4QJF
X-ray crystal structure of Thermocuccus kodakarensis RNA polymerase Rpp4/Rpo7 (RpoF/RpoE) complex
Domain Annotation: SCOP2 Classification SCOP2 Database Homepage
Domain Annotation: ECOD Classification ECOD Database Homepage
Chains | Family Name | Domain Identifier | Architecture | Possible Homology | Homology | Topology | Family | Provenance Source (Version) |
---|---|---|---|---|---|---|---|---|
A | S1_1 | e4qjfA2 | A: beta barrels | X: OB-fold | H: Nucleic acid-binding proteins (From Topology) | T: Nucleic acid-binding proteins | F: S1_1 | ECOD (1.6) |
A | SHS2_Rpb7-N | e4qjfA1 | 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) |
B | RNA_pol_Rpb4 | e4qjfB1 | A: alpha arrays | X: HhH/H2TH | H: SAM/DNA-glycosylase | T: SAM domain-like | F: RNA_pol_Rpb4 | ECOD (1.6) |
Domain Annotation: CATH CATH Database Homepage
Chain | Domain | Class | Architecture | Topology | Homology | Provenance Source (Version) |
---|---|---|---|---|---|---|
A | 3.30.1490.120 | Alpha Beta | 2-Layer Sandwich | Dna Ligase | domain 1 | CATH (4.3.0) |
A | 2.40.50.140 | Mainly Beta | Beta Barrel | OB fold (Dihydrolipoamide Acetyltransferase, E2P) | Nucleic acid-binding proteins | CATH (4.3.0) |
B | 6.10.140.10 | Special | Helix non-globular | Helix Hairpins | CATH (4.3.0) | |
B | 1.10.150.80 | Mainly Alpha | Orthogonal Bundle | DNA polymerase | domain 1 | CATH (4.3.0) |
Protein Family Annotation Pfam Database Homepage
Chains | Accession | Name | Description | Comments | Source |
---|---|---|---|---|---|
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 | |
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 | |
PF03874 | RNA polymerase Rpb4 (RNA_pol_Rpb4) | RNA polymerase Rpb4 | - | Family |
Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage
InterPro: Protein Family Classification InterPro Database Homepage
Chains | Accession | Name | Type |
---|---|---|---|
IPR046399 | DNA-directed RNA polymerase subunit Rpo7 | Family | |
IPR036898 | RNA polymerase Rpb7-like, N-terminal domain superfamily | Homologous Superfamily | |
IPR004519 | DNA-directed RNA polymerase, subunit E/RPC8 | Family | |
IPR003029 | S1 domain | Domain | |
IPR012340 | Nucleic acid-binding, OB-fold | Homologous Superfamily | |
IPR045113 | RNA polymerase subunit Rpb7-like | Family | |
IPR005576 | RNA polymerase Rpb7-like , N-terminal | Domain | |
IPR005574 | RNA polymerase subunit Rpb4/RPC9 | Family | |
IPR044876 | HRDC domain superfamily | Homologous Superfamily | |
IPR010997 | HRDC-like superfamily | Homologous Superfamily | |
IPR010924 | DNA-directed RNA polymerase subunit Rpo4 | Family |