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Conserved domains on  [gi|564356676|ref|XP_006240409|]
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DDB1- and CUL4-associated factor 4 isoform X1 [Rattus norvegicus]

Protein Classification

WD40 repeat domain-containing protein( domain architecture ID 1000017)

WD40 repeat domain-containing protein folds into a beta-propeller structure and functions as a scaffold, providing a platform for the interaction and assembly of several proteins into a signalosome; similar to a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly

CATH:  2.130.10.10
Gene Ontology:  GO:0005515
PubMed:  10322433|8090199|30069656|29026209
SCOP:  4002744

Graphical summary

 Zoom to residue level

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List of domain hits

 Name Accession Description Interval E-value
WD40 super family cl29593
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 311-471 3.68e-10

WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment.


The actual alignment was detected with superfamily member cd00200:

Pssm-ID: 475233 [Multi-domain]  Cd Length: 289  Bit Score: 60.81  E-value: 3.68e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564356676 311 LTNVVTGHRqsywtnSDVLAQQFAVKTPLLFNGCRSGEIFAIDLRSPSQakgwKATQIFHDSAVTSVQVFKEEQYLMASD 390
Cdd:cd00200    1 LRRTLKGHT------GGVTCVAFSPDGKLLATGSGDGTIKVWDLETGEL----LRTLKGHTGPVRDVAASADGTYLASGS 70

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564356676 391 MAGKIKLWDLRATKCVRQYEGH---VNEYAYLPLHmheeeGILVAVGQDCYTRIWSLHDARLLRTIPSPcptsKANIPSV 467
Cdd:cd00200   71 SDKTIRLWDLETGECVRTLTGHtsyVSSVAFSPDG-----RILSSSSRDKTIKVWDVETGKCLTTLRGH----TDWVNSV 141


                 ....
gi 564356676 468 AFSP 471
Cdd:cd00200  142 AFSP 145
 
Name Accession Description Interval E-value
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 311-471 3.68e-10

WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment.


Pssm-ID: 238121 [Multi-domain]  Cd Length: 289  Bit Score: 60.81  E-value: 3.68e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564356676 311 LTNVVTGHRqsywtnSDVLAQQFAVKTPLLFNGCRSGEIFAIDLRSPSQakgwKATQIFHDSAVTSVQVFKEEQYLMASD 390
Cdd:cd00200    1 LRRTLKGHT------GGVTCVAFSPDGKLLATGSGDGTIKVWDLETGEL----LRTLKGHTGPVRDVAASADGTYLASGS 70

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564356676 391 MAGKIKLWDLRATKCVRQYEGH---VNEYAYLPLHmheeeGILVAVGQDCYTRIWSLHDARLLRTIPSPcptsKANIPSV 467
Cdd:cd00200   71 SDKTIRLWDLETGECVRTLTGHtsyVSSVAFSPDG-----RILSSSSRDKTIKVWDVETGKCLTTLRGH----TDWVNSV 141


                 ....
gi 564356676 468 AFSP 471
Cdd:cd00200  142 AFSP 145
WD40 COG2319
WD40 repeat [General function prediction only];
370-471 2.36e-09

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 59.15  E-value: 2.36e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564356676 370 HDSAVTSVQVFKEEQYLMASDMAGKIKLWDLRATKCVRQYEGH---VNEYAYLPlhmheeEG-ILVAVGQDCYTRIWSLH 445
Cdd:COG2319  161 HSGAVTSVAFSPDGKLLASGSDDGTVRLWDLATGKLLRTLTGHtgaVRSVAFSP------DGkLLASGSADGTVRLWDLA 234

                         90       100
                 ....*....|....*....|....*.
gi 564356676 446 DARLLRTIPSPcptsKANIPSVAFSP 471
Cdd:COG2319  235 TGKLLRTLTGH----SGSVRSVAFSP 256
 
Name Accession Description Interval E-value
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 311-471 3.68e-10

WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment.


Pssm-ID: 238121 [Multi-domain]  Cd Length: 289  Bit Score: 60.81  E-value: 3.68e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564356676 311 LTNVVTGHRqsywtnSDVLAQQFAVKTPLLFNGCRSGEIFAIDLRSPSQakgwKATQIFHDSAVTSVQVFKEEQYLMASD 390
Cdd:cd00200    1 LRRTLKGHT------GGVTCVAFSPDGKLLATGSGDGTIKVWDLETGEL----LRTLKGHTGPVRDVAASADGTYLASGS 70

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564356676 391 MAGKIKLWDLRATKCVRQYEGH---VNEYAYLPLHmheeeGILVAVGQDCYTRIWSLHDARLLRTIPSPcptsKANIPSV 467
Cdd:cd00200   71 SDKTIRLWDLETGECVRTLTGHtsyVSSVAFSPDG-----RILSSSSRDKTIKVWDVETGKCLTTLRGH----TDWVNSV 141


                 ....
gi 564356676 468 AFSP 471
Cdd:cd00200  142 AFSP 145
WD40 COG2319
WD40 repeat [General function prediction only];
370-471 2.36e-09

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 59.15  E-value: 2.36e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564356676 370 HDSAVTSVQVFKEEQYLMASDMAGKIKLWDLRATKCVRQYEGH---VNEYAYLPlhmheeEG-ILVAVGQDCYTRIWSLH 445
Cdd:COG2319  161 HSGAVTSVAFSPDGKLLASGSDDGTVRLWDLATGKLLRTLTGHtgaVRSVAFSP------DGkLLASGSADGTVRLWDLA 234

                         90       100
                 ....*....|....*....|....*.
gi 564356676 446 DARLLRTIPSPcptsKANIPSVAFSP 471
Cdd:COG2319  235 TGKLLRTLTGH----SGSVRSVAFSP 256
WD40 COG2319
WD40 repeat [General function prediction only];
345-471 3.05e-09

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 59.15  E-value: 3.05e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564356676 345 RSGEIFAIDLRSPSQAKGWKATQIFHDSAVTSVQVFKEEQYLMASDMAGKIKLWDLRATKCVRQYEGH---VNEYAYLPl 421
Cdd:COG2319   52 AAGAGDLTLLLLDAAAGALLATLLGHTAAVLSVAFSPDGRLLASASADGTVRLWDLATGLLLRTLTGHtgaVRSVAFSP- 130

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 564356676 422 hmheeEG-ILVAVGQDCYTRIWSLHDARLLRTIPSPcptsKANIPSVAFSP 471
Cdd:COG2319  131 -----DGkTLASGSADGTVRLWDLATGKLLRTLTGH----SGAVTSVAFSP 172
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 316-443 5.59e-09

WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment.


Pssm-ID: 238121 [Multi-domain]  Cd Length: 289  Bit Score: 57.34  E-value: 5.59e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564356676 316 TGHrqsywtNSDVLAQQFAVKTPLLFNGCRSGEIFAIDLRSPSqakgWKATQIFHDSAVTSVQVFKEEQYLMASDMAGKI 395
Cdd:cd00200  174 TGH------TGEVNSVAFSPDGEKLLSSSSDGTIKLWDLSTGK----CLGTLRGHENGVNSVAFSPDGYLLASGSEDGTI 243

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 564356676 396 KLWDLRATKCVRQYEGHVNE-YAylpLHMHEEEGILVAVGQDCYTRIWS 443
Cdd:cd00200  244 RVWDLRTGECVQTLSGHTNSvTS---LAWSPDGKRLASGSADGTIRIWD 289
WD40 cd00200
WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions ...
 287-471 1.48e-08

WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment.


Pssm-ID: 238121 [Multi-domain]  Cd Length: 289  Bit Score: 56.19  E-value: 1.48e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564356676 287 WSCAWSLNvqANNCFSTGLSRRVLLTNVVTGHRQSYWT--NSDVLAQQFAVKTPLLFNGCRSGEIFAIDLRSPSQakgwK 364
Cdd:cd00200   55 RDVAASAD--GTYLASGSSDKTIRLWDLETGECVRTLTghTSYVSSVAFSPDGRILSSSSRDKTIKVWDVETGKC----L 128

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564356676 365 ATQIFHDSAVTSVQVFKEEQYLMASDMAGKIKLWDLRATKCVRQYEGHVNEYAYLPLhmHEEEGILVAVGQDCYTRIWSL 444
Cdd:cd00200  129 TTLRGHTDWVNSVAFSPDGTFVASSSQDGTIKLWDLRTGKCVATLTGHTGEVNSVAF--SPDGEKLLSSSSDGTIKLWDL 206

                        170       180
                 ....*....|....*....|....*..
gi 564356676 445 HDARLLRTIPSpcptSKANIPSVAFSP 471
Cdd:cd00200  207 STGKCLGTLRG----HENGVNSVAFSP 229
WD40 COG2319
WD40 repeat [General function prediction only];
370-471 1.83e-08

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 56.46  E-value: 1.83e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564356676 370 HDSAVTSVQVFKEEQYLMASDMAGKIKLWDLRATKCVRQYEGH---VNEYAYLPlhmheeEG-ILVAVGQDCYTRIWSLH 445
Cdd:COG2319  203 HTGAVRSVAFSPDGKLLASGSADGTVRLWDLATGKLLRTLTGHsgsVRSVAFSP------DGrLLASGSADGTVRLWDLA 276

                         90       100
                 ....*....|....*....|....*.
gi 564356676 446 DARLLRTIPSPcptsKANIPSVAFSP 471
Cdd:COG2319  277 TGELLRTLTGH----SGGVNSVAFSP 298
WD40 COG2319
WD40 repeat [General function prediction only];
370-471 2.04e-08

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 56.46  E-value: 2.04e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564356676 370 HDSAVTSVQVFKEEQYLMASDMAGKIKLWDLRATKCVRQYEGH---VNEYAYLPlhmheEEGILVAVGQDCYTRIWSLHD 446
Cdd:COG2319  287 HSGGVNSVAFSPDGKLLASGSDDGTVRLWDLATGKLLRTLTGHtgaVRSVAFSP-----DGKTLASGSDDGTVRLWDLAT 361

                         90       100
                 ....*....|....*....|....*
gi 564356676 447 ARLLRTIPSPcptsKANIPSVAFSP 471
Cdd:COG2319  362 GELLRTLTGH----TGAVTSVAFSP 382
WD40 COG2319
WD40 repeat [General function prediction only];
370-471 3.11e-08

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 55.69  E-value: 3.11e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564356676 370 HDSAVTSVQVFKEEQYLMASDMAGKIKLWDLRATKCVRQYEGH---VNEYAYLPlhmheeEG-ILVAVGQDCYTRIWSLH 445
Cdd:COG2319  245 HSGSVRSVAFSPDGRLLASGSADGTVRLWDLATGELLRTLTGHsggVNSVAFSP------DGkLLASGSDDGTVRLWDLA 318

                         90       100
                 ....*....|....*....|....*.
gi 564356676 446 DARLLRTIPSPcptsKANIPSVAFSP 471
Cdd:COG2319  319 TGKLLRTLTGH----TGAVRSVAFSP 340
WD40 COG2319
WD40 repeat [General function prediction only];
284-446 2.99e-05

WD40 repeat [General function prediction only];


Pssm-ID: 441893 [Multi-domain]  Cd Length: 403  Bit Score: 46.44  E-value: 2.99e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564356676 284 PGAWSCAWSLNVQAnnCFSTGLSRRVLLTNVVTGHRQSYWTNSDVLAQQFAVkTP---LLFNGCRSGEIFAIDLRSPSQA 360
Cdd:COG2319  247 GSVRSVAFSPDGRL--LASGSADGTVRLWDLATGELLRTLTGHSGGVNSVAF-SPdgkLLASGSDDGTVRLWDLATGKLL 323

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564356676 361 KGWKAtqifHDSAVTSVQVFKEEQYLMASDMAGKIKLWDLRATKCVRQYEGH---VNEYAYLPlhmheEEGILVAVGQDC 437
Cdd:COG2319  324 RTLTG----HTGAVRSVAFSPDGKTLASGSDDGTVRLWDLATGELLRTLTGHtgaVTSVAFSP-----DGRTLASGSADG 394


                 ....*....
gi 564356676 438 YTRIWSLHD 446
Cdd:COG2319  395 TVRLWDLAT 403
 
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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