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Conserved domains on  [gi|1907176927|ref|XP_036008507|]
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B-lymphocyte antigen CD19 isoform X1 [Mus musculus]

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
CD19_double_Ig super family cl49627
CD19 (Cluster of Differentiation 19), a unique double immunoglobulin (Ig)-fold domain; CD19, ...
 63-152 2.17e-44

CD19 (Cluster of Differentiation 19), a unique double immunoglobulin (Ig)-fold domain; CD19, also known as B-Lymphocyte Surface Antigen B4, T-Cell Surface Antigen Leu-12, and CVID3, is a transmembrane receptor present on various types of B cells, including progenitor, naive, and memory B cells, as well as plasmablasts. Until recently, it was believed to comprise two extracellular immunoglobulin (Ig) structural domains arranged in tandem with C2 topology. However, recent crystal structures have shown that the CD19 extracellular domain contains a unique double Ig domain that is responsible for its binding to proteins such as CD21, CD81, and CD225, which regulate B cell activation and survival. A recent analysis of the CD19 extracellular domain sequence reveals two "Ig domains", but the structure demonstrates that these two domains are not folded independently and connected in tandem. Rather, they fold together as one intertwined domain that can be referred to as a "double Ig" domain. Each of the two regular Ig domain sequences has a noticeably short linker that forms a loop between strands C' and D, rather than allowing the formation of a C" strand. Additionally, the two Ig-domain sequences are separated by a long linker that is structured as a small insertion domain, enabling both Ig sequences to fold together as a unique double Ig-domain. The CD19 domain comprises four "protodomains": two formed by A'B-CC' strands and two by DE-FG strands that interdigitate to form a novel double Ig fold. When analyzing this double Ig domain in terms of the usual Ig-fold, A'B-CC' protodomain of the first Ig sequence combines with DE-FG protodomain of the second, and vice versa. Hence, the second combined Ig fold is inverted, with DE-FG protodomain of the first Ig sequence combining with A'B-CC' protodomain of the second Ig sequence and in that order, as if it were a circular permutation, obtained only through structural folding.


The actual alignment was detected with superfamily member cd23998:

Pssm-ID: 483967  Cd Length: 95  Bit Score: 149.56  E-value: 2.17e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907176927  63 QDLTVAPGSTLWLSCGVPPVPVAKGSISWTHVHPRRPNVSLLSLSLGGEHPVREMWV-----WGSLLLLPQATALDEGTY 137
Cdd:cd23998     1 QDLTVAPGSTLWLSCGVPPDSGTRGPISWTHVHPKPSNTSLLSLELKEDRPAREKWVlgtlrGGALLLLPRATAQDAGIY 80

                          90
                  ....*....|....*
gi 1907176927 138 YCLRGNLTIERHVKV 152
Cdd:cd23998    81 HCHLGNRTISMELTV 95
 
Name Accession Description Interval E-value
CD19_protodomain_3_4 cd23998
CD19 (Cluster of Differentiation 19), a unique double immunoglobulin (Ig)-fold protodomain 3 ...
 63-152 2.17e-44

CD19 (Cluster of Differentiation 19), a unique double immunoglobulin (Ig)-fold protodomain 3 and 4; CD19, also known as B-Lymphocyte Surface Antigen B4, T-Cell Surface Antigen Leu-12, and CVID3, is a transmembrane receptor present on various types of B cells, including progenitor, naive, and memory B cells, as well as plasmablasts. Until recently, it was believed to comprise two extracellular immunoglobulin (Ig) structural domains arranged in tandem with C2 topology. However, recent crystal structures have shown that the CD19 extracellular domain contains a unique double Ig domain that is responsible for its binding to proteins such as CD21, CD81, and CD225, which regulate B cell activation and survival. A recent analysis of the CD19 extracellular domain sequence reveals two "Ig domains", but the structure demonstrates that these two domains are not folded independently and connected in tandem. Rather, they fold together as one intertwined domain that can be referred to as a "double Ig" domain. Each of the two regular Ig domain sequences has a noticeably short linker that forms a loop between strands C' and D, rather than allowing the formation of a C" strand. Additionally, the two Ig-domain sequences are separated by a long linker that is structured as a small insertion domain, enabling both Ig sequences to fold together as a unique double Ig-domain. The CD19 domain comprises four "protodomains": two formed by A'B-CC' strands and two by DE-FG strands that interdigitate to form a novel double Ig fold. When analyzing this double Ig domain in terms of the usual Ig-fold, A'B-CC' protodomain of the first Ig sequence combines with DE-FG protodomain of the second, and vice versa. Hence, the second combined Ig fold is inverted, with DE-FG protodomain of the first Ig sequence combining with A'B-CC' protodomain of the second Ig sequence and in that order, as if it were a circular permutation, obtained only through structural folding. This group contains the protodomains 3 and 4 of the CD19 double Ig domain.


Pssm-ID: 467825  Cd Length: 95  Bit Score: 149.56  E-value: 2.17e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907176927  63 QDLTVAPGSTLWLSCGVPPVPVAKGSISWTHVHPRRPNVSLLSLSLGGEHPVREMWV-----WGSLLLLPQATALDEGTY 137
Cdd:cd23998     1 QDLTVAPGSTLWLSCGVPPDSGTRGPISWTHVHPKPSNTSLLSLELKEDRPAREKWVlgtlrGGALLLLPRATAQDAGIY 80

                          90
                  ....*....|....*
gi 1907176927 138 YCLRGNLTIERHVKV 152
Cdd:cd23998    81 HCHLGNRTISMELTV 95
IG_like smart00410
Immunoglobulin like; IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
 63-143 4.13e-04

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: 39.03  E-value: 4.13e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907176927   63 QDLTVAPGSTLWLSCGVPPVPVAkgSISWthvhpRRPNVSLLSlslggeHPVREMWVWGSL---LLLPQATALDEGTYYC 139
Cdd:smart00410   2 PSVTVKEGESVTLSCEASGSPPP--EVTW-----YKQGGKLLA------ESGRFSVSRSGStstLTISNVTPEDSGTYTC 68


                   ....
gi 1907176927  140 LRGN 143
Cdd:smart00410  69 AATN 72
Ig_3 pfam13927
Immunoglobulin domain; This family contains immunoglobulin-like domains.
 62-139 3.77e-03

Immunoglobulin domain; This family contains immunoglobulin-like domains.


Pssm-ID: 464046 [Multi-domain]  Cd Length: 78  Bit Score: 36.00  E-value: 3.77e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907176927  62 NQDLTVAPGSTLWLSCGV--PPVPvakgSISWTHVHPRRPNVSLLSLSLGGEhpvremwvwGSLLLLPQATALDEGTYYC 139
Cdd:pfam13927   8 PSSVTVREGETVTLTCEAtgSPPP----TITWYKNGEPISSGSTRSRSLSGS---------NSTLTISNVTRSDAGTYTC 74
 
Name Accession Description Interval E-value
CD19_protodomain_3_4 cd23998
CD19 (Cluster of Differentiation 19), a unique double immunoglobulin (Ig)-fold protodomain 3 ...
 63-152 2.17e-44

CD19 (Cluster of Differentiation 19), a unique double immunoglobulin (Ig)-fold protodomain 3 and 4; CD19, also known as B-Lymphocyte Surface Antigen B4, T-Cell Surface Antigen Leu-12, and CVID3, is a transmembrane receptor present on various types of B cells, including progenitor, naive, and memory B cells, as well as plasmablasts. Until recently, it was believed to comprise two extracellular immunoglobulin (Ig) structural domains arranged in tandem with C2 topology. However, recent crystal structures have shown that the CD19 extracellular domain contains a unique double Ig domain that is responsible for its binding to proteins such as CD21, CD81, and CD225, which regulate B cell activation and survival. A recent analysis of the CD19 extracellular domain sequence reveals two "Ig domains", but the structure demonstrates that these two domains are not folded independently and connected in tandem. Rather, they fold together as one intertwined domain that can be referred to as a "double Ig" domain. Each of the two regular Ig domain sequences has a noticeably short linker that forms a loop between strands C' and D, rather than allowing the formation of a C" strand. Additionally, the two Ig-domain sequences are separated by a long linker that is structured as a small insertion domain, enabling both Ig sequences to fold together as a unique double Ig-domain. The CD19 domain comprises four "protodomains": two formed by A'B-CC' strands and two by DE-FG strands that interdigitate to form a novel double Ig fold. When analyzing this double Ig domain in terms of the usual Ig-fold, A'B-CC' protodomain of the first Ig sequence combines with DE-FG protodomain of the second, and vice versa. Hence, the second combined Ig fold is inverted, with DE-FG protodomain of the first Ig sequence combining with A'B-CC' protodomain of the second Ig sequence and in that order, as if it were a circular permutation, obtained only through structural folding. This group contains the protodomains 3 and 4 of the CD19 double Ig domain.


Pssm-ID: 467825  Cd Length: 95  Bit Score: 149.56  E-value: 2.17e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907176927  63 QDLTVAPGSTLWLSCGVPPVPVAKGSISWTHVHPRRPNVSLLSLSLGGEHPVREMWV-----WGSLLLLPQATALDEGTY 137
Cdd:cd23998     1 QDLTVAPGSTLWLSCGVPPDSGTRGPISWTHVHPKPSNTSLLSLELKEDRPAREKWVlgtlrGGALLLLPRATAQDAGIY 80

                          90
                  ....*....|....*
gi 1907176927 138 YCLRGNLTIERHVKV 152
Cdd:cd23998    81 HCHLGNRTISMELTV 95
CD19_double_Ig cd23997
CD19 (Cluster of Differentiation 19), a unique double immunoglobulin (Ig)-fold domain; CD19, ...
 63-152 1.66e-23

CD19 (Cluster of Differentiation 19), a unique double immunoglobulin (Ig)-fold domain; CD19, also known as B-Lymphocyte Surface Antigen B4, T-Cell Surface Antigen Leu-12, and CVID3, is a transmembrane receptor present on various types of B cells, including progenitor, naive, and memory B cells, as well as plasmablasts. Until recently, it was believed to comprise two extracellular immunoglobulin (Ig) structural domains arranged in tandem with C2 topology. However, recent crystal structures have shown that the CD19 extracellular domain contains a unique double Ig domain that is responsible for its binding to proteins such as CD21, CD81, and CD225, which regulate B cell activation and survival. A recent analysis of the CD19 extracellular domain sequence reveals two "Ig domains", but the structure demonstrates that these two domains are not folded independently and connected in tandem. Rather, they fold together as one intertwined domain that can be referred to as a "double Ig" domain. Each of the two regular Ig domain sequences has a noticeably short linker that forms a loop between strands C' and D, rather than allowing the formation of a C" strand. Additionally, the two Ig-domain sequences are separated by a long linker that is structured as a small insertion domain, enabling both Ig sequences to fold together as a unique double Ig-domain. The CD19 domain comprises four "protodomains": two formed by A'B-CC' strands and two by DE-FG strands that interdigitate to form a novel double Ig fold. When analyzing this double Ig domain in terms of the usual Ig-fold, A'B-CC' protodomain of the first Ig sequence combines with DE-FG protodomain of the second, and vice versa. Hence, the second combined Ig fold is inverted, with DE-FG protodomain of the first Ig sequence combining with A'B-CC' protodomain of the second Ig sequence and in that order, as if it were a circular permutation, obtained only through structural folding.


Pssm-ID: 467824  Cd Length: 89  Bit Score: 93.56  E-value: 1.66e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907176927  63 QDLTVAPGSTLWLSCGVPPVPVAKGSISWTHVHPRrpnVSLLSLSLGGehpvREMWV----WGSLLLLPQATALDEGTYY 138
Cdd:cd23997     1 LDVTVAEGSTLWLPCLVPPSDGPRGPLTWSRGHPK---TPLLSLELGS----PGLWVlvgpLGILLLLPNVSAQMGGFYL 73

                          90
                  ....*....|....*.
gi 1907176927 139 CLRGNL--TIERHVKV 152
Cdd:cd23997    74 CELGNLswTIGWTVSV 89
Ig_Semaphorin_C cd04979
Immunoglobulin (Ig)-like domain at the C-terminus of semaphorins; The members here are ...
 65-147 2.92e-09

Immunoglobulin (Ig)-like domain at the C-terminus of semaphorins; The members here are composed of the immunoglobulin (Ig)-like domain in semaphorins. Semaphorins are transmembrane protein that have important roles in a variety of tissues. Functionally, semaphorins were initially characterized for their importance in the development of the nervous system and in axonal guidance. Later they have been found to be important for the formation and functioning of the cardiovascular, endocrine, gastrointestinal, hepatic, immune, musculoskeletal, renal, reproductive, and respiratory systems. Semaphorins function through binding to their receptors and transmembrane semaphorins also serves as receptors themselves. Although molecular mechanism of semaphorins is poorly understood, the Ig-like domains may be involved in ligand binding or dimerization.


Pssm-ID: 409368  Cd Length: 88  Bit Score: 53.62  E-value: 2.92e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907176927  65 LTVAPGSTLWLSCGVPPvpvAKGSISWTHVHPRRPnvsllslslgGEHPVREMWVWGSLLLLPQATALDEGTYYCLRGNL 144
Cdd:cd04979     6 ISVKEGDTVILSCSVKS---NNAPVTWIHNGKKVP----------RYRSPRLVLKTERGLLIRSAQEADAGVYECHSGER 72


                  ...
gi 1907176927 145 TIE 147
Cdd:cd04979    73 VLG 75
IG_like smart00410
Immunoglobulin like; IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
 63-143 4.13e-04

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: 39.03  E-value: 4.13e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907176927   63 QDLTVAPGSTLWLSCGVPPVPVAkgSISWthvhpRRPNVSLLSlslggeHPVREMWVWGSL---LLLPQATALDEGTYYC 139
Cdd:smart00410   2 PSVTVKEGESVTLSCEASGSPPP--EVTW-----YKQGGKLLA------ESGRFSVSRSGStstLTISNVTPEDSGTYTC 68


                   ....
gi 1907176927  140 LRGN 143
Cdd:smart00410  69 AATN 72
Ig_3 pfam13927
Immunoglobulin domain; This family contains immunoglobulin-like domains.
 62-139 3.77e-03

Immunoglobulin domain; This family contains immunoglobulin-like domains.


Pssm-ID: 464046 [Multi-domain]  Cd Length: 78  Bit Score: 36.00  E-value: 3.77e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907176927  62 NQDLTVAPGSTLWLSCGV--PPVPvakgSISWTHVHPRRPNVSLLSLSLGGEhpvremwvwGSLLLLPQATALDEGTYYC 139
Cdd:pfam13927   8 PSSVTVREGETVTLTCEAtgSPPP----TITWYKNGEPISSGSTRSRSLSGS---------NSTLTISNVTRSDAGTYTC 74
ig pfam00047
Immunoglobulin domain; Members of the immunoglobulin superfamily are found in hundreds of ...
 60-139 4.92e-03

Immunoglobulin domain; Members of the immunoglobulin superfamily are found in hundreds of proteins of different functions. Examples include antibodies, the giant muscle kinase titin and receptor tyrosine kinases. Immunoglobulin-like domains may be involved in protein-protein and protein-ligand interactions.


Pssm-ID: 395002  Cd Length: 86  Bit Score: 36.02  E-value: 4.92e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907176927  60 LINQDLTVAPGSTLWLSCGVPPVPVAkGSISWthvhpRRPNVSLLSLSLGGEHPVREMwvwGSLLLLPQATALDEGTYYC 139
Cdd:pfam00047   1 SAPPTVTVLEGDSATLTCSASTGSPG-PDVTW-----SKEGGTLIESLKVKHDNGRTT---QSSLLISNVTKEDAGTYTC 71
 
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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