


Pssm-ID: 409464  Cd Length: 116  Bit Score: 42.51  E-value: 4.60e-06
                         10        20
                 ....*....|....*....|....*..
gi 215272334   2 NNISIVLRDLEFSDTGKYTCHVKNPKE 28
Cdd:cd05880   78 RDASILIWQLQPTDNGTYTCQVKNPPD 104
IgV_P0 cd05879
Immunoglobulin (Ig)-like domain of protein zero (P0); The members here are composed of the ...
 5-41 1.24e-04

Immunoglobulin (Ig)-like domain of protein zero (P0); The members here are composed of the immunoglobulin (Ig) domain of protein zero (P0), a myelin membrane adhesion molecule. P0 accounts for over 50% of the total protein in peripheral nervous system (PNS) myelin. P0 is a single-pass transmembrane glycoprotein with a highly basic intracellular domain and an Ig domain. The extracellular domain of P0 (P0-ED) is similar to the Ig variable domain, carrying one acceptor sequence for N-linked glycosylation. P0 plays a role in membrane adhesion in the spiral wraps of the myelin sheath. The intracellular domain is thought to mediate membrane apposition of the cytoplasmic faces and may, through electrostatic interactions, interact directly with lipid headgroups. It is thought that homophilic interactions of the P0 extracellular domain mediate membrane juxtaposition in the extracellular space of PNS myelin.


Pssm-ID: 409463  Cd Length: 117  Bit Score: 38.70  E-value: 1.24e-04
                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 215272334   5 SIVLRDLEFSDTGKYTCHVKNPKEnNLQHHATIFLQV 41
Cdd:cd05879   82 SIVIHNLDYTDNGTFTCDVKNPPD-IVGKSSQVTLYV 117
V-set pfam07686
Immunoglobulin V-set domain; This domain is found in antibodies as well as neural protein P0 ...
 2-34 1.08e-03

Immunoglobulin V-set domain; This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.


Pssm-ID: 462230  Cd Length: 109  Bit Score: 35.90  E-value: 1.08e-03
                          10        20        30
                  ....*....|....*....|....*....|...
gi 215272334    2 NNISIVLRDLEFSDTGKYTCHVKNPKENNLQHH 34
Cdd:pfam07686  71 GDGSLTIQNLTLSDSGTYTCAVIPSGEGVFGKG 103
IG_like smart00410
Immunoglobulin like; IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
 2-41 2.59e-03

Immunoglobulin like; IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.


Pssm-ID: 214653 [Multi-domain]  Cd Length: 85  Bit Score: 34.40  E-value: 2.59e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|
gi 215272334     2 NNISIVLRDLEFSDTGKYTCHVKNpkeNNLQHHATIFLQV 41
Cdd:smart00410  49 STSTLTISNVTPEDSGTYTCAATN---SSGSASSGTTLTV 85
 
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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