5M1S
Cryo-EM structure of the E. coli replicative DNA polymerase-clamp-exonuclase-theta complex bound to DNA in the editing mode
Domain Annotation: SCOP2 Classification SCOP2 Database Homepage
Chains | Type | Family Name | Domain Identifier | Family Identifier | Provenance Source (Version) |
---|---|---|---|---|---|
B | SCOP2B Superfamily | DNA clamp | 8038076 | 3000780 | SCOP2B (2022-06-29) |
B | SCOP2B Superfamily | DNA clamp | 8038082 | 3000780 | SCOP2B (2022-06-29) |
B | SCOP2B Superfamily | DNA clamp | 8038081 | 3000780 | SCOP2B (2022-06-29) |
C | SCOP2B Superfamily | DNA clamp | 8038082 | 3000780 | SCOP2B (2022-06-29) |
C | SCOP2B Superfamily | DNA clamp | 8038081 | 3000780 | SCOP2B (2022-06-29) |
C | SCOP2B Superfamily | DNA clamp | 8038076 | 3000780 | SCOP2B (2022-06-29) |
D | SCOP2B Superfamily | Ribonuclease H-like | 8042074 | 3000143 | 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) |
---|---|---|---|---|---|---|---|---|
A | HHH_6 | e5m1sA4 | A: alpha arrays | X: HhH/H2TH | H: SAM/DNA-glycosylase | T: SAM domain-like | F: HHH_6 | ECOD (1.6) |
A | DNA_pol3_alpha_C | e5m1sA2 | A: alpha arrays | X: DNA polymerase III finger domain (From Topology) | H: DNA polymerase III finger domain (From Topology) | T: DNA polymerase III finger domain | F: DNA_pol3_alpha_C | ECOD (1.6) |
A | DNA_pol3_alpha_N | e5m1sA1 | A: a+b three layers | X: Nucleotidyltransferase-like | H: Nucleotidyltransferase (From Topology) | T: Nucleotidyltransferase | F: DNA_pol3_alpha_N | ECOD (1.6) |
A | PHP | e5m1sA3 | A: a/b barrels | X: TIM beta/alpha-barrel | H: TIM barrels (From Topology) | T: TIM barrels | F: PHP | ECOD (1.6) |
B | DNA_pol3_beta | e5m1sB2 | A: a+b two layers | X: DNA clamp (From Topology) | H: DNA clamp (From Topology) | T: DNA clamp | F: DNA_pol3_beta | ECOD (1.6) |
B | DNA_pol3_beta_2 | e5m1sB1 | A: a+b two layers | X: DNA clamp (From Topology) | H: DNA clamp (From Topology) | T: DNA clamp | F: DNA_pol3_beta_2 | ECOD (1.6) |
B | DNA_pol3_beta_3 | e5m1sB3 | A: a+b two layers | X: DNA clamp (From Topology) | H: DNA clamp (From Topology) | T: DNA clamp | F: DNA_pol3_beta_3 | ECOD (1.6) |
C | DNA_pol3_beta | e5m1sC3 | A: a+b two layers | X: DNA clamp (From Topology) | H: DNA clamp (From Topology) | T: DNA clamp | F: DNA_pol3_beta | ECOD (1.6) |
C | DNA_pol3_beta_2 | e5m1sC1 | A: a+b two layers | X: DNA clamp (From Topology) | H: DNA clamp (From Topology) | T: DNA clamp | F: DNA_pol3_beta_2 | ECOD (1.6) |
C | DNA_pol3_beta_3 | e5m1sC2 | A: a+b two layers | X: DNA clamp (From Topology) | H: DNA clamp (From Topology) | T: DNA clamp | F: DNA_pol3_beta_3 | ECOD (1.6) |
D | RNase_T | e5m1sD1 | A: mixed a+b and a/b | X: Ribonuclease H-like | H: Ribonuclease H-like (From Topology) | T: Ribonuclease H-like | F: RNase_T | ECOD (1.6) |
G [auth F] | DNA_pol3_theta | e5m1sF1 | A: alpha arrays | X: DNA polymerase III theta subunit-like | H: DNA polymerase III theta subunit-like (From Topology) | T: DNA polymerase III theta subunit-like | F: DNA_pol3_theta | ECOD (1.6) |
Protein Family Annotation Pfam Database Homepage
Chains | Accession | Name | Description | Comments | Source |
---|---|---|---|---|---|
PF02811 | PHP domain (PHP) | PHP domain | - | Family | |
PF07733 | Bacterial DNA polymerase III alpha NTPase domain (DNA_pol3_alpha) | Bacterial DNA polymerase III alpha NTPase domain | - | Domain | |
PF17657 | Bacterial DNA polymerase III alpha subunit finger domain (DNA_pol3_finger) | Bacterial DNA polymerase III alpha subunit finger domain | - | Domain | |
PF14579 | Helix-hairpin-helix motif (HHH_6) | Helix-hairpin-helix motif | The HHH domain is a short DNA-binding domain [1]. | Domain | |
PF02768 | DNA polymerase III beta subunit, C-terminal domain (DNA_pol3_beta_3) | DNA polymerase III beta subunit, C-terminal domain | A dimer of the beta subunit of DNA polymerase beta forms a ring which encircles duplex DNA. Each monomer contains three domains of identical topology and DNA clamp fold. | Domain | |
PF02767 | DNA polymerase III beta subunit, central domain (DNA_pol3_beta_2) | DNA polymerase III beta subunit, central domain | A dimer of the beta subunit of DNA polymerase beta forms a ring which encircles duplex DNA. Each monomer contains three domains of identical topology and DNA clamp fold. | Domain | |
PF00712 | DNA polymerase III beta subunit, N-terminal domain (DNA_pol3_beta) | DNA polymerase III beta subunit, N-terminal domain | A dimer of the beta subunit of DNA polymerase beta forms a ring which encircles duplex DNA. Each monomer contains three domains of identical topology and DNA clamp fold. | Domain | |
PF00929 | Exonuclease (RNase_T) | Exonuclease | - | Family | |
G [auth F] | PF06440 | DNA polymerase III, theta subunit (DNA_pol3_theta) | DNA polymerase III, theta subunit | DNA polymerase III (EC 2.7.7.7) is comprised of three tightly associated subunits, alpha, epsilon and theta. This family contains the theta subunit. The structure of the theta subunit shows that the N-terminal two thirds is comprised of three helic ... | Domain |