6X6T

Cryo-EM structure of an Escherichia coli coupled transcription-translation complex B1 (TTC-B1) containing an mRNA with a 24 nt long spacer, transcription factors NusA and NusG, and fMet-tRNAs at P-site and E-site


Protein Family Annotation Pfam Database Homepage

ChainsAccessionIdentifierDescriptionCommentsSource
PF17136Ribosomal proteins 50S L24/mitochondrial 39S L24 (ribosomal_L24)Ribosomal proteins 50S L24/mitochondrial 39S L24- Family
PF00467KOW motif (KOW)KOW motif- Family
PF01193RNA polymerase Rpb3/Rpb11 dimerisation domain (RNA_pol_L)RNA polymerase Rpb3/Rpb11 dimerisation domainThe 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 ...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.
Domain
PF01000RNA polymerase Rpb3/RpoA insert domain (RNA_pol_A_bac)RNA polymerase Rpb3/RpoA insert domainMembers of this family include: alpha subunit from eubacteria alpha subunits from chloroplasts Rpb3 subunits from eukaryotes RpoD subunits from archaealDomain
PF03118Bacterial RNA polymerase, alpha chain C terminal domain (RNA_pol_A_CTD)Bacterial RNA polymerase, alpha chain C terminal domainThe alpha subunit of RNA polymerase consists of two independently folded domains, referred to as amino-terminal and carboxyl terminal domains. The amino terminal domain is involved in the interaction with the other subunits of the RNA polymerase. T ...The alpha subunit of RNA polymerase consists of two independently folded domains, referred to as amino-terminal and carboxyl terminal domains. The amino terminal domain is involved in the interaction with the other subunits of the RNA polymerase. The carboxyl-terminal domain interacts with the DNA and activators. The amino acid sequence of the alpha subunit is conserved in prokaryotic and chloroplast RNA polymerases. There are three regions of particularly strong conservation, two in the amino-terminal and one in the carboxyl- terminal [2].
Domain
PF13184NusA-like KH domain (KH_5)NusA-like KH domain- Domain
PF14520Helix-hairpin-helix domain (HHH_5)Helix-hairpin-helix domain- Domain
PF08529NusA N-terminal domain (NusA_N)NusA N-terminal domainThis domain represents the RNA polymerase binding domain of NusA.Domain
PF00575S1 RNA binding domain (S1)S1 RNA binding domainThe 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
PF01084Ribosomal protein S18 (Ribosomal_S18)Ribosomal protein S18- Family
PF01649Ribosomal protein S20 (Ribosomal_S20p)Ribosomal protein S20- Family
PF03719Ribosomal protein S5, C-terminal domain (Ribosomal_S5_C)Ribosomal protein S5, C-terminal domain- Domain
PF00333Ribosomal protein S5, N-terminal domain (Ribosomal_S5)Ribosomal protein S5, N-terminal domain- Domain
PF00338Ribosomal protein S10p/S20e (Ribosomal_S10)Ribosomal protein S10p/S20eThis family includes small ribosomal subunit S10 from prokaryotes and S20 from eukaryotes.Domain
PF00411Ribosomal protein S11 (Ribosomal_S11)Ribosomal protein S11- Family
PF00253Ribosomal protein S14p/S29e (Ribosomal_S14)Ribosomal protein S14p/S29e- Family
PF00312Ribosomal protein S15 (Ribosomal_S15)Ribosomal protein S15- Domain
PF00886Ribosomal protein S16 (Ribosomal_S16)Ribosomal protein S16- Family
PF00203Ribosomal protein S19 (Ribosomal_S19)Ribosomal protein S19- Domain
PF03946Ribosomal protein L11, N-terminal domain (Ribosomal_L11_N)Ribosomal protein L11, N-terminal domainThe N-terminal domain of Ribosomal protein L11 adopts an alpha/beta fold and is followed by the RNA binding C-terminal domain.Domain
PF00298Ribosomal protein L11, RNA binding domain (Ribosomal_L11)Ribosomal protein L11, RNA binding domain- Domain
PF16320Ribosomal protein L7/L12 dimerisation domain (Ribosomal_L12_N)Ribosomal protein L7/L12 dimerisation domainThis is the N-terminal dimerisation domain of ribosomal protein L7/L12 [1].Domain
PF01016Ribosomal L27 protein (Ribosomal_L27)Ribosomal L27 protein- Family
PF00830Ribosomal L28 family (Ribosomal_L28)Ribosomal L28 family- Family
PF00327Ribosomal protein L30p/L7e (Ribosomal_L30)Ribosomal protein L30p/L7eThis family includes prokaryotic L30 and eukaryotic L7.Domain
PF01783Ribosomal L32p protein family (Ribosomal_L32p)Ribosomal L32p protein family- Family
PF00444Ribosomal protein L36 (Ribosomal_L36)Ribosomal protein L36- Domain
PF00828Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A (Ribosomal_L27A)Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A- Family
PF01196Ribosomal protein L17 (Ribosomal_L17)Ribosomal protein L17- Family
PF01245Ribosomal protein L19 (Ribosomal_L19)Ribosomal protein L19- Family
PF00453Ribosomal protein L20 (Ribosomal_L20)Ribosomal protein L20- Family
PF00829Ribosomal prokaryotic L21 protein (Ribosomal_L21p)Ribosomal prokaryotic L21 protein- Family
PF04561RNA polymerase Rpb2, domain 2 (RNA_pol_Rpb2_2)RNA polymerase Rpb2, domain 2RNA 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 ...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).
Domain
PF10385RNA polymerase beta subunit external 1 domain (RNA_pol_Rpb2_45)RNA polymerase beta subunit external 1 domainRNA polymerases catalyse the DNA-dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared with three in eukaryotes (not including mitochondrial or chloroplast polymerases). This domain in prokaryotes spans the gap between ...RNA polymerases catalyse the DNA-dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared with three in eukaryotes (not including mitochondrial or chloroplast polymerases). This domain in prokaryotes spans the gap between domains 4 and 5 of the yeast protein. It is also known as the external 1 region of the polymerase and is bound in association with the external 2 region [1].
Domain
PF04560RNA polymerase Rpb2, domain 7 (RNA_pol_Rpb2_7)RNA polymerase Rpb2, domain 7RNA 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 ...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].
Domain
PF04565RNA polymerase Rpb2, domain 3 (RNA_pol_Rpb2_3)RNA polymerase Rpb2, domain 3RNA 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 ...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].
Domain
PF04563RNA polymerase beta subunit (RNA_pol_Rpb2_1)RNA polymerase beta subunit- Family
PF00562RNA polymerase Rpb2, domain 6 (RNA_pol_Rpb2_6)RNA polymerase Rpb2, domain 6RNA 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 ...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).
Domain
PF02357Transcription termination factor nusG (NusG)Transcription termination factor nusG- Domain
PF00467KOW motif (KOW)KOW motif- Family
PF00623RNA polymerase Rpb1, domain 2 (RNA_pol_Rpb1_2)RNA polymerase Rpb1, domain 2RNA 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 ...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].
Domain
PF05000RNA polymerase Rpb1, domain 4 (RNA_pol_Rpb1_4)RNA polymerase Rpb1, domain 4RNA 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 ...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].
Domain
PF04983RNA polymerase Rpb1, domain 3 (RNA_pol_Rpb1_3)RNA polymerase Rpb1, domain 3RNA 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 ...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].
Domain
PF04998RNA polymerase Rpb1, domain 5 (RNA_pol_Rpb1_5)RNA polymerase Rpb1, domain 5RNA 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 ...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].
Domain
PF04997RNA polymerase Rpb1, domain 1 (RNA_pol_Rpb1_1)RNA polymerase Rpb1, domain 1RNA 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 ...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].
Domain
PF01192RNA polymerase Rpb6 (RNA_pol_Rpb6)RNA polymerase Rpb6- Family
PF00237Ribosomal protein L22p/L17e (Ribosomal_L22)Ribosomal protein L22p/L17eThis family includes L22 from prokaryotes and chloroplasts and L17 from eukaryotes.Domain
PF01165Ribosomal protein S21 (Ribosomal_S21)Ribosomal protein S21- Family
PF00318Ribosomal protein S2 (Ribosomal_S2)Ribosomal protein S2- Family
PF00575S1 RNA binding domain (S1)S1 RNA binding domainThe 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
PF07650KH domain (KH_2)KH domain- Domain
PF00189Ribosomal protein S3, C-terminal domain (Ribosomal_S3_C)Ribosomal protein S3, C-terminal domainThis family contains a central domain Pfam:PF00013, hence the amino and carboxyl terminal domains are stored separately. This is a minimal carboxyl-terminal domain. Some are much longer.Domain
PF00163Ribosomal protein S4/S9 N-terminal domain (Ribosomal_S4)Ribosomal protein S4/S9 N-terminal domain- Family
PF01479S4 domain (S4)S4 domainThe S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4, eukaryotic ribosomal S9, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast pro ...The S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4, eukaryotic ribosomal S9, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast protein containing a pseudouridine synthetase and a deaminase domain, bacterial tyrosyl-tRNA synthetases, and a number of uncharacterized, small proteins that may be involved in translation regulation [1]. The S4 domain probably mediates binding to RNA.
Domain
PF01250Ribosomal protein S6 (Ribosomal_S6)Ribosomal protein S6- Domain
PF00177Ribosomal protein S7p/S5e (Ribosomal_S7)Ribosomal protein S7p/S5eThis family contains ribosomal protein S7 from prokaryotes and S5 from eukaryotes.Domain
PF00410Ribosomal protein S8 (Ribosomal_S8)Ribosomal protein S8- Domain
PF00380Ribosomal protein S9/S16 (Ribosomal_S9)Ribosomal protein S9/S16- Family
PF00276Ribosomal protein L23 (Ribosomal_L23)Ribosomal protein L23- Family
PF00164Ribosomal protein S12/S23 (Ribosom_S12_S23)Ribosomal protein S12/S23- Family
PF00366Ribosomal protein S17 (Ribosomal_S17)Ribosomal protein S17- Domain
PF00416Ribosomal protein S13/S18 (Ribosomal_S13)Ribosomal protein S13/S18- Family
PF00831Ribosomal L29 protein (Ribosomal_L29)Ribosomal L29 protein- Family
PF01197Ribosomal protein L31 (Ribosomal_L31)Ribosomal protein L31- Family
PF03947Ribosomal Proteins L2, C-terminal domain (Ribosomal_L2_C)Ribosomal Proteins L2, C-terminal domain- Domain
PF00181Ribosomal Proteins L2, RNA binding domain (Ribosomal_L2)Ribosomal Proteins L2, RNA binding domain- Domain
PF01386Ribosomal L25p family (Ribosomal_L25p)Ribosomal L25p familyRibosomal protein L25 is an RNA binding protein, that binds 5S rRNA. This family includes Ctc from B. subtilis Swiss:P14194, which is induced by stress.Domain
PF00297Ribosomal protein L3 (Ribosomal_L3)Ribosomal protein L3- Family
PF00471Ribosomal protein L33 (Ribosomal_L33)Ribosomal protein L33- Family
PF00573Ribosomal protein L4/L1 family (Ribosomal_L4)Ribosomal protein L4/L1 family- Family
PF00468Ribosomal protein L34 (Ribosomal_L34)Ribosomal protein L34- Family
PF00281Ribosomal protein L5 (Ribosomal_L5)Ribosomal protein L5- Domain
PF00673ribosomal L5P family C-terminus (Ribosomal_L5_C)ribosomal L5P family C-terminusThis region is found associated with Pfam:PF00281.Domain
PF01632Ribosomal protein L35 (Ribosomal_L35p)Ribosomal protein L35- Family
PF00347Ribosomal protein L6 (Ribosomal_L6)Ribosomal protein L6- Domain
PF01281Ribosomal protein L9, N-terminal domain (Ribosomal_L9_N)Ribosomal protein L9, N-terminal domain- Domain
PF03948Ribosomal protein L9, C-terminal domain (Ribosomal_L9_C)Ribosomal protein L9, C-terminal domain- Domain
PF00572Ribosomal protein L13 (Ribosomal_L13)Ribosomal protein L13- Family
PF00238Ribosomal protein L14p/L23e (Ribosomal_L14)Ribosomal protein L14p/L23e- Domain
PF00252Ribosomal protein L16p/L10e (Ribosomal_L16)Ribosomal protein L16p/L10e- Domain
PF00861Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast (Ribosomal_L18p)Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast- Family
PF00466Ribosomal protein L10 (Ribosomal_L10)Ribosomal protein L10- Family

Gene Product Annotation Gene Product Annotation

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
50S ribosomal protein L24
    DNA-directed RNA polymerase subunit alpha
        Transcription termination/antitermination protein NusA
          30S ribosomal protein S18
            30S ribosomal protein S20
              30S ribosomal protein S5
                30S ribosomal protein S10
                  30S ribosomal protein S11
                    30S ribosomal protein S14
                      30S ribosomal protein S15
                        30S ribosomal protein S16
                          30S ribosomal protein S19
                            50S ribosomal protein L11
                              50S ribosomal protein L7/L12
                                23S rRNAnonenonenone
                                50S ribosomal protein L27
                                50S ribosomal protein L28
                                  50S ribosomal protein L30
                                    50S ribosomal protein L32
                                      50S ribosomal protein L36
                                        50S ribosomal protein L15
                                          50S ribosomal protein L17
                                            50S ribosomal protein L19
                                              50S ribosomal protein L20
                                                50S ribosomal protein L21
                                                  E-site and P-site tRNA (fMet)nonenonenone
                                                  DNA-directed RNA polymerase subunit beta
                                                      Transcription termination/antitermination protein NusG
                                                            DNA-directed RNA polymerase subunit beta'
                                                                DNA-directed RNA polymerase subunit omega
                                                                    16S rRNAnonenonenone
                                                                    50S ribosomal protein L22
                                                                      30S ribosomal protein S21
                                                                        30S ribosomal protein S2
                                                                          30S ribosomal protein S1
                                                                            30S ribosomal protein S3
                                                                              30S ribosomal protein S4
                                                                                30S ribosomal protein S6
                                                                                  30S ribosomal protein S7
                                                                                    30S ribosomal protein S8
                                                                                      30S ribosomal protein S9
                                                                                        50S ribosomal protein L23
                                                                                          30S ribosomal protein S12
                                                                                            30S ribosomal protein S17
                                                                                              30S ribosomal protein S13
                                                                                                5S rRNAnonenonenone
                                                                                                50S ribosomal protein L29
                                                                                                  50S ribosomal protein L31
                                                                                                    50S ribosomal protein L2
                                                                                                      50S ribosomal protein L25
                                                                                                        50S ribosomal protein L3
                                                                                                          50S ribosomal protein L33
                                                                                                            50S ribosomal protein L4
                                                                                                              50S ribosomal protein L34
                                                                                                                50S ribosomal protein L5
                                                                                                                  50S ribosomal protein L35
                                                                                                                    50S ribosomal protein L6
                                                                                                                      50S ribosomal protein L9
                                                                                                                        50S ribosomal protein L13
                                                                                                                          NT DNAnonenonenone
                                                                                                                          50S ribosomal protein L14
                                                                                                                            50S ribosomal protein L16
                                                                                                                              50S ribosomal protein L18
                                                                                                                                T DNAnonenonenone
                                                                                                                                mRNA with 24 nt long spacernonenonenone
                                                                                                                                50S ribosomal protein L10