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RNA POLYMERASE II INITIAL TRANSCRIBING COMPLEX WITH A 6NT DNA-RNA HYBRID AND SOAKED WITH AMPCPP
Annotation data related to this entry.
4A3F
  •   Protein Family Annotation: Pfam Classification   Hide
    Chain Pfam Accession Pfam Family Identifier Pfam Description Type Comment
    A PF04983   RNA_pol_Rpb1_3 RNA polymerase Rpb1, domain 3 Domain 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 domain. The 3' end of RNA is positioned close to this domain. The pore delimited by this domain is thought to act as a channel through which nucleotides enter the active site and/or where the 3' end of the RNA may be extruded during back-tracking [1,2]. Source: Pfam  
    A PF04992   RNA_pol_Rpb1_6 RNA polymerase Rpb1, domain 6 Domain 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 module of the RNA polymerase. Domain 6 forms part of the shelf module [1,2]. This family appears to be specific to the largest subunit of RNA polymerase II. Source: Pfam  
    F PF01192   RNA_pol_Rpb6 RNA polymerase Rpb6 Family
    E PF03871   RNA_pol_Rpb5_N RNA polymerase Rpb5, N-terminal domain 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 pol II structure [3]. This module is important for positioning the downstream DNA. Source: Pfam  
    H PF03870   RNA_pol_Rpb8 RNA polymerase Rpb8 Family
    B PF04561   RNA_pol_Rpb2_2 RNA polymerase Rpb2, domain 2 Domain 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 polymerase. This domain forms one of the two distinctive lobes of the Rpb2 structure. This domain is also known as the lobe domain [1]. DNA has been demonstrated to bind to the concave surface of the lobe domain, and plays a role in maintaining the transcription bubble [1]. Many of the bacterial members contain large insertions within this domain, as region known as dispensable region 1 (DRI). Source: Pfam  
    C PF01000   RNA_pol_A_bac RNA polymerase Rpb3/RpoA insert domain Domain Members of this family include: alpha subunit from eubacteria alpha subunits from chloroplasts Rpb3 subunits from eukaryotes RpoD subunits from archaeal Source: Pfam  
    G PF08292   RNA_pol_Rbc25 RNA polymerase III subunit Rpc25 Domain Rpc25 is a strongly conserved subunit of RNA polymerase III and has homology to Rpa43 in RNA polymerase I, Rpb7 in RNA polymerase II and the archaeal RpoE subunit. Rpc25 is required for transcription initiation and is not essential for the elongating properties of RNA polymerase III [1]. Source: Pfam  
    E PF01191   RNA_pol_Rpb5_C RNA polymerase Rpb5, C-terminal domain Domain The assembly domain of Rpb5 [1]. The archaeal equivalent to this domain is subunit H. Subunit H lacks the N-terminal domain. Source: Pfam  
    B PF00562   RNA_pol_Rpb2_6 RNA polymerase Rpb2, domain 6 Domain 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 and the wall domain [1]. The hybrid binding domain binds the nascent RNA strand / template DNA strand in the Pol II transcription elongation complex. This domain contains the important structural motifs, switch 3 and the flap loop and binds an active site metal ion[1]. This domain is also involved in binding to Rpb1 and Rpb3 [1]. Many of the bacterial members contain large insertions within this domain, as region known as dispensable region 2 (DRII). Source: Pfam  
    D PF03874   RNA_pol_Rpb4 RNA polymerase Rpb4 Family
    A PF04998   RNA_pol_Rpb1_5 RNA polymerase Rpb1, domain 5 Domain 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 discontinuous cleft domain that is required to from the central cleft or channel where the DNA is bound [1,2]. Source: Pfam  
    B PF04563   RNA_pol_Rpb2_1 RNA polymerase beta subunit Family
    C PF01193   RNA_pol_L RNA polymerase Rpb3/Rpb11 dimerisation domain 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 domain of the alpha subunit/Rpb3 is interrupted by an insert domain (Pfam:PF01000). Some of the alpha subunits also contain iron-sulphur binding domains (Pfam:PF00037). Rpb11 is found as a continuous domain. Members of this family include: alpha subunit from eubacteria, alpha subunits from chloroplasts, Rpb3 subunits from eukaryotes, Rpb11 subunits from eukaryotes, RpoD subunits from archaeal spp, and RpoL subunits from archaeal spp. Source: Pfam  
    B PF04560   RNA_pol_Rpb2_7 RNA polymerase Rpb2, domain 7 Domain 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 polymerase. This domain comprised of the structural domains anchor and clamp [1]. The clamp region (C-terminal) contains a zinc-binding motif [1]. The clamp region is named due to its interaction with the clamp domain found in Rpb1. The domain also contains a region termed "switch 4". The switches within the polymerase are thought to signal different stages of transcription [1]. Source: Pfam  
    A PF04990   RNA_pol_Rpb1_7 RNA polymerase Rpb1, domain 7 Domain 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 module of the RNA polymerase. Domain 7 forms a substantial interaction with the lobe domain of Rpb2 (Pfam:PF04561) [1,2]. Source: Pfam  
    J PF01194   RNA_pol_N RNA polymerases N / 8 kDa subunit Domain Source: Pfam  
    B PF04565   RNA_pol_Rpb2_3 RNA polymerase Rpb2, domain 3 Domain 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 proximal to catalytic site [1]. Source: Pfam  
    A PF00623   RNA_pol_Rpb1_2 RNA polymerase Rpb1, domain 2 Domain 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. The invariant motif -NADFDGD- binds the active site magnesium ion [1,2]. Source: Pfam  
    A PF05000   RNA_pol_Rpb1_4 RNA polymerase Rpb1, domain 4 Domain 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 domain. The funnel contain the binding site for some elongation factors [1,2]. Source: Pfam  
    K PF01193   RNA_pol_L RNA polymerase Rpb3/Rpb11 dimerisation domain 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 domain of the alpha subunit/Rpb3 is interrupted by an insert domain (Pfam:PF01000). Some of the alpha subunits also contain iron-sulphur binding domains (Pfam:PF00037). Rpb11 is found as a continuous domain. Members of this family include: alpha subunit from eubacteria, alpha subunits from chloroplasts, Rpb3 subunits from eukaryotes, Rpb11 subunits from eukaryotes, RpoD subunits from archaeal spp, and RpoL subunits from archaeal spp. Source: Pfam  
    I PF02150   RNA_POL_M_15KD RNA polymerases M/15 Kd subunit Domain Source: Pfam  
    G PF00575   S1 S1 RNA binding domain 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. Source: Pfam  
    K PF13656   RNA_pol_L_2 RNA polymerase Rpb3/Rpb11 dimerisation domain 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 domain of the alpha subunit/Rpb3 is interrupted by an insert domain (Pfam:PF01000). Some of the alpha subunits also contain iron-sulphur binding domains (Pfam:PF00037). Rpb11 is found as a continuous domain. Members of this family include: alpha subunit from eubacteria, alpha subunits from chloroplasts, Rpb3 subunits from eukaryotes, Rpb11 subunits from eukaryotes, RpoD subunits from archaeal spp, and RpoL subunits from archaeal spp. Many of the members of this family carry only the N-terminal region of Rpb11. Source: Pfam  
    B PF04566   RNA_pol_Rpb2_4 RNA polymerase Rpb2, domain 4 Domain 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 [1]. Source: Pfam  
    B PF04567   RNA_pol_Rpb2_5 RNA polymerase Rpb2, domain 5 Domain 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 [1]. Source: Pfam  
    L PF03604   DNA_RNApol_7kD DNA directed RNA polymerase, 7 kDa subunit Domain Source: Pfam  
    A PF04997   RNA_pol_Rpb1_1 RNA polymerase Rpb1, domain 1 Domain 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 domain, which a mobile domain involved in positioning the DNA, maintenance of the transcription bubble and positioning of the nascent RNA strand [1,2]. Source: Pfam  
    I PF01096   TFIIS_C Transcription factor S-II (TFIIS) Domain Source: Pfam  
    G PF03876   SHS2_Rpb7-N SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 Domain 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]. Source: Pfam  
     
  •   Gene Product Annotation: GO Terms   Hide
    Polymer Molecular Function Biological Process Cellular Component
    DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB1 (4A3F:A)
    • none
    DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2 (4A3F:B)
    • none
    DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3 (4A3F:C)
    • none
    DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 (4A3F:D)
    DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 1 (4A3F:E)
    DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 2 (4A3F:F)
    RPB7, DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 (4A3F:G)
    • none
    DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 3 (4A3F:H)
    DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9 (4A3F:I)
    DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 5 (4A3F:J)
    DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 (4A3F:K)
    • none
    DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 4 (4A3F:L)
    NON TEMPLATE DNA 5'-D(*TP*AP*AP*GP*TP*AP*CP*TP*TP*GP*AP *GP*CP*TP)- 3' (4A3F:N)
    • none
    • none
    • none
    TRANSCRIPT RNA 5'-R(*CP*CP*AP*GP*GP*AP)-3' (4A3F:P)
    • none
    • none
    • none
    5'-D(*AP*GP*CP*TP*CP*AP*AP*GP*TP*AP*CP*TP*TP*DTP *TP*TP*CP*C BRU*GP*GP*TP*CP*AP*TP*T)- 3' (4A3F:T)
    • none
    • none
    • none
     
  •   Structural Biology Knowledgebase Data Hide
     
 
Annotations in orange boxes have been gathered from external resources.