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- PDB-8urx: Escherichia coli transcription-translation coupled complex class ... -

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Basic information

Entry
Database: PDB / ID: 8urx
TitleEscherichia coli transcription-translation coupled complex class B (TTC-B) containing RfaH bound to ops signal, mRNA with a 30 nt long spacer, and fMet-tRNAs in E-site and P-site of the ribosome
Components
  • (30S ribosomal protein ...) x 21
  • (50S ribosomal protein ...) x 31
  • (DNA-directed RNA polymerase subunit ...) x 4
  • 16S rRNA
  • 23S rRNA
  • 5S rRNA
  • E-site and P-site fMet-tRNA
  • NT DNA ops
  • Ribosomal protein L21
  • T DNA ops
  • Transcription antitermination protein RfaH
  • mRNA with 30 nt long spacer
KeywordsTRANSCRIPTION / translation / RfaH / gene expression / regulation / ops / ribosome / coupling
Function / homology
Function and homology information


transcription antitermination factor activity, DNA binding / negative regulation of cytoplasmic translational initiation / transcription elongation-coupled chromatin remodeling / RNA polymerase complex / submerged biofilm formation / stringent response / cellular response to cell envelope stress / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / bacterial-type flagellum assembly ...transcription antitermination factor activity, DNA binding / negative regulation of cytoplasmic translational initiation / transcription elongation-coupled chromatin remodeling / RNA polymerase complex / submerged biofilm formation / stringent response / cellular response to cell envelope stress / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / bacterial-type flagellum assembly / misfolded RNA binding / Group I intron splicing / RNA folding / bacterial-type flagellum-dependent cell motility / positive regulation of ribosome biogenesis / nitrate assimilation / translational termination / DnaA-L2 complex / negative regulation of translational initiation / negative regulation of DNA-templated DNA replication initiation / translational initiation / ribosome assembly / mRNA regulatory element binding translation repressor activity / positive regulation of RNA splicing / assembly of large subunit precursor of preribosome / transcription elongation factor complex / cytosolic ribosome assembly / regulation of DNA-templated transcription elongation / transcription antitermination / DNA-templated transcription initiation / regulation of cell growth / cell motility / DNA-templated transcription termination / maintenance of translational fidelity / ribosomal large subunit assembly / ribonucleoside binding / mRNA 5'-UTR binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / large ribosomal subunit / ribosome binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / response to heat / protein-containing complex assembly / cytosolic small ribosomal subunit / intracellular iron ion homeostasis / cytosolic large ribosomal subunit / tRNA binding / cytoplasmic translation / rRNA binding / protein dimerization activity / negative regulation of translation / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / response to antibiotic / mRNA binding / magnesium ion binding / DNA binding / RNA binding / zinc ion binding / membrane / cytoplasm / cytosol
Similarity search - Function
Transcription antitermination protein RfaH / Ribosomal protein S1 / Ribosomal protein S1-like / Ribosomal protein L7/L12, oligomerisation / Ribosomal protein L7/L12, oligomerisation domain superfamily / NusG-like / Transcription termination factor nusG / Ribosomal protein L7/L12 dimerisation domain / Ribosomal protein L7/L12 / Ribosomal protein L7/L12, C-terminal ...Transcription antitermination protein RfaH / Ribosomal protein S1 / Ribosomal protein S1-like / Ribosomal protein L7/L12, oligomerisation / Ribosomal protein L7/L12, oligomerisation domain superfamily / NusG-like / Transcription termination factor nusG / Ribosomal protein L7/L12 dimerisation domain / Ribosomal protein L7/L12 / Ribosomal protein L7/L12, C-terminal / Ribosomal protein L7/L12 C-terminal domain / RNA-binding domain, S1 / Ribosomal protein L7/L12, C-terminal/adaptor protein ClpS-like / NusG, N-terminal / In Spt5p, this domain may confer affinity for Spt4p. It possesses a RNP-like fold. / NusG, N-terminal domain superfamily / Ribosomal protein L10, eubacterial, conserved site / Ribosomal protein L10 signature. / Ribosomal protein L10 / : / S1 domain profile. / DNA-directed RNA polymerase, omega subunit / Ribosomal protein S21, conserved site / Ribosomal protein S21 signature. / DNA-directed RNA polymerase, subunit beta-prime, bacterial type / DNA-directed RNA polymerase, beta subunit, external 1 domain superfamily / DNA-directed RNA polymerase, beta subunit, external 1 domain / RNA polymerase beta subunit external 1 domain / RNA polymerase, alpha subunit, C-terminal / Bacterial RNA polymerase, alpha chain C terminal domain / Ribosomal protein L25, short-form / DNA-directed RNA polymerase, alpha subunit / DNA-directed RNA polymerase beta subunit, bacterial-type / Ribosomal protein S14, bacterial/plastid / Ribosomal protein S1-like RNA-binding domain / Ribosomal protein L11, bacterial-type / S1 RNA binding domain / Ribosomal protein L31 type A / Ribosomal protein S21 superfamily / S1 domain / Ribosomal protein S21 / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein S21 / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein L11, conserved site / Ribosomal protein L11 signature. / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L10-like domain superfamily / Ribosomal protein L10 / Ribosomal protein L16 signature 1. / Ribosomal protein L10P / : / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal protein L16, conserved site / Ribosomal protein L16 signature 2. / Ribosomal protein L9 signature. / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L9, C-terminal / Ribosomal protein L9, C-terminal domain / Ribosomal protein L17 signature. / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L11, N-terminal / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11, RNA binding domain / Ribosomal protein L11/L12 / Ribosomal protein L36 signature. / Ribosomal protein L28/L24 superfamily / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Ribosomal protein L32p, bacterial type / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9 / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / Ribosomal protein L28 / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L5, bacterial-type / Ribosomal protein L6, bacterial-type / Ribosomal protein L18, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36
Similarity search - Domain/homology
: / : / : / : / DNA / DNA (> 10) / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) ...: / : / : / : / DNA / DNA (> 10) / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL15 / Small ribosomal subunit protein bS18 / Large ribosomal subunit protein bL36 / Small ribosomal subunit protein bS21 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein bL17 / 30S ribosomal protein S1 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS13 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein bL21 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein bL20 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS3 / Large ribosomal subunit protein bL34 / Transcription antitermination protein RfaH / Large ribosomal subunit protein uL6 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein bS20 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein bL25 / Large ribosomal subunit protein bL32 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS15 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein bL33 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein uL10 / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL31 / Large ribosomal subunit protein bL35 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS5 / DNA-directed RNA polymerase subunit alpha / DNA-directed RNA polymerase subunit omega / DNA-directed RNA polymerase subunit beta' / DNA-directed RNA polymerase subunit beta / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL22 / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein uL14 / Small ribosomal subunit protein uS14 / Large ribosomal subunit protein bL12 / Large ribosomal subunit protein bL19 / Small ribosomal subunit protein uS10 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein bL9
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.6 Å
AuthorsMolodtsov, V. / Wang, C. / Ebright, R.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2024
Title: Escherichia coli transcription-translation coupled complex class A (TTC-A) containing RfaH bound to ops signal, mRNA with a 21 nt long spacer, and fMet-tRNAs in E-site and P-site of the ribosome
Authors: Molodtsov, V. / Wang, C. / Zhang, J. / Kaelber, J.T. / Blaha, G. / Ebright, R.H.
History
DepositionOct 27, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
0: Ribosomal protein L21
1: 50S ribosomal protein L22
2: 50S ribosomal protein L23
3: 50S ribosomal protein L24
4: 50S ribosomal protein L25
5: NT DNA ops
6: T DNA ops
7: mRNA with 30 nt long spacer
9: 50S ribosomal protein L10
A: E-site and P-site fMet-tRNA
AA: DNA-directed RNA polymerase subunit beta
AB: Transcription antitermination protein RfaH
AC: DNA-directed RNA polymerase subunit alpha
AD: DNA-directed RNA polymerase subunit alpha
AE: DNA-directed RNA polymerase subunit beta'
AF: DNA-directed RNA polymerase subunit omega
B: E-site and P-site fMet-tRNA
C: 30S ribosomal protein S18
D: 16S rRNA
E: 30S ribosomal protein S20
F: 30S ribosomal protein S21
G: 30S ribosomal protein S2
H: 30S ribosomal protein S1
I: 30S ribosomal protein S3
J: 30S ribosomal protein S4
K: 30S ribosomal protein S5
L: 30S ribosomal protein S6
M: 30S ribosomal protein S7
N: 30S ribosomal protein S8
O: 30S ribosomal protein S9
P: 30S ribosomal protein S10
Q: 30S ribosomal protein S11
R: 30S ribosomal protein S12
S: 30S ribosomal protein S14
T: 30S ribosomal protein S15
U: 30S ribosomal protein S16
V: 30S ribosomal protein S17
W: 30S ribosomal protein S19
X: 30S ribosomal protein S13
Y: 50S ribosomal protein L11
Z: 50S ribosomal protein L7/L12
a: 23S rRNA
b: 50S ribosomal protein L27
c: 50S ribosomal protein L28
d: 5S rRNA
e: 50S ribosomal protein L29
f: 50S ribosomal protein L30
g: 50S ribosomal protein L31
h: 50S ribosomal protein L2
i: 50S ribosomal protein L32
j: 50S ribosomal protein L3
k: 50S ribosomal protein L33
l: 50S ribosomal protein L4
m: 50S ribosomal protein L34
n: 50S ribosomal protein L5
o: 50S ribosomal protein L35
p: 50S ribosomal protein L6
q: 50S ribosomal protein L36
r: 50S ribosomal protein L9
s: 50S ribosomal protein L13
t: 50S ribosomal protein L14
u: 50S ribosomal protein L15
v: 50S ribosomal protein L16
w: 50S ribosomal protein L17
x: 50S ribosomal protein L18
y: 50S ribosomal protein L19
z: 50S ribosomal protein L20
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,741,39770
Polymers2,741,24267
Non-polymers1553
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 2 types, 2 molecules 0AB

#1: Protein Ribosomal protein L21


Mass: 11586.374 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rplU, ECMP0215528_3699 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A829CSJ4
#12: Protein Transcription antitermination protein RfaH


Mass: 18364.217 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rfaH / Production host: Escherichia coli (E. coli) / References: UniProt: C3SK02

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50S ribosomal protein ... , 31 types, 31 molecules 12349YZbcefghijklmnopqrstuvwxyz

#2: Protein 50S ribosomal protein L22 / Large ribosomal subunit protein uL22


Mass: 12253.359 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rplV, eryB, b3315, JW3277 / Production host: Escherichia coli (E. coli) / References: UniProt: P61175
#3: Protein 50S ribosomal protein L23


Mass: 11222.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rplW, ECMP0215528_3828 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A829CFV1
#4: Protein 50S ribosomal protein L24


Mass: 11339.250 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rplX, EAVG_03047 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1X3KWX7
#5: Protein 50S ribosomal protein L25


Mass: 10713.465 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rplY / Production host: Escherichia coli (E. coli) / References: UniProt: D7XH79
#9: Protein 50S ribosomal protein L10 / 50S ribosomal protein L8 / Large ribosomal subunit protein uL10


Mass: 17736.596 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rplJ, b3985, JW3948 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7J3
#38: Protein 50S ribosomal protein L11 / Large ribosomal subunit protein uL11


Mass: 14894.362 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rplK, relC, b3983, JW3946 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7J7
#39: Protein 50S ribosomal protein L7/L12


Mass: 12309.155 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rplL / Production host: Escherichia coli (E. coli) / References: UniProt: V0AEG5
#41: Protein 50S ribosomal protein L27 / Large ribosomal subunit protein bL27


Mass: 9146.540 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpmA, b3185, JW3152 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7L8
#42: Protein 50S ribosomal protein L28


Mass: 9027.551 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpmB, ECVG_03476 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1X3JA73
#44: Protein 50S ribosomal protein L29


Mass: 7286.464 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpmC, ECDG_03892 / Production host: Escherichia coli (E. coli) / References: UniProt: D6IEL0
#45: Protein 50S ribosomal protein L30


Mass: 6554.820 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpmD, HMPREF1611_03432 / Production host: Escherichia coli (E. coli) / References: UniProt: V0YKA9
#46: Protein 50S ribosomal protein L31 / Large ribosomal subunit protein bL31-A


Mass: 7887.117 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpmE, b3936, JW3907 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7M9
#47: Protein 50S ribosomal protein L2 / Large ribosomal subunit protein uL2


Mass: 29923.619 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rplB, b3317, JW3279 / Production host: Escherichia coli (E. coli) / References: UniProt: P60422
#48: Protein 50S ribosomal protein L32


Mass: 6463.445 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpmF, HMPREF9536_00655 / Production host: Escherichia coli (E. coli) / References: UniProt: D7XI28
#49: Protein 50S ribosomal protein L3 / Large ribosomal subunit protein uL3


Mass: 22277.535 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rplC, b3320, JW3282 / Production host: Escherichia coli (E. coli) / References: UniProt: P60438
#50: Protein 50S ribosomal protein L33


Mass: 6388.631 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpmG, SSJG_04343 / Production host: Escherichia coli (E. coli) / References: UniProt: F4NQ61
#51: Protein 50S ribosomal protein L4


Mass: 22121.566 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: A1AGK6
#52: Protein/peptide 50S ribosomal protein L34


Mass: 5397.463 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpmH / Production host: Escherichia coli (E. coli) / References: UniProt: B7MGC4
#53: Protein 50S ribosomal protein L5


Mass: 20333.611 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rplE, ECMP0215528_3818 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A829CFT8
#54: Protein 50S ribosomal protein L35 / Large ribosomal subunit protein bL35 / Ribosomal protein A


Mass: 7313.032 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpmI, b1717, JW1707 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7Q1
#55: Protein 50S ribosomal protein L6


Mass: 18932.791 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: rplF, A5U30_004539, A8499_003319, A8502_004036, A9X72_02250, AAG43_004459, AAS29_002175, ACN68_01830, ACN81_25455, ACU57_21025, AM464_09155, APX88_16140, AT845_004391, AW118_24835, AW119_26645, ...Gene: rplF, A5U30_004539, A8499_003319, A8502_004036, A9X72_02250, AAG43_004459, AAS29_002175, ACN68_01830, ACN81_25455, ACU57_21025, AM464_09155, APX88_16140, AT845_004391, AW118_24835, AW119_26645, AWP47_12710, B6R12_002820, B6R15_004082, B6R31_004981, B6R48_005048, B6R87_004958, BANRA_04315, BANRA_04463, BEA19_23360, BER14_25125, BF481_004943, BG944_001120, BGM66_003606, BHS81_19770, BJI68_08740, BJJ90_02190, BK292_20440, BK383_24710, BKL28_004556, BLM69_000027, BMC79_004432, BMT50_12280, BON92_01205, BR158_003777, BRV02_004610, BRV34_003983, BRV41_004371, BSR05_22725, BTB68_004369, BTQ06_10625, BUO55_004710, BvCmsKKP061_03017, BXT93_05540, BZL69_25965, C0P57_002655, C1Q91_004917, C2121_004175, C2M16_25470, C2R31_004620, C3F40_19785, C5N07_23555, C9114_23825, C9E67_02790, C9Z68_22570, CA593_09715, CCS08_00150, CDL36_25575, CDL37_18610, CF22_004862, CG831_003636, CIG67_10740, CO706_15220, CQ986_004894, CR538_02485, CR539_21835, CR628_001353, CTR35_003617, CWS33_24875, CX938_003818, CY655_21255, D0X26_24515, D3G36_23115, D4M65_20590, D4N09_20190, D4U49_16165, D9D43_22615, D9E34_23590, D9E49_05175, D9H94_20815, D9J03_20070, D9J61_16670, DD762_23565, DIV22_15240, DN627_24350, DNQ45_03775, DNX30_25460, DRW19_25065, DS732_24280, DTL43_20980, DTL90_24710, DTM45_24535, DU321_12020, E0I42_22210, E3N34_07180, E4K51_21510, E5H86_24505, E6D34_21740, EA239_22810, EA435_23050, EAI46_07495, EAN77_23505, EAX79_10730, EBP16_21855, EC95NR1_02696, ECs4170, EHD79_24220, EIZ93_12450, EKI52_17645, EL79_0411, ELT17_22420, ELT48_22940, ELX68_21470, ELX76_22960, ELX79_22070, ELX96_16825, ELY41_18740, ELY48_23180, EN85_004362, EPS76_07195, ERS085406_04403, ERS139208_04351, EWK56_25015, ExPECSC038_03653, F3N40_22345, F7F11_22705, F7N46_23990, F9413_21215, F9461_25635, F9B07_24665, F9S83_19010, FA868_22765, FDM60_20820, FEJ01_22495, FFF58_25435, FGG80_25115, FHD44_21285, FIJ20_21175, FJQ40_18325, FJQ53_22895, FKO60_25655, FOI11_019240, FOI11_03940, FPI65_20325, FPS11_25410, FTV90_00770, FTV93_20880, FV293_22445, FVB16_04890, FWK02_06290, FZN31_02615, FZU14_21840, G3565_26335, G3V95_19865, G3W53_20975, G4A38_21530, G4A47_20800, G9448_17055, GAI89_24810, GAJ12_24700, GAJ26_22030, GF699_19755, GFY34_22880, GIB53_19380, GJ11_21405, GJO56_22755, GKF66_21565, GKF89_18490, GNW61_16650, GNZ05_25965, GOP25_22725, GP711_23325, GP944_18810, GP954_00925, GP965_04315, GP975_01205, GP979_01985, GQA06_03930, GQM04_10585, GQM13_25220, GQM21_11250, GQN34_23285, GQW07_21530, GRC73_21730, GRO95_20795, GRW05_09080, GRW24_04735, GRW56_00315, GRW57_03520, GSM54_23310, GSY44_20020, GUC01_21200, GUI33_20065, H0O51_24755, H0O53_20810, H0O72_19435, H6Y26_003167, HCQ42_003945, HEP30_018655, HEP34_004767, HHH44_004532, HI055_004143, HIE29_005190, HJ942_004435, HJQ60_005008, HKA49_005032, HL563_21530, HLV18_23320, HLX92_10055, HLZ50_22160, HMV95_19625, HV109_02170, HV209_14695, HVV39_09285, HVW43_18650, HVX31_01950, HVY77_02155, HVZ30_02035, HVZ71_02340, HX136_02175, I6H00_20905, I6H02_12010, IA00_004091, IFB95_004809, IH772_23995, IT029_004950, J0541_004400, J4S20_004799, J5U05_004084, JE86ST02C_37730, JE86ST05C_37760, JFD_03716, JNP96_25325, NCTC10082_02836, NCTC10089_00499, NCTC10090_03524, NCTC10418_00687, NCTC10764_03860, NCTC10767_01513, NCTC11112_01039, NCTC11126_02768, NCTC11181_02735, NCTC11341_01892, NCTC12950_00476, NCTC13127_00783, NCTC13148_03444, NCTC13216_01355, NCTC4450_02472, NCTC7927_00548, NCTC7928_02519, NCTC8009_01508, NCTC8333_00486, NCTC8450_04934, NCTC8621_00505, NCTC8959_03264, NCTC8960_03067, NCTC8985_04979, NCTC9001_04251, NCTC9044_01360, NCTC9077_00601, NCTC9081_00914, NCTC9111_00864, NCTC9117_00753, NCTC9702_00534, NCTC9706_02734, NCTC9775_04000, NCTC9777_01888, ND22_005153, RG28_21630, SAMEA3472044_01159, SAMEA3472056_05414, SAMEA3472147_04289, SAMEA3751407_00027, SAMEA3752557_01955, SAMEA3753106_04631, TUM18780_04330, WR15_19625
Production host: Escherichia coli (E. coli) / References: UniProt: C3SR17
#56: Protein/peptide 50S ribosomal protein L36


Mass: 4377.390 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpmJ / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0E2L017
#57: Protein 50S ribosomal protein L9


Mass: 15789.020 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rplI, HMPREF1611_02665 / Production host: Escherichia coli (E. coli) / References: UniProt: V0YZK9
#58: Protein 50S ribosomal protein L13


Mass: 16050.606 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rplM, A1UI_03510 / Production host: Escherichia coli (E. coli) / References: UniProt: S1EW51
#59: Protein 50S ribosomal protein L14


Mass: 13565.067 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rplN, A13A_03633 / Production host: Escherichia coli (E. coli) / References: UniProt: S1NW45
#60: Protein 50S ribosomal protein L15


Mass: 15008.471 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rplO / Production host: Escherichia coli (E. coli) / References: UniProt: A0A037Y8L6
#61: Protein 50S ribosomal protein L16 / Large ribosomal subunit protein uL16


Mass: 15312.269 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rplP, b3313, JW3275 / Production host: Escherichia coli (E. coli) / References: UniProt: P0ADY7
#62: Protein 50S ribosomal protein L17


Mass: 14393.657 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rplQ, EAXG_02993 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1X3LC97
#63: Protein 50S ribosomal protein L18


Mass: 12794.668 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rplR, ETEC_3556 / Production host: Escherichia coli (E. coli) / References: UniProt: E3PKY8
#64: Protein 50S ribosomal protein L19


Mass: 13159.278 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rplS, HMPREF1620_00384 / Production host: Escherichia coli (E. coli) / References: UniProt: V0AJX1
#65: Protein 50S ribosomal protein L20


Mass: 13528.024 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rplT / Production host: Escherichia coli (E. coli) / References: UniProt: B7MAS6

-
DNA chain , 2 types, 2 molecules 56

#6: DNA chain NT DNA ops


Mass: 11786.552 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others)
#7: DNA chain T DNA ops


Mass: 11534.374 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others)

-
RNA chain , 5 types, 6 molecules 7ABDad

#8: RNA chain mRNA with 30 nt long spacer


Mass: 14749.310 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others)
#10: RNA chain E-site and P-site fMet-tRNA


Mass: 24496.617 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: GenBank: 1870104878
#17: RNA chain 16S rRNA


Mass: 499690.031 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: GenBank: 1732209707
#40: RNA chain 23S rRNA


Mass: 941635.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: GenBank: 937521852
#43: RNA chain 5S rRNA


Mass: 38790.090 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: GenBank: 1273279017

-
DNA-directed RNA polymerase subunit ... , 4 types, 5 molecules AAACADAEAF

#11: Protein DNA-directed RNA polymerase subunit beta / RNAP subunit beta / RNA polymerase subunit beta / Transcriptase subunit beta


Mass: 150820.875 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: rpoB, groN, nitB, rif, ron, stl, stv, tabD, b3987, JW3950
Production host: Escherichia coli (E. coli) / References: UniProt: P0A8V2, DNA-directed RNA polymerase
#13: Protein DNA-directed RNA polymerase subunit alpha / RNAP subunit alpha / RNA polymerase subunit alpha / Transcriptase subunit alpha


Mass: 36558.680 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpoA, pez, phs, sez, b3295, JW3257 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7Z4, DNA-directed RNA polymerase
#14: Protein DNA-directed RNA polymerase subunit beta' / RNAP subunit beta' / RNA polymerase subunit beta' / Transcriptase subunit beta'


Mass: 155366.781 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpoC, tabB, b3988, JW3951 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A8T7, DNA-directed RNA polymerase
#15: Protein DNA-directed RNA polymerase subunit omega / RNAP omega subunit / RNA polymerase omega subunit / Transcriptase subunit omega


Mass: 10249.547 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpoZ, b3649, JW3624 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A800, DNA-directed RNA polymerase

+
30S ribosomal protein ... , 21 types, 21 molecules CEFGHIJKLMNOPQRSTUVWX

#16: Protein 30S ribosomal protein S18


Mass: 9005.472 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsR / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0E2KXL3
#18: Protein 30S ribosomal protein S20


Mass: 9708.464 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsT / Production host: Escherichia coli (E. coli) / References: UniProt: C3TRH7
#19: Protein 30S ribosomal protein S21


Mass: 8524.039 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsU / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0E2L2J1
#20: Protein 30S ribosomal protein S2


Mass: 26781.670 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsB / Production host: Escherichia coli (E. coli) / References: UniProt: C3TPN2
#21: Protein 30S ribosomal protein S1


Mass: 61238.887 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: EAXG_00304 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1X3LHG1
#22: Protein 30S ribosomal protein S3


Mass: 26031.316 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsC / Production host: Escherichia coli (E. coli) / References: UniProt: B7MCS9
#23: Protein 30S ribosomal protein S4


Mass: 23514.199 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsD, ramA, b3296, JW3258 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7V8
#24: Protein 30S ribosomal protein S5


Mass: 17629.398 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsE, spc, b3303, JW3265 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7W1
#25: Protein 30S ribosomal protein S6 / Small ribosomal subunit protein bS6


Mass: 15727.512 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsF, b4200, JW4158 / Production host: Escherichia coli (E. coli) / References: UniProt: P02358
#26: Protein 30S ribosomal protein S7 / Small ribosomal subunit protein uS7


Mass: 20055.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsG, b3341, JW3303 / Production host: Escherichia coli (E. coli) / References: UniProt: P02359
#27: Protein 30S ribosomal protein S8


Mass: 14146.557 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsH, HMPREF9536_01683 / Production host: Escherichia coli (E. coli) / References: UniProt: D7XKZ3
#28: Protein 30S ribosomal protein S9


Mass: 14886.270 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1X3LT86
#29: Protein 30S ribosomal protein S10


Mass: 11755.597 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsJ, HMPREF1620_00582 / Production host: Escherichia coli (E. coli) / References: UniProt: V0ANK5
#30: Protein 30S ribosomal protein S11


Mass: 13870.975 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsK / Production host: Escherichia coli (E. coli) / References: UniProt: B7MCR3
#31: Protein 30S ribosomal protein S12


Mass: 13768.157 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsL, strA, b3342, JW3304 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7S3
#32: Protein 30S ribosomal protein S14


Mass: 11606.560 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsN, HMPREF1591_00914 / Production host: Escherichia coli (E. coli) / References: UniProt: U9Y6H3
#33: Protein 30S ribosomal protein S15


Mass: 10290.816 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsO, HMPREF9346_03742 / Production host: Escherichia coli (E. coli) / References: UniProt: D8EB41
#34: Protein 30S ribosomal protein S16


Mass: 9207.572 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsP / Production host: Escherichia coli (E. coli) / References: UniProt: C3SYP2
#35: Protein 30S ribosomal protein S17


Mass: 9724.491 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsQ / Production host: Escherichia coli (E. coli) / References: UniProt: A0A8E0MHL6
#36: Protein 30S ribosomal protein S19


Mass: 10455.355 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsS, A1UI_03589 / Production host: Escherichia coli (E. coli) / References: UniProt: S1EA57
#37: Protein 30S ribosomal protein S13


Mass: 13128.467 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpsM, G711_03878 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7U9IV78

-
Non-polymers , 2 types, 3 molecules

#66: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#67: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Escherichia coli transcription-translation coupled complex class B (TTC-B) containing RfaH bound to ops signal, mRNA with a 30 nt long spacer, and fMet-tRNAs in E-site and P-site of the ribosome
Type: COMPLEX / Entity ID: #1-#65 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1250 nm
Image recordingElectron dose: 28 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

-
Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 6.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 2632 / Symmetry type: POINT

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