E.coli transcription translation coupling complex in TTC-B state 3 (subclass1) containing mRNA with 30-mer spacer, NusG, NusA, fMet-tRNA(iMet), Phe-tRNA(Phe), and viomycin
Domain Annotation: SCOP2 Classification SCOP2 Database Homepage
Chains | Type | Family Name | Domain Identifier | Family Identifier | Provenance Source (Version) |
---|---|---|---|---|---|
I | SCOP2B Superfamily | Alpha-L RNA-binding motif | 8083400 | 3001473 | SCOP2B (2022-06-29) |
G | SCOP2B Superfamily | SIS domain/Ribosomal protein S2-like | 8063838 | 3001397 | SCOP2B (2022-06-29) |
KB [auth NG] | SCOP2B Superfamily | N-utilization substance G protein NusG, N-terminal domain | 8080353 | 3000474 | SCOP2B (2022-06-29) |
KB [auth NG] | SCOP2B Superfamily | Translation proteins SH3-like KOW motif containing domain | 8080349 | 3000334 | SCOP2B (2022-06-29) |
JB [auth NA] | SCOP2B Superfamily | Rad51 N-terminal domain-like | 8040765 | 3000529 | SCOP2B (2022-06-29) |
F | SCOP2B Superfamily | Ribosomal protein L36 | 8035391 | 3001346 | SCOP2B (2022-06-29) |
FB [auth A2] | SCOP2B Superfamily | RBP11-like subunits of RNA polymerase | 8035907 | 3001655 | SCOP2B (2022-06-29) |
FB [auth A2] | SCOP2B Superfamily | C-terminal domain of RNA polymerase alpha subunit | 8042964 | 3000519 | SCOP2B (2022-06-29) |
FB [auth A2] | SCOP2B Superfamily | RBP11-like subunits of RNA polymerase | 8035907 | 3001655 | SCOP2B (2022-06-29) |
FB [auth A2] | SCOP2B Superfamily | Insert subdomain of RNA polymerase alpha subunit | 8037279 | 3001500 | SCOP2B (2022-06-29) |
EB [auth A1] | SCOP2B Superfamily | RBP11-like subunits of RNA polymerase | 8035907 | 3001655 | SCOP2B (2022-06-29) |
EB [auth A1] | SCOP2B Superfamily | C-terminal domain of RNA polymerase alpha subunit | 8042964 | 3000519 | SCOP2B (2022-06-29) |
EB [auth A1] | SCOP2B Superfamily | RBP11-like subunits of RNA polymerase | 8035907 | 3001655 | SCOP2B (2022-06-29) |
EB [auth A1] | SCOP2B Superfamily | Insert subdomain of RNA polymerase alpha subunit | 8037279 | 3001500 | SCOP2B (2022-06-29) |
XA [auth z] | SCOP2B Superfamily | Ribosomal protein L30p/L7e | 8096372 | 3001378 | SCOP2B (2022-06-29) |
E | SCOP2B Superfamily | L35p-like | 8035388 | 3000790 | SCOP2B (2022-06-29) |
WA [auth y] | SCOP2B Superfamily | Ribosomal protein L29 (L29p) | 8096370 | 3000713 | SCOP2B (2022-06-29) |
VA [auth x] | SCOP2B Superfamily | L28p-like | 8035424 | 3001966 | SCOP2B (2022-06-29) |
UA [auth w] | SCOP2B Superfamily | Ribosomal L27 protein-like | 8096338 | 3000539 | SCOP2B (2022-06-29) |
TA [auth v] | SCOP2B Superfamily | Ribosomal protein L25-like | 8042538 | 3001161 | SCOP2B (2022-06-29) |
SA [auth u] | SCOP2B Superfamily | Translation proteins SH3-like KOW motif containing domain | 8096358 | 3000334 | SCOP2B (2022-06-29) |
RA [auth t] | SCOP2B Superfamily | Ribosomal proteins S24e, L23 and L15e | 8035415 | 3000210 | SCOP2B (2022-06-29) |
QA [auth s] | SCOP2B Superfamily | Ribosomal protein L22 | 8096336 | 3001078 | SCOP2B (2022-06-29) |
PA [auth r] | SCOP2B Superfamily | l21p-like | 8096354 | 3002005 | SCOP2B (2022-06-29) |
OA [auth q] | SCOP2B Superfamily | Ribosomal protein L20 | 8096382 | 3000563 | SCOP2B (2022-06-29) |
NA [auth p] | SCOP2B Superfamily | Translation proteins SH3-like KOW motif containing domain | 8096364 | 3000334 | SCOP2B (2022-06-29) |
MA [auth o] | SCOP2B Superfamily | Translational machinery components | 8032969 | 3000571 | SCOP2B (2022-06-29) |
LA [auth n] | SCOP2B Superfamily | Prokaryotic ribosomal protein L17 | 8035409 | 3000995 | SCOP2B (2022-06-29) |
KA [auth m] | SCOP2B Superfamily | Ribosomal protein L16p/L10e | 8096366 | 3000884 | SCOP2B (2022-06-29) |
JA [auth l] | SCOP2B Superfamily | Ribosomal proteins L15p and L18e | 8070553 | 3001045 | SCOP2B (2022-06-29) |
IA [auth k] | SCOP2B Superfamily | 50S Ribosomal protein L14-like | 8103358 | 3000433 | SCOP2B (2022-06-29) |
HA [auth j] | SCOP2B Superfamily | Ribosomal protein L13 | 8096350 | 3001134 | SCOP2B (2022-06-29) |
GA [auth i] | SCOP2B Superfamily | Ribosomal L11/L12e N-terminal domain-like | 8032963 | 3000950 | SCOP2B (2022-06-29) |
GA [auth i] | SCOP2B Superfamily | Ribosomal protein L11, C-terminal domain | 8032961 | 3001186 | SCOP2B (2022-06-29) |
FA [auth g] | SCOP2B Superfamily | L9 N-domain-like | 8032960 | 3000338 | SCOP2B (2022-06-29) |
FA [auth g] | SCOP2B Superfamily | Ribosomal protein L9 C-domain | 8032958 | 3000329 | SCOP2B (2022-06-29) |
EA [auth f] | SCOP2B Superfamily | Ribosomal protein L6 | 8035397 | 3000724 | SCOP2B (2022-06-29) |
EA [auth f] | SCOP2B Superfamily | Ribosomal protein L6 | 8035398 | 3000724 | SCOP2B (2022-06-29) |
DA [auth e] | SCOP2B Superfamily | RL5-like | 8096352 | 3001709 | SCOP2B (2022-06-29) |
C | SCOP2B Superfamily | Zn-binding ribosomal proteins | 8096362 | 3001320 | SCOP2B (2022-06-29) |
CA [auth d] | SCOP2B Superfamily | Ribosomal protein L4 | 8096356 | 3001146 | SCOP2B (2022-06-29) |
BA [auth c] | SCOP2B Superfamily | Translational proteins | 8032955 | 3000811 | SCOP2B (2022-06-29) |
AA [auth b] | SCOP2B Superfamily | Translation proteins SH3-like KOW motif containing domain | 8035393 | 3000334 | SCOP2B (2022-06-29) |
AA [auth b] | SCOP2B Superfamily | Nucleic acid-binding proteins | 8035394 | 3000135 | SCOP2B (2022-06-29) |
Z | SCOP2B Superfamily | Ribosomal protein S21 | 8053090 | 3002159 | SCOP2B (2022-06-29) |
X | SCOP2B Superfamily | Ribosomal protein S19 | 8103915 | 3000686 | SCOP2B (2022-06-29) |
V | SCOP2B Superfamily | Nucleic acid-binding proteins | 8059276 | 3000135 | SCOP2B (2022-06-29) |
U | SCOP2B Superfamily | Ribosomal protein S16 | 8106547 | 3000680 | SCOP2B (2022-06-29) |
T | SCOP2B Superfamily | S15/NS1 RNA-binding domain | 8032375 | 3001284 | SCOP2B (2022-06-29) |
B | SCOP2B Superfamily | Zn-binding ribosomal proteins | 8096380 | 3001320 | SCOP2B (2022-06-29) |
S | SCOP2B Superfamily | Glucocorticoid receptor-like (DNA-binding domain) | 8052568 | 3000068 | SCOP2B (2022-06-29) |
R | SCOP2B Superfamily | S13-like H2TH domain | 8098358 | 3000053 | SCOP2B (2022-06-29) |
Q | SCOP2B Superfamily | Nucleic acid-binding proteins | 8106545 | 3000135 | SCOP2B (2022-06-29) |
P | SCOP2B Superfamily | Translational machinery components | 8035368 | 3000571 | SCOP2B (2022-06-29) |
O | SCOP2B Superfamily | Ribosomal protein S10 | 8102681 | 3001336 | SCOP2B (2022-06-29) |
N | SCOP2B Superfamily | Ribosomal protein S5 domain 2-like | 8082661 | 3000100 | SCOP2B (2022-06-29) |
M | SCOP2B Superfamily | Ribosomal protein S8 | 8079059 | 3000709 | SCOP2B (2022-06-29) |
L | SCOP2B Superfamily | Ribosomal protein S7 | 8077979 | 3000799 | SCOP2B (2022-06-29) |
K | SCOP2B Superfamily | Ribosomal protein S6 | 8066495 | 3001323 | SCOP2B (2022-06-29) |
Protein Family Annotation Pfam Database Homepage
Chains | Accession | Name | Description | Comments | Source |
---|---|---|---|---|---|
PF03946 | Ribosomal protein L11, N-terminal domain (Ribosomal_L11_N) | Ribosomal protein L11, N-terminal domain | The N-terminal domain of Ribosomal protein L11 adopts an alpha/beta fold and is followed by the RNA binding C-terminal domain. | Domain | |
PF00163 | Ribosomal protein S4/S9 N-terminal domain (Ribosomal_S4) | Ribosomal protein S4/S9 N-terminal domain | - | Family | |
PF00298 | Ribosomal protein L11, RNA binding domain (Ribosomal_L11) | Ribosomal protein L11, RNA binding domain | Domain | ||
PF01479 | S4 domain (S4) | S4 domain | 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 pro ... | Domain | |
PF07650 | KH domain (KH_2) | KH domain | Domain | ||
PF00189 | Ribosomal protein S3, C-terminal domain (Ribosomal_S3_C) | Ribosomal protein S3, C-terminal domain | This 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 | |
PF00318 | Ribosomal protein S2 (Ribosomal_S2) | Ribosomal protein S2 | - | Family | |
PF01281 | Ribosomal protein L9, N-terminal domain (Ribosomal_L9_N) | Ribosomal protein L9, N-terminal domain | Domain | ||
PF03948 | Ribosomal protein L9, C-terminal domain (Ribosomal_L9_C) | Ribosomal protein L9, C-terminal domain | Domain | ||
OB [auth 0] | PF00679 | Elongation factor G C-terminus (EFG_C) | Elongation factor G C-terminus | This domain includes the carboxyl terminal regions of Elongation factor G, elongation factor 2 and some tetracycline resistance proteins and adopt a ferredoxin-like fold. | Domain |
OB [auth 0] | PF00009 | Elongation factor Tu GTP binding domain (GTP_EFTU) | Elongation factor Tu GTP binding domain | This domain contains a P-loop motif, also found in several other families such as Pfam:PF00071, Pfam:PF00025 and Pfam:PF00063. Elongation factor Tu consists of three structural domains, this plus two C-terminal beta barrel domains. | Domain |
OB [auth 0] | PF14492 | Elongation Factor G, domain III (EFG_III) | Elongation Factor G, domain III | This domain is found in Elongation Factor G. It shares a similar structure with domain V (Pfam:PF00679). Structural studies in drosophila indicate this is domain 3 [1]. | Domain |
OB [auth 0] | PF03144 | Elongation factor Tu domain 2 (GTP_EFTU_D2) | Elongation factor Tu domain 2 | Elongation factor Tu consists of three structural domains, this is the second domain. This domain adopts a beta barrel structure. This the second domain is involved in binding to charged tRNA [1]. This domain is also found in other proteins such as e ... | Domain |
OB [auth 0] | PF03764 | Elongation factor G, domain IV (EFG_IV) | Elongation factor G, domain IV | This domain is found in elongation factor G, elongation factor 2 and some tetracycline resistance proteins and adopts a ribosomal protein S5 domain 2-like fold. | Domain |
KB [auth NG] | PF02357 | Transcription termination factor nusG (NusG) | Transcription termination factor nusG | Domain | |
KB [auth NG] | PF00467 | KOW motif (KOW) | KOW motif | - | Family |
JB [auth NA] | PF13184 | NusA-like KH domain (KH_5) | NusA-like KH domain | Domain | |
JB [auth NA] | PF14520 | Helix-hairpin-helix domain (HHH_5) | Helix-hairpin-helix domain | Domain | |
JB [auth NA] | PF08529 | NusA N-terminal domain (NusA_N) | NusA N-terminal domain | This domain represents the RNA polymerase binding domain of NusA. | Domain |
JB [auth NA] | 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 |
IB [auth W0] | PF01192 | RNA polymerase Rpb6 (RNA_pol_Rpb6) | RNA polymerase Rpb6 | - | Family |
PF00347 | Ribosomal protein L6 (Ribosomal_L6) | Ribosomal protein L6 | Domain | ||
PF00444 | Ribosomal protein L36 (Ribosomal_L36) | Ribosomal protein L36 | Domain | ||
HB [auth B2] | PF04561 | RNA polymerase Rpb2, domain 2 (RNA_pol_Rpb2_2) | RNA polymerase Rpb2, domain 2 | 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 po ... | Domain |
HB [auth B2] | PF10385 | RNA polymerase beta subunit external 1 domain (RNA_pol_Rpb2_45) | RNA polymerase beta subunit external 1 domain | 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 ... | Domain |
HB [auth B2] | PF04560 | RNA polymerase Rpb2, domain 7 (RNA_pol_Rpb2_7) | RNA polymerase Rpb2, domain 7 | 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 p ... | Domain |
HB [auth B2] | PF04565 | RNA polymerase Rpb2, domain 3 (RNA_pol_Rpb2_3) | RNA polymerase Rpb2, domain 3 | 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 ... | Domain |
HB [auth B2] | PF04563 | RNA polymerase beta subunit (RNA_pol_Rpb2_1) | RNA polymerase beta subunit | - | Family |
HB [auth B2] | PF00562 | RNA polymerase Rpb2, domain 6 (RNA_pol_Rpb2_6) | RNA polymerase Rpb2, domain 6 | 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 ... | Domain |
GB [auth B1] | PF00623 | RNA polymerase Rpb1, domain 2 (RNA_pol_Rpb1_2) | RNA polymerase Rpb1, domain 2 | 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 ... | Domain |
GB [auth B1] | PF05000 | RNA polymerase Rpb1, domain 4 (RNA_pol_Rpb1_4) | RNA polymerase Rpb1, domain 4 | 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 do ... | Domain |
GB [auth B1] | PF04983 | RNA polymerase Rpb1, domain 3 (RNA_pol_Rpb1_3) | RNA polymerase Rpb1, domain 3 | 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 doma ... | Domain |
GB [auth B1] | PF04998 | RNA polymerase Rpb1, domain 5 (RNA_pol_Rpb1_5) | RNA polymerase Rpb1, domain 5 | 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 discontin ... | Domain |
EB [auth A1], FB [auth A2] | PF01193 | RNA polymerase Rpb3/Rpb11 dimerisation domain (RNA_pol_L) | RNA polymerase Rpb3/Rpb11 dimerisation 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 do ... | Domain |
EB [auth A1], FB [auth A2] | PF01000 | RNA polymerase Rpb3/RpoA insert domain (RNA_pol_A_bac) | RNA polymerase Rpb3/RpoA insert domain | Members of this family include: alpha subunit from eubacteria alpha subunits from chloroplasts Rpb3 subunits from eukaryotes RpoD subunits from archaeal | Domain |
PF00281 | Ribosomal protein L5 (Ribosomal_L5) | Ribosomal protein L5 | Domain | ||
PF01632 | Ribosomal protein L35 (Ribosomal_L35p) | Ribosomal protein L35 | - | Family | |
PF00468 | Ribosomal protein L34 (Ribosomal_L34) | Ribosomal protein L34 | - | Family | |
PF00573 | Ribosomal protein L4/L1 family (Ribosomal_L4) | Ribosomal protein L4/L1 family | - | Family | |
PF00471 | Ribosomal protein L33 (Ribosomal_L33) | Ribosomal protein L33 | - | Family | |
PF00297 | Ribosomal protein L3 (Ribosomal_L3) | Ribosomal protein L3 | - | Family | |
PF00327 | Ribosomal protein L30p/L7e (Ribosomal_L30) | Ribosomal protein L30p/L7e | This family includes prokaryotic L30 and eukaryotic L7. | Domain | |
PF00831 | Ribosomal L29 protein (Ribosomal_L29) | Ribosomal L29 protein | - | Family | |
PF00203 | Ribosomal protein S19 (Ribosomal_S19) | Ribosomal protein S19 | Domain | ||
PF00830 | Ribosomal L28 family (Ribosomal_L28) | Ribosomal L28 family | - | Family | |
PF01084 | Ribosomal protein S18 (Ribosomal_S18) | Ribosomal protein S18 | - | Family | |
PF01386 | Ribosomal L25p family (Ribosomal_L25p) | Ribosomal L25p family | Ribosomal 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 | |
PF00366 | Ribosomal protein S17 (Ribosomal_S17) | Ribosomal protein S17 | Domain | ||
PF00886 | Ribosomal protein S16 (Ribosomal_S16) | Ribosomal protein S16 | - | Family | |
PF17136 | Ribosomal proteins 50S L24/mitochondrial 39S L24 (ribosomal_L24) | Ribosomal proteins 50S L24/mitochondrial 39S L24 | - | Family | |
PF00467 | KOW motif (KOW) | KOW motif | - | Family | |
PF00276 | Ribosomal protein L23 (Ribosomal_L23) | Ribosomal protein L23 | - | Family | |
PF00312 | Ribosomal protein S15 (Ribosomal_S15) | Ribosomal protein S15 | Domain | ||
PF00181 | Ribosomal Proteins L2, RNA binding N-terminal domain (Ribosomal_L2_N) | Ribosomal Proteins L2, RNA binding N-terminal domain | Domain | ||
PF01783 | Ribosomal L32p protein family (Ribosomal_L32p) | Ribosomal L32p protein family | - | Family | |
PF00237 | Ribosomal protein L22p/L17e (Ribosomal_L22) | Ribosomal protein L22p/L17e | This family includes L22 from prokaryotes and chloroplasts and L17 from eukaryotes. | Domain | |
PF00253 | Ribosomal protein S14p/S29e (Ribosomal_S14) | Ribosomal protein S14p/S29e | - | Family | |
PF00416 | Ribosomal protein S13/S18 (Ribosomal_S13) | Ribosomal protein S13/S18 | - | Family | |
PF00829 | Ribosomal prokaryotic L21 protein (Ribosomal_L21p) | Ribosomal prokaryotic L21 protein | - | Family | |
PF00164 | Ribosomal protein S12/S23 (Ribosom_S12_S23) | Ribosomal protein S12/S23 | This protein is known as S12 in bacteria and archaea and S23 in eukaryotes. | Domain | |
PF00453 | Ribosomal protein L20 (Ribosomal_L20) | Ribosomal protein L20 | - | Family | |
PF01245 | Ribosomal protein L19 (Ribosomal_L19) | Ribosomal protein L19 | - | Family | |
PF00411 | Ribosomal protein S11 (Ribosomal_S11) | Ribosomal protein S11 | - | Family | |
PF00338 | Ribosomal protein S10p/S20e (Ribosomal_S10) | Ribosomal protein S10p/S20e | This family includes small ribosomal subunit S10 from prokaryotes and S20 from eukaryotes. | Domain | |
PF00380 | Ribosomal protein S9/S16 (Ribosomal_S9) | Ribosomal protein S9/S16 | - | Family | |
PF01196 | Ribosomal protein L17 (Ribosomal_L17) | Ribosomal protein L17 | - | Family | |
PF00252 | Ribosomal protein L16p/L10e (Ribosomal_L16) | Ribosomal protein L16p/L10e | Domain | ||
PF00410 | Ribosomal protein S8 (Ribosomal_S8) | Ribosomal protein S8 | Domain | ||
PF00828 | Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A (Ribosomal_L27A) | Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A | This family includes higher eukaryotic ribosomal 60S L27A, archaeal 50S L18e, prokaryotic 50S L15, fungal mitochondrial L10, plant L27A, mitochondrial L15 and chloroplast L18-3 proteins. | Domain | |
PF00238 | Ribosomal protein L14p/L23e (Ribosomal_L14) | Ribosomal protein L14p/L23e | Domain | ||
PF01250 | Ribosomal protein S6 (Ribosomal_S6) | Ribosomal protein S6 | Domain | ||
PF03719 | Ribosomal protein S5, C-terminal domain (Ribosomal_S5_C) | Ribosomal protein S5, C-terminal domain | Domain | ||
PF00572 | Ribosomal protein L13 (Ribosomal_L13) | Ribosomal protein L13 | - | Family | |
PF00333 | Ribosomal protein S5, N-terminal domain (Ribosomal_S5) | Ribosomal protein S5, N-terminal domain | Domain | ||
PF01197 | Ribosomal protein L31 (Ribosomal_L31) | Ribosomal protein L31 | - | Family | |
PF00687 | Ribosomal protein L1p/L10e family (Ribosomal_L1) | Ribosomal protein L1p/L10e family | This family includes prokaryotic L1 and eukaryotic L10. | Domain |