8GXQ
PIC-Mediator in complex with +1 nucleosome (T40N) in MH-binding state
Domain Annotation: SCOP2 Classification SCOP2 Database Homepage
Chains | Type | Family Name | Domain Identifier | Family Identifier | Provenance Source (Version) |
---|---|---|---|---|---|
K [auth EB] | SCOP2B Superfamily | Winged helix DNA-binding domain | 8003067 | 3000034 | SCOP2B (2022-06-29) |
L [auth FB] | SCOP2B Superfamily | Rap30/74 heterodimerisation domain-like | 8003550 | 3000142 | SCOP2B (2022-06-29) |
L [auth FB] | SCOP2B Superfamily | Winged helix DNA-binding domain | 8003005 | 3000034 | SCOP2B (2022-06-29) |
M [auth HB] | SCOP2B Superfamily | BSD domain-like | 8039783 | 3001039 | SCOP2B (2022-06-29) |
CC [auth NF] | SCOP2B Superfamily | Core histone-like | 8042439 | 3001387 | SCOP2B (2022-06-29) |
N [auth NB] | SCOP2B Superfamily | Core histone-like | 8042439 | 3001387 | SCOP2B (2022-06-29) |
S [auth PF] | SCOP2B Superfamily | RPB6/omega subunit-like | 8106082 | 3000189 | SCOP2B (2022-06-29) |
W [auth PK] | SCOP2B Superfamily | RBP11-like subunits of RNA polymerase | 8080728 | 3001655 | SCOP2B (2022-06-29) |
X [auth PL] | SCOP2B Superfamily | RNA polymerase subunits | 8103068 | 3001823 | SCOP2B (2022-06-29) |
Y [auth DP] | SCOP2B Superfamily | TATA-box binding protein-like | 8036293 | 3000705 | SCOP2B (2022-06-29) |
Y [auth DP] | SCOP2B Superfamily | TATA-box binding protein-like | 8036295 | 3000705 | SCOP2B (2022-06-29) |
Z [auth DQ] | SCOP2B Superfamily | Transcription factor IIA (TFIIA), beta-barrel domain | 8037002 | 3001281 | SCOP2B (2022-06-29) |
Z [auth DQ] | SCOP2B Superfamily | Transcription factor IIA (TFIIA), alpha-helical domain | 8037001 | 3001887 | SCOP2B (2022-06-29) |
AA [auth DO] | SCOP2B Superfamily | Transcription factor IIA (TFIIA), beta-barrel domain | 8037007 | 3001281 | SCOP2B (2022-06-29) |
AA [auth DO] | SCOP2B Superfamily | Transcription factor IIA (TFIIA), alpha-helical domain | 8037005 | 3001887 | SCOP2B (2022-06-29) |
BA [auth Dc] | SCOP2B Superfamily | Core histone-like | 8086844 | 3001387 | SCOP2B (2022-06-29) |
CA [auth Dd] | SCOP2B Superfamily | Core histone-like | 8042407 | 3001387 | SCOP2B (2022-06-29) |
JA [auth DD] | SCOP2B Superfamily | Core histone-like | 8042407 | 3001387 | SCOP2B (2022-06-29) |
C [auth BA] | SCOP2B Superfamily | Cyclin-like | 8043880 | 3000768 | SCOP2B (2022-06-29) |
C [auth BA] | SCOP2B Superfamily | Cyclin-like | 8043882 | 3000768 | SCOP2B (2022-06-29) |
DA [auth De] | SCOP2B Superfamily | Taf5 N-terminal domain-like | 8034920 | 3001495 | SCOP2B (2022-06-29) |
LA [auth DE] | SCOP2B Superfamily | Taf5 N-terminal domain-like | 8034920 | 3001495 | SCOP2B (2022-06-29) |
EA [auth Df] | SCOP2B Superfamily | Core histone-like | 8081687 | 3001387 | SCOP2B (2022-06-29) |
MA [auth DF] | SCOP2B Superfamily | Core histone-like | 8081687 | 3001387 | SCOP2B (2022-06-29) |
GA [auth Dj] | SCOP2B Superfamily | Core histone-like | 8053233 | 3001387 | SCOP2B (2022-06-29) |
QA [auth DJ] | SCOP2B Superfamily | Core histone-like | 8053233 | 3001387 | SCOP2B (2022-06-29) |
HA [auth Dk] | SCOP2B Superfamily | Core histone-like | 8036824 | 3001387 | SCOP2B (2022-06-29) |
IA [auth Dl] | SCOP2B Superfamily | Core histone-like | 8042408 | 3001387 | SCOP2B (2022-06-29) |
RA [auth DL] | SCOP2B Superfamily | Core histone-like | 8042408 | 3001387 | SCOP2B (2022-06-29) |
KA [auth Dm] | SCOP2B Superfamily | Core histone-like | 8036818 | 3001387 | SCOP2B (2022-06-29) |
NA [auth DG] | SCOP2B Superfamily | Rap30/74 heterodimerisation domain-like | 8054049 | 3000142 | SCOP2B (2022-06-29) |
OA [auth DH] | SCOP2B Superfamily | Core histone-like | 8053232 | 3001387 | SCOP2B (2022-06-29) |
SA [auth HD] | SCOP2B Superfamily | RING/U-box like | 8039298 | 3000160 | SCOP2B (2022-06-29) |
TA [auth HE] | SCOP2B Superfamily | vWA-like | 8054198 | 3000832 | SCOP2B (2022-06-29) |
UA [auth HG] | SCOP2B Superfamily | Cysteine-rich domain | 8033482 | 3001452 | SCOP2B (2022-06-29) |
UA [auth HG] | SCOP2B Superfamily | vWA-like | 8057086 | 3000832 | SCOP2B (2022-06-29) |
VA [auth HH] | SCOP2B Superfamily | RecA-like P-loop NTPases | 8054245 | 3002019 | SCOP2B (2022-06-29) |
WA [auth HF] | SCOP2B Superfamily | TFB5-like | 8034306 | 3000733 | SCOP2B (2022-06-29) |
XA [auth HI] | SCOP2B Superfamily | Protein kinase-like (PK-like) | 8042855 | 3000066 | SCOP2B (2022-06-29) |
YA [auth HJ] | SCOP2B Superfamily | Cyclin-like | 8037909 | 3000768 | SCOP2B (2022-06-29) |
YA [auth HJ] | SCOP2B Superfamily | Cyclin-like | 8037906 | 3000768 | SCOP2B (2022-06-29) |
ZA [auth PD] | SCOP2B Superfamily | HRDC-like | 8106072 | 3000132 | SCOP2B (2022-06-29) |
E [auth EA] | SCOP2B Superfamily | Zinc beta-ribbon | 8043056 | 3001238 | SCOP2B (2022-06-29) |
KB [auth m] | SCOP2B Superfamily | Mediator of RNA polymerase II transcription subunit 31 | 8105987 | 3002846 | SCOP2B (2022-06-29) |
BC [auth NE] | SCOP2B Superfamily | Core histone-like | 8096712 | 3001387 | SCOP2B (2022-06-29) |
H [auth NA] | SCOP2B Superfamily | Core histone-like | 8096712 | 3001387 | SCOP2B (2022-06-29) |
Domain Annotation: ECOD Classification ECOD Database Homepage
Chains | Family Name | Domain Identifier | Architecture | Possible Homology | Homology | Topology | Family | Provenance Source (Version) |
---|---|---|---|---|---|---|---|---|
J [auth DB] | Peptidase_M1_2 | e8gxqDB3 | A: beta sandwiches | X: Baculovirus p35 protein-related (From Topology) | H: Baculovirus p35 protein-related (From Topology) | T: Baculovirus p35 protein-related | F: Peptidase_M1_2 | ECOD (1.6) |
J [auth DB] | CLASP_N_2 | e8gxqDB1 | A: alpha superhelices | X: Repetitive alpha hairpins | H: ARM repeat (From Topology) | T: ARM repeat | F: CLASP_N_2 | ECOD (1.6) |
J [auth DB] | Peptidase_M1 | e8gxqDB2 | A: mixed a+b and a/b | X: Zincin-like | H: Metalloproteases (zincins) catalytic domain (From Topology) | T: Metalloproteases (zincins) catalytic domain | F: Peptidase_M1 | ECOD (1.6) |
K [auth EB] | TFIIE_beta | e8gxqEB3 | A: alpha arrays | X: HTH | H: HTH | T: winged | F: TFIIE_beta | ECOD (1.6) |
K [auth EB] | KOG3095 | e8gxqEB1 | A: alpha arrays | X: HTH | H: HTH | T: winged | F: KOG3095 | ECOD (1.6) |
K [auth EB] | EF-hand_11 | e8gxqEB2 | A: alpha arrays | X: HTH | H: HTH | T: winged | F: EF-hand_11 | ECOD (1.6) |
CC [auth NF] | Histone_1 | e8gxqNF1 | A: alpha arrays | X: Histone-like | H: Histone-related | T: Histone | F: Histone_1 | ECOD (1.6) |
N [auth NB] | Histone_1 | e8gxqNB1 | A: alpha arrays | X: Histone-like | H: Histone-related | T: Histone | F: Histone_1 | ECOD (1.6) |
O [auth PB] | RNA_pol_Rpb2_6_3rd_2 | e8gxqPB7 | A: beta barrels | X: cradle loop barrel | H: RIFT-related | T: double psi | F: RNA_pol_Rpb2_6_3rd_2 | ECOD (1.6) |
O [auth PB] | RNA_pol_Rpb2_6_2nd_1 | e8gxqPB3 | A: a+b complex topology | X: alpha/beta-Hammerhead/Barrel-sandwich hybrid | H: alpha/beta-Hammerhead/Barrel-sandwich hybrid | T: Single hybrid motif | F: RNA_pol_Rpb2_6_2nd_1 | ECOD (1.6) |
O [auth PB] | RNA_pol_Rpb2_3 | e8gxqPB1 | A: a+b complex topology | X: N-terminal domain in beta subunit of DNA dependent RNA-polymerase (From Topology) | H: N-terminal domain in beta subunit of DNA dependent RNA-polymerase (From Topology) | T: N-terminal domain in beta subunit of DNA dependent RNA-polymerase | F: RNA_pol_Rpb2_3 | ECOD (1.6) |
O [auth PB] | RNA_pol_Rpb2_1 | e8gxqPB2 | A: a+b complex topology | X: insertion domain in beta subunit of DNA dependent RNA-polymerase (From Topology) | H: insertion domain in beta subunit of DNA dependent RNA-polymerase (From Topology) | T: insertion domain in beta subunit of DNA dependent RNA-polymerase | F: RNA_pol_Rpb2_1 | ECOD (1.6) |
O [auth PB] | RNA_pol_Rpb2_45_1 | e8gxqPB6 | A: a+b complex topology | X: barrel domain in beta subunit of DNA dependent RNA-polymerase (From Topology) | H: barrel domain in beta subunit of DNA dependent RNA-polymerase (From Topology) | T: barrel domain in beta subunit of DNA dependent RNA-polymerase | F: RNA_pol_Rpb2_45_1 | ECOD (1.6) |
O [auth PB] | RNA_pol_Rpb2_7 | e8gxqPB4 | A: a+b complex topology | X: C-terminal domain in beta subunit of DNA dependent RNA-polymerase (From Topology) | H: C-terminal domain in beta subunit of DNA dependent RNA-polymerase (From Topology) | T: C-terminal domain in beta subunit of DNA dependent RNA-polymerase | F: RNA_pol_Rpb2_7 | ECOD (1.6) |
O [auth PB] | RNA_pol_Rpb2_4 | e8gxqPB5 | A: a+b complex topology | X: inserted a+b domain in yeast RNA polymerase beta subunit (From Topology) | H: inserted a+b domain in yeast RNA polymerase beta subunit (From Topology) | T: inserted a+b domain in yeast RNA polymerase beta subunit | F: RNA_pol_Rpb2_4 | ECOD (1.6) |
Q [auth PC] | RNA_pol_L_1 | e8gxqPC2 | A: a+b two layers | X: DCoH-like | H: RBP11-like subunits of RNA polymerase (From Topology) | T: RBP11-like subunits of RNA polymerase | F: RNA_pol_L_1 | ECOD (1.6) |
Q [auth PC] | RNA_pol_A_bac_1 | e8gxqPC1 | A: a+b complex topology | X: Ribosomal protein TL5/L25 C-terminal domain-like | H: Insert subdomain of RNA polymerase alpha subunit (From Topology) | T: Insert subdomain of RNA polymerase alpha subunit | F: RNA_pol_A_bac_1 | ECOD (1.6) |
R [auth PE] | RNA_pol_Rpb5_C | e8gxqPE1 | A: a+b two layers | X: RPB5-like RNA polymerase subunit (From Topology) | H: RPB5-like RNA polymerase subunit (From Topology) | T: RPB5-like RNA polymerase subunit | F: RNA_pol_Rpb5_C | ECOD (1.6) |
R [auth PE] | RNA_pol_Rpb5_N | e8gxqPE2 | A: a/b three-layered sandwiches | X: Restriction endonuclease-like | H: Eukaryotic RPB5 N-terminal domain (From Topology) | T: Eukaryotic RPB5 N-terminal domain | F: RNA_pol_Rpb5_N | ECOD (1.6) |
S [auth PF] | RNA_pol_Rpb6_1 | e8gxqPF1 | A: alpha arrays | X: RPB6/omega subunit-like (From Homology) | H: RPB6/omega subunit-like | T: RPB6 | F: RNA_pol_Rpb6_1 | ECOD (1.6) |
T [auth PH] | RNA_pol_Rpb8 | e8gxqPH1 | A: beta barrels | X: OB-fold | H: Nucleic acid-binding proteins (From Topology) | T: Nucleic acid-binding proteins | F: RNA_pol_Rpb8 | ECOD (1.6) |
U [auth PI] | RNA_POL_M_15KD | e8gxqPI2 | A: few secondary structure elements | X: Rubredoxin-like | H: Rubredoxin-related | T: Rubredoxin-related | F: RNA_POL_M_15KD | ECOD (1.6) |
U [auth PI] | TFIIS_C | e8gxqPI1 | A: few secondary structure elements | X: Rubredoxin-like | H: Rubredoxin-related | T: Rubredoxin-related | F: TFIIS_C | ECOD (1.6) |
V [auth PJ] | RNA_pol_N | e8gxqPJ1 | A: alpha arrays | X: HTH | H: RPB10 (From Topology) | T: RPB10 | F: RNA_pol_N | ECOD (1.6) |
W [auth PK] | RNA_pol_L_2 | e8gxqPK1 | A: a+b two layers | X: DCoH-like | H: RBP11-like subunits of RNA polymerase (From Topology) | T: RBP11-like subunits of RNA polymerase | F: RNA_pol_L_2 | ECOD (1.6) |
X [auth PL] | DNA_RNApol_7kD | e8gxqPL1 | A: few secondary structure elements | X: Rubredoxin-like | H: Rubredoxin-related | T: Rubredoxin-related | F: DNA_RNApol_7kD | ECOD (1.6) |
Y [auth DP] | TBP | e8gxqDP2 | A: a+b two layers | X: TBP-like | H: TATA-box binding protein-like (From Topology) | T: TATA-box binding protein-like | F: TBP | ECOD (1.6) |
Z [auth DQ] | TFIIA_C | e8gxqDQ2 | A: beta duplicates or obligate multimers | X: Transcription factor IIA (TFIIA), beta-barrel domain (From Topology) | H: Transcription factor IIA (TFIIA), beta-barrel domain (From Topology) | T: Transcription factor IIA (TFIIA), beta-barrel domain | F: TFIIA_C | ECOD (1.6) |
Z [auth DQ] | TFIIA_N | e8gxqDQ1 | A: alpha duplicates or obligate multimers | X: TFIIA, alpha-helical domain (From Topology) | H: TFIIA, alpha-helical domain (From Topology) | T: TFIIA, alpha-helical domain | F: TFIIA_N | ECOD (1.6) |
AA [auth DO] | TFIIA_gamma_C | e8gxqDO2 | A: beta duplicates or obligate multimers | X: Transcription factor IIA (TFIIA), beta-barrel domain (From Topology) | H: Transcription factor IIA (TFIIA), beta-barrel domain (From Topology) | T: Transcription factor IIA (TFIIA), beta-barrel domain | F: TFIIA_gamma_C | ECOD (1.6) |
AA [auth DO] | TFIIA_gamma_N | e8gxqDO1 | A: alpha duplicates or obligate multimers | X: TFIIA, alpha-helical domain (From Topology) | H: TFIIA, alpha-helical domain (From Topology) | T: TFIIA, alpha-helical domain | F: TFIIA_gamma_N | ECOD (1.6) |
C [auth BA] | TFIIB | e8gxqBA3 | A: alpha arrays | X: HTH | H: HTH | T: Cyclin-like | F: TFIIB | ECOD (1.6) |
C [auth BA] | TF_Zn_Ribbon | e8gxqBA1 | A: few secondary structure elements | X: Rubredoxin-like | H: Rubredoxin-related | T: Rubredoxin-related | F: TF_Zn_Ribbon | ECOD (1.6) |
DA [auth De] | ANAPC4_WD40_10 | e8gxqDe1 | A: beta duplicates or obligate multimers | X: beta-propeller-like | H: beta-propeller | T: 8-bladed | F: ANAPC4_WD40_10 | ECOD (1.6) |
DA [auth De] | TFIID_NTD2 | e8gxqDe2 | A: alpha superhelices | X: Taf5 N-terminal domain-like (From Topology) | H: Taf5 N-terminal domain-like (From Topology) | T: Taf5 N-terminal domain-like | F: TFIID_NTD2 | ECOD (1.6) |
LA [auth DE] | ANAPC4_WD40_2 | e8gxqDE2 | A: beta duplicates or obligate multimers | X: beta-propeller-like | H: beta-propeller | T: 8-bladed | F: ANAPC4_WD40_2 | ECOD (1.6) |
LA [auth DE] | TFIID_NTD2 | e8gxqDE1 | A: alpha superhelices | X: Taf5 N-terminal domain-like (From Topology) | H: Taf5 N-terminal domain-like (From Topology) | T: Taf5 N-terminal domain-like | F: TFIID_NTD2 | ECOD (1.6) |
GA [auth Dj] | TFIID_30kDa | e8gxqDj1 | A: alpha arrays | X: Histone-like | H: Histone-related | T: Histone | F: TFIID_30kDa | ECOD (1.6) |
QA [auth DJ] | TFIID_30kDa | e8gxqDJ1 | A: alpha arrays | X: Histone-like | H: Histone-related | T: Histone | F: TFIID_30kDa | ECOD (1.6) |
HA [auth Dk] | TAFII28 | e8gxqDk1 | A: alpha arrays | X: Histone-like | H: Histone-related | T: Histone | F: TAFII28 | ECOD (1.6) |
RA [auth DL] | TFIID_20kDa | e8gxqDL1 | A: alpha arrays | X: Histone-like | H: Histone-related | T: Histone | F: TFIID_20kDa | ECOD (1.6) |
TA [auth HE] | Tfb4 | e8gxqHE1 | A: a/b three-layered sandwiches | X: HAD domain-like | H: HAD domain-related | T: vWA-like | F: Tfb4 | ECOD (1.6) |
TA [auth HE] | F_UNCLASSIFIED | e8gxqHE2 | A: few secondary structure elements | X: Rubredoxin-like | H: Rubredoxin-related | T: Rubredoxin-related | F: F_UNCLASSIFIED | ECOD (1.6) |
UA [auth HG] | VWA | e8gxqHG2 | A: a/b three-layered sandwiches | X: HAD domain-like | H: HAD domain-related | T: vWA-like | F: VWA | ECOD (1.6) |
UA [auth HG] | PknG_rubred_like | e8gxqHG3 | A: few secondary structure elements | X: Rubredoxin-like | H: Rubredoxin-related | T: Rubredoxin-related | F: PknG_rubred_like | ECOD (1.6) |
UA [auth HG] | C1_4 | e8gxqHG1 | A: few secondary structure elements | X: RING/U-box-like | H: RING/U-box-like | T: Cysteine-rich domain | F: C1_4 | ECOD (1.6) |
WA [auth HF] | Tfb5 | e8gxqHF1 | A: a+b complex topology | X: TFB5-related (From Topology) | H: TFB5-related (From Topology) | T: TFB5-related | F: Tfb5 | ECOD (1.6) |
XA [auth HI] | Pkinase_Tyr | e8gxqHI1 | A: a+b complex topology | X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology) | H: Protein kinase/SAICAR synthase/ATP-grasp | T: Protein kinase | F: Pkinase_Tyr | ECOD (1.6) |
YA [auth HJ] | Cyclin_N_1 | e8gxqHJ2 | A: alpha arrays | X: HTH | H: HTH | T: Cyclin-like | F: Cyclin_N_1 | ECOD (1.6) |
ZA [auth PD] | RNA_pol_Rpb4 | e8gxqPD1 | A: alpha arrays | X: HhH/H2TH | H: SAM/DNA-glycosylase | T: SAM domain-like | F: RNA_pol_Rpb4 | ECOD (1.6) |
AB [auth PG] | S1_1 | e8gxqPG1 | A: beta barrels | X: OB-fold | H: Nucleic acid-binding proteins (From Topology) | T: Nucleic acid-binding proteins | F: S1_1 | ECOD (1.6) |
AB [auth PG] | SHS2_Rpb7-N | e8gxqPG2 | A: a+b two layers | X: Dodecin subunit-like | H: Flavin-binding protein dodecin-like (From Topology) | T: Flavin-binding protein dodecin-like | F: SHS2_Rpb7-N | ECOD (1.6) |
BB [auth g] | Med7 | e8gxqg1 | A: alpha duplicates or obligate multimers | X: Mediator hinge subcomplex-like (From Homology) | H: Mediator hinge subcomplex-like | T: MED7 hinge region | F: Med7 | ECOD (1.6) |
E [auth EA] | TFIIE_alpha | e8gxqEA1 | A: alpha arrays | X: HTH | H: HTH | T: winged | F: TFIIE_alpha | ECOD (1.6) |
E [auth EA] | TF_Zn_Ribbon | e8gxqEA2 | A: few secondary structure elements | X: Rubredoxin-like | H: Rubredoxin-related | T: Rubredoxin-related | F: TF_Zn_Ribbon | ECOD (1.6) |
FB [auth u] | Med21 | e8gxqu1 | A: alpha duplicates or obligate multimers | X: Mediator hinge subcomplex-like (From Homology) | H: Mediator hinge subcomplex-like | T: RNA polymerase II holoenzyme component SRB7 (MED21) | F: Med21 | ECOD (1.6) |
IB [auth f] | Med6 | e8gxqf1 | A: extended segments | X: Mediator of RNA polymerase II transcription subunit 6 (From Topology) | H: Mediator of RNA polymerase II transcription subunit 6 (From Topology) | T: Mediator of RNA polymerase II transcription subunit 6 | F: Med6 | ECOD (1.6) |
KB [auth m] | Med31 | e8gxqm1 | A: a+b complex topology | X: Mediator of RNA polymerase II transcription submodule Med7N/31 (From Topology) | H: Mediator of RNA polymerase II transcription submodule Med7N/31 (From Topology) | T: Mediator of RNA polymerase II transcription submodule Med7N/31 | F: Med31 | ECOD (1.6) |
F [auth FA] | TFIIF_alpha_N | e8gxqFA1 | A: beta complex topology | X: triple barrel (From Homology) | H: triple barrel | T: Rap30/74 interaction domains-like | F: TFIIF_alpha_N | ECOD (1.6) |
PB [auth e] | F_UNCLASSIFIED | e8gxqe1 | A: alpha duplicates or obligate multimers | X: Mediator hinge subcomplex-like (From Homology) | H: Mediator hinge subcomplex-like | T: RNA polymerase II holoenzyme component SRB7 (MED21) | F: F_UNCLASSIFIED | ECOD (1.6) |
UB [auth r] | Med18 | e8gxqr1 | A: a+b complex topology | X: mRNA triphosphatase CET1-related (From Topology) | H: mRNA triphosphatase CET1-related (From Topology) | T: mRNA triphosphatase CET1-related | F: Med18 | ECOD (1.6) |
VB [auth t] | F_UNCLASSIFIED | e8gxqt1 | A: a+b complex topology | X: mRNA triphosphatase CET1-related (From Topology) | H: mRNA triphosphatase CET1-related (From Topology) | T: mRNA triphosphatase CET1-related | F: F_UNCLASSIFIED | ECOD (1.6) |
WB [auth v] | Med22 | e8gxqv1 | A: a+b complex topology | X: Mediator of RNA polymerase II transcription subunit 22 (From Topology) | H: Mediator of RNA polymerase II transcription subunit 22 (From Topology) | T: Mediator of RNA polymerase II transcription subunit 22 | F: Med22 | ECOD (1.6) |
G [auth HA] | HBB | e8gxqHA3 | A: a+b two layers | X: XPD arch domain (From Topology) | H: XPD arch domain (From Topology) | T: XPD arch domain | F: HBB | ECOD (1.6) |
G [auth HA] | DEAD_2 | e8gxqHA1 | A: a/b three-layered sandwiches | X: P-loop domains-like | H: P-loop domains-related | T: P-loop containing nucleoside triphosphate hydrolases | F: DEAD_2 | ECOD (1.6) |
G [auth HA] | HBB,Helicase_C_2 | e8gxqHA2 | A: a/b three-layered sandwiches | X: P-loop domains-like | H: P-loop domains-related | T: P-loop containing nucleoside triphosphate hydrolases | F: HBB,Helicase_C_2 | ECOD (1.6) |
AC [auth y] | F_UNCLASSIFIED | e8gxqy1 | A: a/b three-layered sandwiches | X: HAD domain-like | H: HAD domain-related | T: vWA-like | F: F_UNCLASSIFIED | ECOD (1.6) |
DC [auth NG] | Histone_1 | e8gxqNG1 | A: alpha arrays | X: Histone-like | H: Histone-related | T: Histone | F: Histone_1 | ECOD (1.6) |
EC [auth NC] | Histone_1 | e8gxqNC1 | A: alpha arrays | X: Histone-like | H: Histone-related | T: Histone | F: Histone_1 | ECOD (1.6) |
FC [auth ND] | Histone | e8gxqND1 | A: alpha arrays | X: Histone-like | H: Histone-related | T: Histone | F: Histone | ECOD (1.6) |
GC [auth NH] | Histone | e8gxqNH1 | A: alpha arrays | X: Histone-like | H: Histone-related | T: Histone | F: Histone | ECOD (1.6) |
BC [auth NE] | Histone | e8gxqNE1 | A: alpha arrays | X: Histone-like | H: Histone-related | T: Histone | F: Histone | ECOD (1.6) |
H [auth NA] | Histone | e8gxqNA1 | A: alpha arrays | X: Histone-like | H: Histone-related | T: Histone | F: Histone | ECOD (1.6) |
Protein Family Annotation Pfam Database Homepage
Chains | Accession | Name | Description | Comments | Source |
---|---|---|---|---|---|
K [auth EB] | PF18121 | TFA2 Winged helix domain 2 (TFA2_Winged_2) | TFA2 Winged helix domain 2 | This is the second winged helix domain can be found in TFA2 proteins present in Saccharomyces cerevisiae. In form 2, the domain interacts directly with Rad3, a DNA helicase [1]. | Domain |
K [auth EB] | PF02186 | TFIIE beta subunit core domain (TFIIE_beta) | TFIIE beta subunit core domain | General transcription factor TFIIE consists of two subunits, TFIIE alpha Pfam:PF02002 and TFIIE beta. TFIIE beta has been found to bind to the region where the promoter starts to open to be single-stranded upon transcription initiation by RNA polymer ... | Domain |
L [auth FB] | PF02270 | TFIIF, beta subunit HTH domain (TFIIF_beta) | TFIIF, beta subunit HTH domain | Accurate transcription in vivo requires at least six general transcription initiation factors, in addition to RNA polymerase II. Transcription initiation factor IIF (TFIIF) is a tetramer of two beta subunits associate with two alpha subunits which ... | Domain |
L [auth FB] | PF17683 | TFIIF, beta subunit N-terminus (TFIIF_beta_N) | TFIIF, beta subunit N-terminus | - | Family |
CC [auth NF], N [auth NB] | PF15511 | Centromere kinetochore component CENP-T histone fold (CENP-T_C) | Centromere kinetochore component CENP-T histone fold | CENP-T is a family of vertebral kinetochore proteins that associates directly with CENP-W. The N-terminus of CENP-T proteins interacts directly with the Ndc80 complex in the outer kinetochore. Importantly, the CENP-T-W complex does not directly asso ... | Domain |
O [auth PB] | PF04561 | RNA polymerase Rpb2, domain 2 (RNA_pol_Rpb2_2) | RNA polymerase Rpb2, domain 2 | RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Rpb2 is the second largest subunit of the RNA po ... | Domain |
O [auth PB] | PF04560 | RNA polymerase Rpb2, domain 7 (RNA_pol_Rpb2_7) | RNA polymerase Rpb2, domain 7 | RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Rpb2 is the second largest subunit of the RNA p ... | Domain |
O [auth PB] | PF04565 | RNA polymerase Rpb2, domain 3 (RNA_pol_Rpb2_3) | RNA polymerase Rpb2, domain 3 | RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 3, s also known as the fork domain and is ... | Domain |
O [auth PB] | PF04566 | RNA polymerase Rpb2, domain 4 (RNA_pol_Rpb2_4) | RNA polymerase Rpb2, domain 4 | RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 4, is also known as the external 2 domain ... | Domain |
O [auth PB] | PF04563 | RNA polymerase beta subunit (RNA_pol_Rpb2_1) | RNA polymerase beta subunit | - | Family |
O [auth PB] | PF00562 | RNA polymerase Rpb2, domain 6 (RNA_pol_Rpb2_6) | RNA polymerase Rpb2, domain 6 | RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain represents the hybrid binding domain ... | Domain |
O [auth PB] | PF04567 | RNA polymerase Rpb2, domain 5 (RNA_pol_Rpb2_5) | RNA polymerase Rpb2, domain 5 | RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 5, is also known as the external 2 domain ... | Domain |
P [auth HC] | PF03849 | Transcription factor Tfb2 (Tfb2) | Transcription factor Tfb2 | - | Family |
P [auth HC] | PF18307 | Transcription factor Tfb2 (p52) C-terminal domain (Tfb2_C) | Transcription factor Tfb2 (p52) C-terminal domain | This is the C-terminal domain of Transcription factor Tfb2 present in Saccharomyces cerevisiae. Tfb2 is referred to as p52 in humans. The interaction between p8-Tfb5 and p52-Tfb2 has a key role in the maintenance of the transcription factor TFIIH arc ... | Domain |
Q [auth PC] | PF01193 | RNA polymerase Rpb3/Rpb11 dimerisation domain (RNA_pol_L) | RNA polymerase Rpb3/Rpb11 dimerisation domain | The two eukaryotic subunits Rpb3 and Rpb11 dimerise to from a platform onto which the other subunits of the RNA polymerase assemble (D/L in archaea). The prokaryotic equivalent of the Rpb3/Rpb11 platform is the alpha-alpha dimer. The dimerisation do ... | Domain |
Q [auth PC] | PF01000 | RNA polymerase Rpb3/RpoA insert domain (RNA_pol_A_bac) | RNA polymerase Rpb3/RpoA insert domain | Members of this family include: alpha subunit from eubacteria alpha subunits from chloroplasts Rpb3 subunits from eukaryotes RpoD subunits from archaeal | Domain |
R [auth PE] | PF01191 | RNA polymerase Rpb5, C-terminal domain (RNA_pol_Rpb5_C) | RNA polymerase Rpb5, C-terminal domain | The assembly domain of Rpb5 [1]. The archaeal equivalent to this domain is subunit H. Subunit H lacks the N-terminal domain. | Domain |
R [auth PE] | PF03871 | RNA polymerase Rpb5, N-terminal domain (RNA_pol_Rpb5_N) | RNA polymerase Rpb5, N-terminal domain | Rpb5 has a bipartite structure which includes a eukaryote-specific N-terminal domain and a C-terminal domain resembling the archaeal RNAP subunit H [1,2]. The N-terminal domain is involved in DNA binding and is part of the jaw module in the RNA p ... | Domain |
S [auth PF] | PF01192 | RNA polymerase Rpb6 (RNA_pol_Rpb6) | RNA polymerase Rpb6 | - | Family |
T [auth PH] | PF03870 | RNA polymerase Rpb8 (RNA_pol_Rpb8) | RNA polymerase Rpb8 | - | Family |
U [auth PI] | PF02150 | RNA polymerases M/15 Kd subunit (RNA_POL_M_15KD) | RNA polymerases M/15 Kd subunit | - | Domain |
U [auth PI] | PF01096 | Transcription factor S-II (TFIIS) (TFIIS_C) | Transcription factor S-II (TFIIS) | - | Domain |
V [auth PJ] | PF01194 | RNA polymerases N / 8 kDa subunit (RNA_pol_N) | RNA polymerases N / 8 kDa subunit | - | Domain |
W [auth PK] | PF13656 | RNA polymerase Rpb3/Rpb11 dimerisation domain (RNA_pol_L_2) | RNA polymerase Rpb3/Rpb11 dimerisation domain | The two eukaryotic subunits Rpb3 and Rpb11 dimerise to from a platform onto which the other subunits of the RNA polymerase assemble (D/L in archaea). The prokaryotic equivalent of the Rpb3/Rpb11 platform is the alpha-alpha dimer. The dimerisation do ... | Domain |
X [auth PL] | PF03604 | DNA directed RNA polymerase, 7 kDa subunit (DNA_RNApol_7kD) | DNA directed RNA polymerase, 7 kDa subunit | - | Domain |
Y [auth DP] | PF00352 | Transcription factor TFIID (or TATA-binding protein, TBP) (TBP) | Transcription factor TFIID (or TATA-binding protein, TBP) | - | Domain |
Z [auth DQ] | PF03153 | Transcription factor IIA, alpha/beta subunit (TFIIA) | Transcription factor IIA, alpha/beta subunit | - | Family |
AA [auth DO] | PF02751 | Transcription initiation factor IIA, gamma subunit (TFIIA_gamma_C) | Transcription initiation factor IIA, gamma subunit | Accurate transcription in vivo requires at least six general transcription initiation factors, in addition to RNA polymerase II. Transcription initiation factor IIA (TFIIA) is a multimeric protein which facilitates the binding of TFIID to the TATA b ... | Domain |
AA [auth DO] | PF02268 | Transcription initiation factor IIA, gamma subunit, helical domain (TFIIA_gamma_N) | Transcription initiation factor IIA, gamma subunit, helical domain | Accurate transcription in vivo requires at least six general transcription initiation factors, in addition to RNA polymerase II. Transcription initiation factor IIA (TFIIA) is a multimeric protein which facilitates the binding of TFIID to the TATA ... | Domain |
C [auth BA] | PF00382 | Transcription factor TFIIB repeat (TFIIB) | Transcription factor TFIIB repeat | - | Domain |
DA [auth De], LA [auth DE] | PF04494 | WD40 associated region in TFIID subunit, NTD2 domain (TFIID_NTD2) | WD40 associated region in TFIID subunit, NTD2 domain | - | Family |
DA [auth De], LA [auth DE] | PF00400 | WD domain, G-beta repeat (WD40) | WD domain, G-beta repeat | - | Repeat |
EA [auth Df], MA [auth DF] | PF07571 | TAF6 C-terminal HEAT repeat domain (TAF6_C) | TAF6 C-terminal HEAT repeat domain | - | Repeat |
EA [auth Df], MA [auth DF] | PF02969 | TATA box binding protein associated factor (TAF) (TAF) | TATA box binding protein associated factor (TAF) | TAF proteins adopt a histone-like fold. | Domain |
GA [auth Dj], QA [auth DJ] | PF03540 | Transcription initiation factor TFIID 23-30kDa subunit (TFIID_30kDa) | Transcription initiation factor TFIID 23-30kDa subunit | - | Family |
IA [auth Dl], RA [auth DL] | PF03847 | Transcription initiation factor TFIID subunit A (TFIID_20kDa) | Transcription initiation factor TFIID subunit A | - | Domain |
NA [auth DG] | PF04658 | TAFII55 protein conserved region (TAFII55_N) | TAFII55 protein conserved region | - | Family |
OA [auth DH] | PF07524 | Bromodomain associated (Bromo_TP) | Bromodomain associated | This domain is predicted to bind DNA [1] and is often found associated with Pfam:PF00439 and in transcription factors. It has a histone-like fold. | Domain |
OA [auth DH] | PF10406 | Transcription factor TFIID complex subunit 8 C-term (TAF8_C) | Transcription factor TFIID complex subunit 8 C-term | This is the C-terminal, Delta, part of the TAF8 protein [1]. The N-terminal is generally the histone fold domain, Bromo_TP (Pfam:PF07524). TAF8 is one of the key subunits of the transcription factor for pol II, TFIID. TAF8 is one of the several gener ... | Domain |
SA [auth HD] | PF17121 | Zinc finger, C3HC4 type (RING finger) (zf-C3HC4_5) | Zinc finger, C3HC4 type (RING finger) | - | Domain |
SA [auth HD] | PF06391 | CDK-activating kinase assembly factor MAT1 (MAT1) | CDK-activating kinase assembly factor MAT1 | - | Family |
D [auth DA] | PF12157 | Protein of unknown function (DUF3591) (DUF3591) | Protein of unknown function (DUF3591) | - | Family |
TA [auth HE] | PF03850 | Transcription factor Tfb4 (Tfb4) | Transcription factor Tfb4 | This family appears to be distantly related to the VWA domain. | Domain |
UA [auth HG] | PF04056 | Ssl1-like (Ssl1) | Ssl1-like | - | Family |
UA [auth HG] | PF07975 | TFIIH C1-like domain (C1_4) | TFIIH C1-like domain | The carboxyl-terminal region of TFIIH is essential for transcription activity. This regions binds three zinc atoms through two independent domain. The first contains a C4 zinc finger motif, whereas the second is characterised by a CX(2)CX(2-4)FCADCD ... | Domain |
VA [auth HH] | PF13625 | Helicase conserved C-terminal domain (Helicase_C_3) | Helicase conserved C-terminal domain | This domain family is found in a wide variety of helicases and helicase-related proteins. | Domain |
VA [auth HH] | PF04851 | Type III restriction enzyme, res subunit (ResIII) | Type III restriction enzyme, res subunit | - | Family |
VA [auth HH] | PF16203 | ERCC3/RAD25/XPB C-terminal helicase (ERCC3_RAD25_C) | ERCC3/RAD25/XPB C-terminal helicase | This is the C-terminal helicase domain of ERCC3, RAD25 and XPB helicases [1]. | Domain |
YA [auth HJ] | PF00134 | Cyclin, N-terminal domain (Cyclin_N) | Cyclin, N-terminal domain | Cyclins regulate cyclin dependent kinases (CDKs). Swiss:P22674 is a Uracil-DNA glycosylase that is related to other cyclins [4]. Cyclins contain two domains of similar all-alpha fold, of which this family corresponds with the N-terminal domain. | Domain |
YA [auth HJ] | PF16899 | Cyclin C-terminal domain (Cyclin_C_2) | Cyclin C-terminal domain | Cyclins contain two domains of similar all-alpha fold, this family corresponds with the C-terminal domain of some cyclins including cyclin C and cyclin H [1]. | Domain |
ZA [auth PD] | PF03874 | RNA polymerase Rpb4 (RNA_pol_Rpb4) | RNA polymerase Rpb4 | - | Family |
AB [auth PG] | PF03876 | SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 (SHS2_Rpb7-N) | SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 | Rpb7 bind to Rpb4 to form a heterodimer. This complex is thought to interact with the nascent RNA strand during RNA polymerase II elongation[1]. This family includes the homologs from RNA polymerase I and III. In RNA polymerase I, Rpa43 is at leas ... | Domain |
AB [auth PG] | PF00575 | S1 RNA binding domain (S1) | S1 RNA binding domain | The S1 domain occurs in a wide range of RNA associated proteins. It is structurally similar to cold shock protein which binds nucleic acids. The S1 domain has an OB-fold structure. | Domain |
E [auth EA] | PF08271 | TFIIB zinc-binding (TF_Zn_Ribbon) | TFIIB zinc-binding | The transcription factor TFIIB contains a zinc-binding motif near the N-terminus. This domain is involved in the interaction with RNA pol II and TFIIF and plays a crucial role in selecting the transcription initiation site. The domain adopts a zinc ... | Domain |
E [auth EA] | PF02002 | TFIIE alpha subunit (TFIIE_alpha) | TFIIE alpha subunit | - | Family |
G [auth HA] | PF13307 | Helicase C-terminal domain (Helicase_C_2) | Helicase C-terminal domain | This domain is found at the C-terminus of DEAD-box helicases. | Domain |
G [auth HA] | PF06733 | DEAD_2 (DEAD_2) | DEAD_2 | - | Family |
G [auth HA] | PF06777 | Helical and beta-bridge domain (HBB) | Helical and beta-bridge domain | HBB is the domain on DEAD-box eukaryotic DNA repair helicases (EC:3.6.1.-) that appears to be a unique fold. It's conformation is of alpha-helices 12-16 plus a short beta-bridge to the FeS-cluster domain at the N-terminal. The full-length XPD protein ... | Domain |
I [auth PA] | PF00623 | RNA polymerase Rpb1, domain 2 (RNA_pol_Rpb1_2) | RNA polymerase Rpb1, domain 2 | RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 2, contains the active site ... | Domain |
I [auth PA] | PF04990 | RNA polymerase Rpb1, domain 7 (RNA_pol_Rpb1_7) | RNA polymerase Rpb1, domain 7 | RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 7, represents a mobile modu ... | Domain |
I [auth PA] | PF05001 | RNA polymerase Rpb1 C-terminal repeat (RNA_pol_Rpb1_R) | RNA polymerase Rpb1 C-terminal repeat | - | Repeat |
I [auth PA] | PF05000 | RNA polymerase Rpb1, domain 4 (RNA_pol_Rpb1_4) | RNA polymerase Rpb1, domain 4 | RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 4, represents the funnel do ... | Domain |
I [auth PA] | PF04983 | RNA polymerase Rpb1, domain 3 (RNA_pol_Rpb1_3) | RNA polymerase Rpb1, domain 3 | RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 3, represents the pore doma ... | Domain |
I [auth PA] | PF04992 | RNA polymerase Rpb1, domain 6 (RNA_pol_Rpb1_6) | RNA polymerase Rpb1, domain 6 | RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 6, represents a mobile modu ... | Domain |
I [auth PA] | PF04998 | RNA polymerase Rpb1, domain 5 (RNA_pol_Rpb1_5) | RNA polymerase Rpb1, domain 5 | RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 5, represents the discontin ... | Domain |
I [auth PA] | PF04997 | RNA polymerase Rpb1, domain 1 (RNA_pol_Rpb1_1) | RNA polymerase Rpb1, domain 1 | RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 1, represents the clamp do ... | Domain |