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Conserved domains on  [gi|1938948715|pdb|4U8U|c]
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Chain c, Linker L2

Protein Classification

LDL receptor domain-containing protein( domain architecture ID 11258030)

Low Density Lipoprotein (LDL) receptor class A domain is a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; similar to Bos taurus CD320 antigen

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
hemoglobin_linker_C super family cl17028
Globular domain of extracellular hemoglobin linker; This family of hemoglobin linker chains is ...
 111-231 1.38e-32

Globular domain of extracellular hemoglobin linker; This family of hemoglobin linker chains is restricted to annelid worms, and participates in the formation of the large erythrocruorin respiratory complex. Via its N-terminal coiled-coil segment (not included in this model), the molecule forms trimers, which are part of a scaffold organizing the overall complex architecture; the latter encompasses 36 linkers and 144 hemoglobins in total. This C-terminal globular domain is involved in trimerization, and also interacts with globins and other C-terminal globular linker domains of neighboring trimers. The structure resembles that of nitrophorins and lipocalins.


The actual alignment was detected with superfamily member pfam16915:

Pssm-ID: 327373  Cd Length: 120  Bit Score: 114.75  E-value: 1.38e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
4U8U_c        111 PVKPGNIFSGTSHWHDCLLRSDHVTRVVIKGTIRRNYFKSRIWVRAQIESDLIHDGKKELSDFDSKGYYNFANRRLVLIP 190
Cdd:pfam16915   1 PTPAGSSFIGDLNWDHCTKRRPKHMDIHITSVKRSSFFPSRPWVKATVDLESHQDGHEQTSTLPVDGFYNFGSRRLILLP 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
4U8U_c        191 iaQDDKHLSVICDFDRGDSRRASCHRVLEGTLHQCANLSVH 231
Cdd:pfam16915  81 --PEGDGLGLVCSFDGGDDDRCKGHIVRESSLDVCAEFILT 119
LDLa smart00192
Low-density lipoprotein receptor domain class A; Cysteine-rich repeat in the low-density ...
 69-102 8.16e-08

Low-density lipoprotein receptor domain class A; Cysteine-rich repeat in the low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. The N-terminal type A repeats in LDL receptor bind the lipoproteins. Other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement. Mutations in the LDL receptor gene cause familial hypercholesterolemia.


:

Pssm-ID: 197566  Cd Length: 33  Bit Score: 47.24  E-value: 8.16e-08
                           10        20        30
                   ....*....|....*....|....*....|....
4U8U_c          69 CAKKEFQCGgyDQECISDLFVCDGHKDCHNGHDE 102
Cdd:smart00192   2 CPPGEFQCD--NGRCIPSSWVCDGVDDCGDGSDE 33
 
Name Accession Description Interval E-value
Eryth_link_C pfam16915
Annelid erythrocruorin linker subunit C-terminus; This domain is found in linker subunits of ...
 111-231 1.38e-32

Annelid erythrocruorin linker subunit C-terminus; This domain is found in linker subunits of the erythrocruorin respiratory complex in annelid worms.


Pssm-ID: 319001  Cd Length: 120  Bit Score: 114.75  E-value: 1.38e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
4U8U_c        111 PVKPGNIFSGTSHWHDCLLRSDHVTRVVIKGTIRRNYFKSRIWVRAQIESDLIHDGKKELSDFDSKGYYNFANRRLVLIP 190
Cdd:pfam16915   1 PTPAGSSFIGDLNWDHCTKRRPKHMDIHITSVKRSSFFPSRPWVKATVDLESHQDGHEQTSTLPVDGFYNFGSRRLILLP 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
4U8U_c        191 iaQDDKHLSVICDFDRGDSRRASCHRVLEGTLHQCANLSVH 231
Cdd:pfam16915  81 --PEGDGLGLVCSFDGGDDDRCKGHIVRESSLDVCAEFILT 119
hemoglobin_linker_C cd11673
Globular domain of extracellular hemoglobin linker; This family of hemoglobin linker chains is ...
 112-231 2.67e-32

Globular domain of extracellular hemoglobin linker; This family of hemoglobin linker chains is restricted to annelid worms, and participates in the formation of the large erythrocruorin respiratory complex. Via its N-terminal coiled-coil segment (not included in this model), the molecule forms trimers, which are part of a scaffold organizing the overall complex architecture; the latter encompasses 36 linkers and 144 hemoglobins in total. This C-terminal globular domain is involved in trimerization, and also interacts with globins and other C-terminal globular linker domains of neighboring trimers. The structure resembles that of nitrophorins and lipocalins.


Pssm-ID: 212563  Cd Length: 120  Bit Score: 114.01  E-value: 2.67e-32
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
4U8U_c      112 VKPGNIFSGTSHWHDCLLRSDHVTRVVIKGTIRRNYFKSRIWVRAQIESDLIHDGKKELSDFDSKGYYNFANRRLVLIPi 191
Cdd:cd11673   1 TAAGSSFSGDLEWDHCTKRRPKHMDIHITSVKRYSFFPSRPKVKATVVIESTKDGDEQTSSLQVKGFYSFGSRRLILLP- 79

                        90       100       110       120
                ....*....|....*....|....*....|....*....|
4U8U_c      192 AQDDKHLSVICDFDRGDSRRASCHRVLEGTLHQCANLSVH 231
Cdd:cd11673  80 PDGLDGLGFVCDFDGGDNDRCKGHIVREASGDVCATFILT 119
LDLa smart00192
Low-density lipoprotein receptor domain class A; Cysteine-rich repeat in the low-density ...
 69-102 8.16e-08

Low-density lipoprotein receptor domain class A; Cysteine-rich repeat in the low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. The N-terminal type A repeats in LDL receptor bind the lipoproteins. Other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement. Mutations in the LDL receptor gene cause familial hypercholesterolemia.


Pssm-ID: 197566  Cd Length: 33  Bit Score: 47.24  E-value: 8.16e-08
                           10        20        30
                   ....*....|....*....|....*....|....
4U8U_c          69 CAKKEFQCGgyDQECISDLFVCDGHKDCHNGHDE 102
Cdd:smart00192   2 CPPGEFQCD--NGRCIPSSWVCDGVDDCGDGSDE 33
LDLa cd00112
Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central ...
 69-103 1.03e-06

Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure


Pssm-ID: 238060  Cd Length: 35  Bit Score: 44.12  E-value: 1.03e-06
                        10        20        30
                ....*....|....*....|....*....|....*
4U8U_c       69 CAKKEFQCGgyDQECISDLFVCDGHKDCHNGHDEA 103
Cdd:cd00112   1 CPPNEFRCA--NGRCIPSSWVCDGEDDCGDGSDEE 33
Ldl_recept_a pfam00057
Low-density lipoprotein receptor domain class A;
69-104 1.48e-05

Low-density lipoprotein receptor domain class A;


Pssm-ID: 395011  Cd Length: 37  Bit Score: 41.08  E-value: 1.48e-05
                          10        20        30
                  ....*....|....*....|....*....|....*.
4U8U_c         69 CAKKEFQCGgyDQECISDLFVCDGHKDCHNGHDEAE 104
Cdd:pfam00057   3 CSPNEFQCG--SGECIPRSWVCDGDPDCGDGSDEEN 36
 
Name Accession Description Interval E-value
Eryth_link_C pfam16915
Annelid erythrocruorin linker subunit C-terminus; This domain is found in linker subunits of ...
 111-231 1.38e-32

Annelid erythrocruorin linker subunit C-terminus; This domain is found in linker subunits of the erythrocruorin respiratory complex in annelid worms.


Pssm-ID: 319001  Cd Length: 120  Bit Score: 114.75  E-value: 1.38e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
4U8U_c        111 PVKPGNIFSGTSHWHDCLLRSDHVTRVVIKGTIRRNYFKSRIWVRAQIESDLIHDGKKELSDFDSKGYYNFANRRLVLIP 190
Cdd:pfam16915   1 PTPAGSSFIGDLNWDHCTKRRPKHMDIHITSVKRSSFFPSRPWVKATVDLESHQDGHEQTSTLPVDGFYNFGSRRLILLP 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
4U8U_c        191 iaQDDKHLSVICDFDRGDSRRASCHRVLEGTLHQCANLSVH 231
Cdd:pfam16915  81 --PEGDGLGLVCSFDGGDDDRCKGHIVRESSLDVCAEFILT 119
hemoglobin_linker_C cd11673
Globular domain of extracellular hemoglobin linker; This family of hemoglobin linker chains is ...
 112-231 2.67e-32

Globular domain of extracellular hemoglobin linker; This family of hemoglobin linker chains is restricted to annelid worms, and participates in the formation of the large erythrocruorin respiratory complex. Via its N-terminal coiled-coil segment (not included in this model), the molecule forms trimers, which are part of a scaffold organizing the overall complex architecture; the latter encompasses 36 linkers and 144 hemoglobins in total. This C-terminal globular domain is involved in trimerization, and also interacts with globins and other C-terminal globular linker domains of neighboring trimers. The structure resembles that of nitrophorins and lipocalins.


Pssm-ID: 212563  Cd Length: 120  Bit Score: 114.01  E-value: 2.67e-32
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
4U8U_c      112 VKPGNIFSGTSHWHDCLLRSDHVTRVVIKGTIRRNYFKSRIWVRAQIESDLIHDGKKELSDFDSKGYYNFANRRLVLIPi 191
Cdd:cd11673   1 TAAGSSFSGDLEWDHCTKRRPKHMDIHITSVKRYSFFPSRPKVKATVVIESTKDGDEQTSSLQVKGFYSFGSRRLILLP- 79

                        90       100       110       120
                ....*....|....*....|....*....|....*....|
4U8U_c      192 AQDDKHLSVICDFDRGDSRRASCHRVLEGTLHQCANLSVH 231
Cdd:cd11673  80 PDGLDGLGFVCDFDGGDNDRCKGHIVREASGDVCATFILT 119
LDLa smart00192
Low-density lipoprotein receptor domain class A; Cysteine-rich repeat in the low-density ...
 69-102 8.16e-08

Low-density lipoprotein receptor domain class A; Cysteine-rich repeat in the low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. The N-terminal type A repeats in LDL receptor bind the lipoproteins. Other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement. Mutations in the LDL receptor gene cause familial hypercholesterolemia.


Pssm-ID: 197566  Cd Length: 33  Bit Score: 47.24  E-value: 8.16e-08
                           10        20        30
                   ....*....|....*....|....*....|....
4U8U_c          69 CAKKEFQCGgyDQECISDLFVCDGHKDCHNGHDE 102
Cdd:smart00192   2 CPPGEFQCD--NGRCIPSSWVCDGVDDCGDGSDE 33
LDLa cd00112
Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central ...
 69-103 1.03e-06

Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure


Pssm-ID: 238060  Cd Length: 35  Bit Score: 44.12  E-value: 1.03e-06
                        10        20        30
                ....*....|....*....|....*....|....*
4U8U_c       69 CAKKEFQCGgyDQECISDLFVCDGHKDCHNGHDEA 103
Cdd:cd00112   1 CPPNEFRCA--NGRCIPSSWVCDGEDDCGDGSDEE 33
Ldl_recept_a pfam00057
Low-density lipoprotein receptor domain class A;
69-104 1.48e-05

Low-density lipoprotein receptor domain class A;


Pssm-ID: 395011  Cd Length: 37  Bit Score: 41.08  E-value: 1.48e-05
                          10        20        30
                  ....*....|....*....|....*....|....*.
4U8U_c         69 CAKKEFQCGgyDQECISDLFVCDGHKDCHNGHDEAE 104
Cdd:pfam00057   3 CSPNEFQCG--SGECIPRSWVCDGDPDCGDGSDEEN 36
 
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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