1GO3

Structure of an archeal homolog of the eukaryotic RNA polymerase II RPB4/RPB7 complex

Domain Annotation: SCOP Classification SCOP Database (version: 2.0) Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species
A	d1go3e1	All beta proteins	OB-fold	Nucleic acid-binding proteins	Cold shock DNA-binding domain-like	C-terminal domain of RNA polymerase II subunit RBP7 (RpoE)	(Methanocaldococcus jannaschii ) [TaxId: 2190 ]
A	d1go3e2	Alpha and beta proteins (a+b)	Dodecin subunit-like	N-terminal, heterodimerisation domain of RBP7 (RpoE)	N-terminal, heterodimerisation domain of RBP7 (RpoE)	N-terminal, heterodimerisation domain of RBP7 (RpoE)	(Methanocaldococcus jannaschii ) [TaxId: 2190 ]
C	d1go3m1	All beta proteins	OB-fold	Nucleic acid-binding proteins	Cold shock DNA-binding domain-like	C-terminal domain of RNA polymerase II subunit RBP7 (RpoE)	(Methanocaldococcus jannaschii ) [TaxId: 2190 ]
C	d1go3m2	Alpha and beta proteins (a+b)	Dodecin subunit-like	N-terminal, heterodimerisation domain of RBP7 (RpoE)	N-terminal, heterodimerisation domain of RBP7 (RpoE)	N-terminal, heterodimerisation domain of RBP7 (RpoE)	(Methanocaldococcus jannaschii ) [TaxId: 2190 ]
B	d1go3f_	All alpha proteins	SAM domain-like	HRDC-like	RNA polymerase II subunit RBP4 (RpoF)	RNA polymerase II subunit RBP4 (RpoF)	(Methanocaldococcus jannaschii ) [TaxId: 2190 ]
D	d1go3n_	All alpha proteins	SAM domain-like	HRDC-like	RNA polymerase II subunit RBP4 (RpoF)	RNA polymerase II subunit RBP4 (RpoF)	(Methanocaldococcus jannaschii ) [TaxId: 2190 ]

Domain Annotation: CATH CATH Database (version 4.2.0) Homepage

Chain	Domain	Class	Architecture	Topology	Homology
A	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins
A	3.30.1490.120	Alpha Beta	2-Layer Sandwich	Dna Ligase	domain 1
C	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins
C	3.30.1490.120	Alpha Beta	2-Layer Sandwich	Dna Ligase	domain 1
B	1.10.150.80	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1
B	6.10.140.10	Special	Helix non-globular	Helix Hairpins
D	1.10.150.80	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1
D	6.10.140.10	Special	Helix non-globular	Helix Hairpins

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Identifier	Description	Comments	Source
A, C	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 ...	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 least one of the subunits contacted by the transcription factor TIF-IA [2]. The N terminus of Rpb7p/Rpc25p/MJ0397 has a SHS2 domain that is involved in protein-protein interaction [3].	Domain
A, C	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
B, D	PF03874	RNA polymerase Rpb4 (RNA_pol_Rpb4)	RNA polymerase Rpb4	-	Family

Gene Product Annotation Gene Product Annotation

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
E, M	DNA-DIRECTED RNA POLYMERASE SUBUNIT E	nucleic acid binding DNA binding binding organic cyclic compound binding heterocyclic compound binding catalytic activity DNA-directed 5'-3' RNA polymerase activity transferase activity transferase activity, transferring phosphorus-containing groups nucleotidyltransferase activity 5'-3' RNA polymerase activity RNA polymerase activity catalytic activity, acting on RNA
F, N	DNA-DIRECTED RNA POLYMERASE SUBUNIT F			RNA polymerase complex protein-containing complex transferase complex, transferring phosphorus-containing groups intracellular protein-containing complex catalytic complex transferase complex

RCSB PDB is funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.