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Conserved domains on  [gi|530417367|ref|XP_005259368|]
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zinc finger protein 541 isoform X2 [Homo sapiens]

Protein Classification

ELM2 and SANT/Myb-like DNA-binding domain-containing protein; SANT/Myb-like DNA-binding domain-containing C2H2 zinc finger protein( domain architecture ID 11473110)

ELM2 and SANT/Myb-like DNA-binding domain-containing protein similar to REST corepressor 3, may act as a component of a corepressor complex that represses transcription| SANT (SWI3, ADA2, N-CoR and TFIIIB)/Myb-like DNA-binding domain-containing C2H2 (Cys2His2) zinc finger protein binds DNA and may function as a transcription factor, and may also bind zinc ions

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
ELM2 pfam01448
ELM2 domain; The ELM2 (Egl-27 and MTA1 homology 2) domain is a small domain of unknown ...
 1055-1110 7.96e-12

ELM2 domain; The ELM2 (Egl-27 and MTA1 homology 2) domain is a small domain of unknown function. It is found in the MTA1 protein that is part of the NuRD complex. The domain is usually found to the N terminus of a myb-like DNA binding domain pfam00249. ELM2 is also found associated with an ARID DNA binding domain pfam01388 in Swiss:O82364. This suggests that ELM2 may also be involved in DNA binding, or perhaps is a protein-protein interaction domain.


:

Pssm-ID: 460214  Cd Length: 53  Bit Score: 61.47  E-value: 7.96e-12
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 530417367  1055 INIGSRFQAEIPELQERSLAGTDEHVA--SLVWKPWGDMmisseTQDRVTELCNVACS 1110
Cdd:pfam01448    1 IRVGPRYQAEIPELLPPSEEEDRYEEEdeLLVWDPNHNL-----PDRKLDEYLVVARS 53
SANT super family cl21498
'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric ...
 1165-1208 1.26e-11

'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA.


The actual alignment was detected with superfamily member cd11661:

Pssm-ID: 473887 [Multi-domain]  Cd Length: 46  Bit Score: 60.71  E-value: 1.26e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 530417367 1165 WTPIEKRLFKKAFYAHKKDFYLIHK-MIQTKTVAQCVEYYYIWKK 1208
Cdd:cd11661     2 WSESEAKLFEEGLRKYGKDFHDIRQdFLPWKSVGELVEFYYMWKK 46
COG5048 COG5048
FOG: Zn-finger [General function prediction only];
150-319 7.92e-05

FOG: Zn-finger [General function prediction only];


:

Pssm-ID: 227381 [Multi-domain]  Cd Length: 467  Bit Score: 47.00  E-value: 7.92e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530417367  150 SSASSLSKHYLTHSQERKHVCKICSKAFKRQDHLTGHMLTHQKTKPFVCIEQGCSKSYCD----YRSLRRHYEVHHGLCI 225
Cdd:COG5048    16 LSSTPKSTLKSLSNAPRPDSCPNCTDSFSRLEHLTRHIRSHTGEKPSQCSYSGCDKSFSRplelSRHLRTHHNNPSDLNS 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530417367  226 LKEAPPEEEACGDSPHAH----------ESAGQPPPSSLRSLVPPEARSPGSLLPHRDLLRRIVSSIVHQKTPSPGPAPA 295
Cdd:COG5048    96 KSLPLSNSKASSSSLSSSssnsndnnllSSHSLPPSSRDPQLPDLLSISNLRNNPLPGNNSSSVNTPQSNSLHPPLPANS 175

                         170       180
                  ....*....|....*....|....
gi 530417367  296 GASDSEGRNTACPCPASSGSSSCT 319
Cdd:COG5048   176 LSKDPSSNLSLLISSNVSTSIPSS 199
 
Name Accession Description Interval E-value
ELM2 pfam01448
ELM2 domain; The ELM2 (Egl-27 and MTA1 homology 2) domain is a small domain of unknown ...
 1055-1110 7.96e-12

ELM2 domain; The ELM2 (Egl-27 and MTA1 homology 2) domain is a small domain of unknown function. It is found in the MTA1 protein that is part of the NuRD complex. The domain is usually found to the N terminus of a myb-like DNA binding domain pfam00249. ELM2 is also found associated with an ARID DNA binding domain pfam01388 in Swiss:O82364. This suggests that ELM2 may also be involved in DNA binding, or perhaps is a protein-protein interaction domain.


Pssm-ID: 460214  Cd Length: 53  Bit Score: 61.47  E-value: 7.96e-12
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 530417367  1055 INIGSRFQAEIPELQERSLAGTDEHVA--SLVWKPWGDMmisseTQDRVTELCNVACS 1110
Cdd:pfam01448    1 IRVGPRYQAEIPELLPPSEEEDRYEEEdeLLVWDPNHNL-----PDRKLDEYLVVARS 53
SANT_MTA3_like cd11661
Myb-Like Dna-Binding Domain of MTA3 and related proteins; Members in this SANT/myb family ...
 1165-1208 1.26e-11

Myb-Like Dna-Binding Domain of MTA3 and related proteins; Members in this SANT/myb family include domains found in mouse metastasis-associated protein 3 (MTA3) proteins and arginine-glutamic dipeptide (RERE) repeats proteins. SANT (SWI3, ADA2, N-CoR and TFIIIB) DNA-binding domains are a diverse set of proteins that share a common 3 alpha-helix bundle. MTA3 has been shown to interact with nucleosome remodeling and deacetylase (NuRD) proteins CHD4 and HDAC1, and the core cohesin complex protein RAD21 in the ovary, and regulate G2/M progression in proliferating granulosa cells. RERE belongs to the atrophin family and has been identified as a nuclear receptor corepressor; altered expression levels of RERE are associated with cancer in humans while mutations of Rere in mice cause failure in closing the anterior neural tube and fusion of the telencephalic and optic vesicles during embryogenesis.


Pssm-ID: 212559 [Multi-domain]  Cd Length: 46  Bit Score: 60.71  E-value: 1.26e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 530417367 1165 WTPIEKRLFKKAFYAHKKDFYLIHK-MIQTKTVAQCVEYYYIWKK 1208
Cdd:cd11661     2 WSESEAKLFEEGLRKYGKDFHDIRQdFLPWKSVGELVEFYYMWKK 46
SANT smart00717
SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains;
1165-1209 3.43e-06

SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains;


Pssm-ID: 197842 [Multi-domain]  Cd Length: 49  Bit Score: 45.29  E-value: 3.43e-06
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*.
gi 530417367   1165 WTPIEKRLFKKAFYAH-KKDFYLIHKMIQTKTVAQCVEYYYIWKKM 1209
Cdd:smart00717    4 WTEEEDELLIELVKKYgKNNWEKIAKELPGRTAEQCRERWRNLLKP 49
COG5048 COG5048
FOG: Zn-finger [General function prediction only];
150-319 7.92e-05

FOG: Zn-finger [General function prediction only];


Pssm-ID: 227381 [Multi-domain]  Cd Length: 467  Bit Score: 47.00  E-value: 7.92e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530417367  150 SSASSLSKHYLTHSQERKHVCKICSKAFKRQDHLTGHMLTHQKTKPFVCIEQGCSKSYCD----YRSLRRHYEVHHGLCI 225
Cdd:COG5048    16 LSSTPKSTLKSLSNAPRPDSCPNCTDSFSRLEHLTRHIRSHTGEKPSQCSYSGCDKSFSRplelSRHLRTHHNNPSDLNS 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530417367  226 LKEAPPEEEACGDSPHAH----------ESAGQPPPSSLRSLVPPEARSPGSLLPHRDLLRRIVSSIVHQKTPSPGPAPA 295
Cdd:COG5048    96 KSLPLSNSKASSSSLSSSssnsndnnllSSHSLPPSSRDPQLPDLLSISNLRNNPLPGNNSSSVNTPQSNSLHPPLPANS 175

                         170       180
                  ....*....|....*....|....
gi 530417367  296 GASDSEGRNTACPCPASSGSSSCT 319
Cdd:COG5048   176 LSKDPSSNLSLLISSNVSTSIPSS 199
zf-C2H2 pfam00096
Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two ...
 168-190 1.05e-04

Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger. #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter.


Pssm-ID: 395048 [Multi-domain]  Cd Length: 23  Bit Score: 40.36  E-value: 1.05e-04
                           10        20
                   ....*....|....*....|...
gi 530417367   168 HVCKICSKAFKRQDHLTGHMLTH 190
Cdd:pfam00096    1 YKCPDCGKSFSRKSNLKRHLRTH 23
Myb_DNA-binding pfam00249
Myb-like DNA-binding domain; This family contains the DNA binding domains from Myb proteins, ...
 1165-1207 2.71e-04

Myb-like DNA-binding domain; This family contains the DNA binding domains from Myb proteins, as well as the SANT domain family.


Pssm-ID: 459731 [Multi-domain]  Cd Length: 46  Bit Score: 39.79  E-value: 2.71e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|...
gi 530417367  1165 WTPIEKRLFKKAFYAHKKDFYLIHKMIQTKTVAQCVEYYYIWK 1207
Cdd:pfam00249    4 WTPEEDELLLEAVEKLGNRWKKIAKLLPGRTDNQCKNRWQNYL 46
PHA00733 PHA00733
hypothetical protein
 142-187 2.86e-03

hypothetical protein


Pssm-ID: 177301  Cd Length: 128  Bit Score: 39.47  E-value: 2.86e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 530417367  142 CSLCGKVFSSASSLSKH--YLTHSQerkhVCKICSKAFKRQDHLTGHM 187
Cdd:PHA00733   76 CPLCLMPFSSSVSLKQHirYTEHSK----VCPVCGKEFRNTDSTLDHV 119
ZnF_C2H2 smart00355
zinc finger;
168-190 9.54e-03

zinc finger;


Pssm-ID: 197676  Cd Length: 23  Bit Score: 34.75  E-value: 9.54e-03
                            10        20
                    ....*....|....*....|...
gi 530417367    168 HVCKICSKAFKRQDHLTGHMLTH 190
Cdd:smart00355    1 YRCPECGKVFKSKSALREHMRTH 23
 
Name Accession Description Interval E-value
ELM2 pfam01448
ELM2 domain; The ELM2 (Egl-27 and MTA1 homology 2) domain is a small domain of unknown ...
 1055-1110 7.96e-12

ELM2 domain; The ELM2 (Egl-27 and MTA1 homology 2) domain is a small domain of unknown function. It is found in the MTA1 protein that is part of the NuRD complex. The domain is usually found to the N terminus of a myb-like DNA binding domain pfam00249. ELM2 is also found associated with an ARID DNA binding domain pfam01388 in Swiss:O82364. This suggests that ELM2 may also be involved in DNA binding, or perhaps is a protein-protein interaction domain.


Pssm-ID: 460214  Cd Length: 53  Bit Score: 61.47  E-value: 7.96e-12
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 530417367  1055 INIGSRFQAEIPELQERSLAGTDEHVA--SLVWKPWGDMmisseTQDRVTELCNVACS 1110
Cdd:pfam01448    1 IRVGPRYQAEIPELLPPSEEEDRYEEEdeLLVWDPNHNL-----PDRKLDEYLVVARS 53
SANT_MTA3_like cd11661
Myb-Like Dna-Binding Domain of MTA3 and related proteins; Members in this SANT/myb family ...
 1165-1208 1.26e-11

Myb-Like Dna-Binding Domain of MTA3 and related proteins; Members in this SANT/myb family include domains found in mouse metastasis-associated protein 3 (MTA3) proteins and arginine-glutamic dipeptide (RERE) repeats proteins. SANT (SWI3, ADA2, N-CoR and TFIIIB) DNA-binding domains are a diverse set of proteins that share a common 3 alpha-helix bundle. MTA3 has been shown to interact with nucleosome remodeling and deacetylase (NuRD) proteins CHD4 and HDAC1, and the core cohesin complex protein RAD21 in the ovary, and regulate G2/M progression in proliferating granulosa cells. RERE belongs to the atrophin family and has been identified as a nuclear receptor corepressor; altered expression levels of RERE are associated with cancer in humans while mutations of Rere in mice cause failure in closing the anterior neural tube and fusion of the telencephalic and optic vesicles during embryogenesis.


Pssm-ID: 212559 [Multi-domain]  Cd Length: 46  Bit Score: 60.71  E-value: 1.26e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 530417367 1165 WTPIEKRLFKKAFYAHKKDFYLIHK-MIQTKTVAQCVEYYYIWKK 1208
Cdd:cd11661     2 WSESEAKLFEEGLRKYGKDFHDIRQdFLPWKSVGELVEFYYMWKK 46
SANT smart00717
SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains;
1165-1209 3.43e-06

SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains;


Pssm-ID: 197842 [Multi-domain]  Cd Length: 49  Bit Score: 45.29  E-value: 3.43e-06
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*.
gi 530417367   1165 WTPIEKRLFKKAFYAH-KKDFYLIHKMIQTKTVAQCVEYYYIWKKM 1209
Cdd:smart00717    4 WTEEEDELLIELVKKYgKNNWEKIAKELPGRTAEQCRERWRNLLKP 49
SANT cd00167
'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric ...
 1165-1207 7.77e-06

'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA.


Pssm-ID: 238096 [Multi-domain]  Cd Length: 45  Bit Score: 44.10  E-value: 7.77e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 530417367 1165 WTPIEKRLFKKAFYAH-KKDFYLIHKMIQTKTVAQCVEYYYIWK 1207
Cdd:cd00167     2 WTEEEDELLLEAVKKYgKNNWEKIAKELPGRTPKQCRERWRNLL 45
COG5048 COG5048
FOG: Zn-finger [General function prediction only];
150-319 7.92e-05

FOG: Zn-finger [General function prediction only];


Pssm-ID: 227381 [Multi-domain]  Cd Length: 467  Bit Score: 47.00  E-value: 7.92e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530417367  150 SSASSLSKHYLTHSQERKHVCKICSKAFKRQDHLTGHMLTHQKTKPFVCIEQGCSKSYCD----YRSLRRHYEVHHGLCI 225
Cdd:COG5048    16 LSSTPKSTLKSLSNAPRPDSCPNCTDSFSRLEHLTRHIRSHTGEKPSQCSYSGCDKSFSRplelSRHLRTHHNNPSDLNS 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530417367  226 LKEAPPEEEACGDSPHAH----------ESAGQPPPSSLRSLVPPEARSPGSLLPHRDLLRRIVSSIVHQKTPSPGPAPA 295
Cdd:COG5048    96 KSLPLSNSKASSSSLSSSssnsndnnllSSHSLPPSSRDPQLPDLLSISNLRNNPLPGNNSSSVNTPQSNSLHPPLPANS 175

                         170       180
                  ....*....|....*....|....
gi 530417367  296 GASDSEGRNTACPCPASSGSSSCT 319
Cdd:COG5048   176 LSKDPSSNLSLLISSNVSTSIPSS 199
zf-C2H2 pfam00096
Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two ...
 168-190 1.05e-04

Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger. #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter.


Pssm-ID: 395048 [Multi-domain]  Cd Length: 23  Bit Score: 40.36  E-value: 1.05e-04
                           10        20
                   ....*....|....*....|...
gi 530417367   168 HVCKICSKAFKRQDHLTGHMLTH 190
Cdd:pfam00096    1 YKCPDCGKSFSRKSNLKRHLRTH 23
Myb_DNA-binding pfam00249
Myb-like DNA-binding domain; This family contains the DNA binding domains from Myb proteins, ...
 1165-1207 2.71e-04

Myb-like DNA-binding domain; This family contains the DNA binding domains from Myb proteins, as well as the SANT domain family.


Pssm-ID: 459731 [Multi-domain]  Cd Length: 46  Bit Score: 39.79  E-value: 2.71e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|...
gi 530417367  1165 WTPIEKRLFKKAFYAHKKDFYLIHKMIQTKTVAQCVEYYYIWK 1207
Cdd:pfam00249    4 WTPEEDELLLEAVEKLGNRWKKIAKLLPGRTDNQCKNRWQNYL 46
zf-C2H2_6 pfam13912
C2H2-type zinc finger;
168-192 2.06e-03

C2H2-type zinc finger;


Pssm-ID: 433576  Cd Length: 27  Bit Score: 36.84  E-value: 2.06e-03
                           10        20
                   ....*....|....*....|....*
gi 530417367   168 HVCKICSKAFKRQDHLTGHMLTHQK 192
Cdd:pfam13912    2 HECSECGKSFPSYQALGGHKKSHRK 26
PHA00733 PHA00733
hypothetical protein
 142-187 2.86e-03

hypothetical protein


Pssm-ID: 177301  Cd Length: 128  Bit Score: 39.47  E-value: 2.86e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 530417367  142 CSLCGKVFSSASSLSKH--YLTHSQerkhVCKICSKAFKRQDHLTGHM 187
Cdd:PHA00733   76 CPLCLMPFSSSVSLKQHirYTEHSK----VCPVCGKEFRNTDSTLDHV 119
COG5048 COG5048
FOG: Zn-finger [General function prediction only];
141-207 8.38e-03

FOG: Zn-finger [General function prediction only];


Pssm-ID: 227381 [Multi-domain]  Cd Length: 467  Bit Score: 40.45  E-value: 8.38e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 530417367  141 DCSLCGKVFSSASSLSKHYLT--HSQE--RKHVC--KICSKAFKRQDHLTGHMLTHQKTKPFVCIEQGCSKSY 207
Cdd:COG5048   291 KSKQCNISFSRSSPLTRHLRSvnHSGEslKPFSCpySLCGKLFSRNDALKRHILLHTSISPAKEKLLNSSSKF 363
ZnF_C2H2 smart00355
zinc finger;
168-190 9.54e-03

zinc finger;


Pssm-ID: 197676  Cd Length: 23  Bit Score: 34.75  E-value: 9.54e-03
                            10        20
                    ....*....|....*....|...
gi 530417367    168 HVCKICSKAFKRQDHLTGHMLTH 190
Cdd:smart00355    1 YRCPECGKVFKSKSALREHMRTH 23
 
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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