PDB-6x9q: Cryo-EM structure of an Escherichia coli coupled transcription-tr...

ID or keywords:

Entry

Database: PDB / ID: 6x9q

Title

Cryo-EM structure of an Escherichia coli coupled transcription-translation complex B3 (TTC-B3) containing an mRNA with a 27 nt long spacer, transcription factors NusA and NusG, and fMet-tRNAs at P-site and E-site

Components

(30S ribosomal protein ...) x 21
(50S ribosomal protein ...) x 32
(DNA-directed RNA polymerase subunit ...) x 4
(Transcription termination/antitermination protein ...) x 2
16S rRNA
23S rRNA
5S rRNA
E-site and P-site tRNA (fMet)
NT DNA
T DNA
mRNA with 27 nt long spacer

Keywords

RIBOSOME / TRANSCRIPTION/TRANSLATION / coupled transcription-translation complex / TRANSCRIPTION / TRANSCRIPTION-TRANSLATION complex

Function / homology

Function and homology information

DNA-templated transcription elongation / positive regulation of ribosome biogenesis / DnaA-L2 complex / DNA-directed RNA polymerase complex / negative regulation of DNA-templated DNA replication initiation / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / regulation of DNA-templated transcription elongation / transcription antitermination / regulation of cell growth ...
Similarity search - Function

Transcription termination factor NusA, C-terminal duplication / Transcription termination factor NusA / Transcription factor NusA, N-terminal / KH domain, NusA-like / NusA, N-terminal domain superfamily / NusA N-terminal domain / NusA-like KH domain / Transcription termination/antitermination protein NusA, bacterial / Ribosomal protein S1 / Ribosomal protein S1-like ...Transcription termination factor NusA, C-terminal duplication / Transcription termination factor NusA / Transcription factor NusA, N-terminal / KH domain, NusA-like / NusA, N-terminal domain superfamily / NusA N-terminal domain / NusA-like KH domain / Transcription termination/antitermination protein NusA, bacterial / Ribosomal protein S1 / Ribosomal protein S1-like / Transcription antitermination protein, NusG / Transcription antitermination protein, NusG, bacteria, conserved site / Transcription termination factor nusG signature. / RNA-binding domain, S1 / Ribosomal protein L7/L12, oligomerisation / Ribosomal protein L7/L12, oligomerisation domain superfamily / Ribosomal protein L7/L12 dimerisation domain / Ribosomal protein L7/L12 / Ribosomal protein L7/L12, C-terminal / Ribosomal protein L7/L12 C-terminal domain / NusG-like / Transcription termination factor nusG / 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. / DNA repair Rad51/transcription factor NusA, alpha-helical / Type-1 KH domain profile. / NusG, N-terminal domain superfamily / Helix-hairpin-helix domain / 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 / DNA-directed RNA polymerase, alpha subunit / DNA-directed RNA polymerase beta subunit, bacterial-type / Ribosomal protein L25, short-form / Ribosomal protein S14, bacterial/plastid / Ribosomal protein L11, bacterial-type / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / Ribosomal protein L31 type A / Ribosomal protein S21 superfamily / Ribosomal protein S21 / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / S1 domain / Ribosomal protein S21 / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L11, conserved site / Ribosomal protein L11 signature. / Ribosomal protein L10-like domain superfamily / Ribosomal protein L16 signature 1. / Ribosomal protein L10P / Ribosomal protein L10 / : / 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 L9, C-terminal domain superfamily / Ribosomal protein L17 signature. / 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 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
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 / DNA-directed RNA polymerase subunit alpha / Small ribosomal subunit protein bS18 / Large ribosomal subunit protein bL36 / Small ribosomal subunit protein bS21 / Large ribosomal subunit protein bL17 / 30S ribosomal protein S1 / DNA-directed RNA polymerase subunit beta' / 30S ribosomal protein S7 / Large ribosomal subunit protein bL20 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS3 / Large ribosomal subunit protein bL34 / Small ribosomal subunit protein bS16 / 50S ribosomal protein L23 / Large ribosomal subunit protein bL25 / 50S ribosomal protein L35 / 30S ribosomal protein S10 / 50S ribosomal protein L4 / 30S ribosomal protein S19 / 50S ribosomal protein L22 / 50S ribosomal protein L29 / 30S ribosomal protein S17 / 50S ribosomal protein L14 / 50S ribosomal protein L24 / 50S ribosomal protein L5 / 30S ribosomal protein S14 / 30S ribosomal protein S8 / 50S ribosomal protein L6 / 50S ribosomal protein L18 / 30S ribosomal protein S5 / 50S ribosomal protein L30 / 30S ribosomal protein S4 / 50S ribosomal protein L33 / 50S ribosomal protein L11 / 50S ribosomal protein L10 / 30S ribosomal protein S12 / 30S ribosomal protein S20 / 30S ribosomal protein S15 / 50S ribosomal protein L21 / 30S ribosomal protein S9 / 50S ribosomal protein L13 / 50S ribosomal protein L31 / 50S ribosomal protein L32 / 50S ribosomal protein L9 / 30S ribosomal protein S2 / 50S ribosomal protein L19 / 50S ribosomal protein L7/L12 / 30S ribosomal protein S13 / Small ribosomal subunit protein bS6 / Large ribosomal subunit protein bL27 / DNA-directed RNA polymerase subunit omega / DNA-directed RNA polymerase subunit beta / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL3 / 50S ribosomal protein L28 / Transcription termination/antitermination protein NusA / Transcription termination/antitermination protein NusG
Similarity search - Component

Biological species

Escherichia coli (E. coli)
synthetic construct (others)

Method

ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.8 Å

Authors

Molodtsov, V. / Ebright, R.H. / Wang, C. / Su, M.

Funding support

United States, 1items

Citation

Journal: Science / Year: 2020
Title: Structural basis of transcription-translation coupling.
Authors: Chengyuan Wang / Vadim Molodtsov / Emre Firlar / Jason T Kaelber / Gregor Blaha / Min Su / Richard H Ebright /

Abstract: In bacteria, transcription and translation are coupled processes in which the movement of RNA polymerase (RNAP)-synthesizing messenger RNA (mRNA) is coordinated with the movement of the first ...

History

Deposition	Jun 3, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 2, 2020	Provider: repository / Type: Initial release
Revision 1.1	Sep 16, 2020	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Sep 23, 2020	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3	Oct 16, 2024	Group: Data collection / Database references / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_admin / pdbx_entry_details / pdbx_modification_feature Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Related structure data

Related structure data	22107MC 21386C 21468C 21469C 21470C 21471C 21472C 21474C 21475C 21476C 21477C 21482C 21483C 21485C 21486C 21494C 22082C 22084C 22087C 22141C 22142C 22181C 22192C 22193C 6vu3C 6vyqC 6vyrC 6vysC 6vytC 6vyuC 6vywC 6vyxC 6vyyC 6vyzC 6vz2C 6vz3C 6vz5C 6vz7C 6vzjC 6x6tC 6x7fC 6x7kC 6xdqC 6xdrC 6xgfC 6xiiC 6xijC M: map data used to model this data C: citing same article (ref.)
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Links

PDB pages	PDBj / wwPDB / NCBI
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PDB pages

PDBj /

wwPDB /

NCBI

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Deposited unit

0: 50S 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

6: T DNA

7: mRNA with 27 nt long spacer

9: 50S ribosomal protein L10

A: E-site and P-site tRNA (fMet)

AA: DNA-directed RNA polymerase subunit beta

AB: Transcription termination/antitermination protein NusG

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

AG: Transcription termination/antitermination protein NusA

B: E-site and P-site tRNA (fMet)

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

2.8 MDa, 68 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author
Evidence: gel filtration

+
50S ribosomal protein ... , 32 types, 32 molecules 012349YZbcefghijklmnopqrstuvwxyz

#1: Protein	50S 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) / Strain: MRE600 / Gene: rplU / Production host: Escherichia coli (E. coli) / References: UniProt: D7ZEN7
#2: Protein	50S ribosomal protein L22 Mass: 12253.359 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: MRE600 / Gene: rplV / Production host: Escherichia coli (E. coli) / References: UniProt: D7Z9G0
#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) / Strain: MRE600 / Gene: rplW / Production host: Escherichia coli (E. coli) / References: UniProt: D7X2Z9
#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) / Strain: MRE600 / Gene: rplX / Production host: Escherichia coli (E. coli) / References: UniProt: D7Z9G6
#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) / Strain: MRE600 / Gene: rplY / Production host: Escherichia coli (E. coli) / References: UniProt: D7XH79
#9: Protein	50S ribosomal protein L10 Mass: 17736.596 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: MRE600 / Gene: rplJ / Production host: Escherichia coli (E. coli) / References: UniProt: D7ZA73
#39: Protein	50S ribosomal protein L11 Mass: 14894.362 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: MRE600 / Gene: rplK / Production host: Escherichia coli (E. coli) / References: UniProt: D7ZA71
#40: 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) / Strain: MRE600 / Gene: rplL, ECDEC2C_4837 / Production host: Escherichia coli (E. coli) / References: UniProt: H4KQ39
#42: 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) / Strain: MRE600 / Gene: rpmA, b3185, JW3152 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7L8
#43: 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) / Strain: MRE600 / Gene: rpmB / Production host: Escherichia coli (E. coli) / References: UniProt: S0YB49
#45: 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) / Strain: MRE600 / Gene: rpmC / Production host: Escherichia coli (E. coli) / References: UniProt: D7Z9G3
#46: 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) / Strain: MRE600 / Gene: rpmD / Production host: Escherichia coli (E. coli) / References: UniProt: D7Z9H3
#47: Protein	50S ribosomal protein L31 Mass: 7887.117 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: MRE600 / Gene: rpmE / Production host: Escherichia coli (E. coli) / References: UniProt: D7ZFP6
#48: 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) / Strain: MRE600 / Gene: rplB, b3317, JW3279 / Production host: Escherichia coli (E. coli) / References: UniProt: P60422
#49: 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) / Strain: MRE600 / Gene: rpmF / Production host: Escherichia coli (E. coli) / References: UniProt: D7ZGG2
#50: 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) / Strain: MRE600 / Gene: rplC, b3320, JW3282 / Production host: Escherichia coli (E. coli) / References: UniProt: P60438
#51: 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) / Strain: MRE600 / Gene: rpmG / Production host: Escherichia coli (E. coli) / References: UniProt: D7Z9P0
#52: 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) / Strain: MRE600 / Gene: rplD / Production host: Escherichia coli (E. coli) / References: UniProt: D7Z9F6
#53: 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) / Strain: MRE600 / Gene: rpmH / Production host: Escherichia coli (E. coli) / References: UniProt: B7MGC4
#54: 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) / Strain: MRE600 / Gene: rplE / Production host: Escherichia coli (E. coli) / References: UniProt: D7Z9G7
#55: Protein	50S ribosomal protein L35 Mass: 7313.032 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: MRE600 / Gene: rpmI / Production host: Escherichia coli (E. coli) / References: UniProt: D7Z814
#56: 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) / Strain: MRE600 / Gene: rplF / Production host: Escherichia coli (E. coli) / References: UniProt: D7Z9H0
#57: 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) / Strain: MRE600 / Gene: rpmJ / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0E2L017
#58: 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) / Strain: MRE600 / Gene: rplI / Production host: Escherichia coli (E. coli) / References: UniProt: D7ZI15
#59: 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) / Strain: MRE600 / Gene: rplM / Production host: Escherichia coli (E. coli) / References: UniProt: D7ZET0
#60: 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) / Strain: MRE600 / Gene: rplN / Production host: Escherichia coli (E. coli) / References: UniProt: D7Z9G5
#61: 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) / Strain: MRE600 / Gene: rplO / Production host: Escherichia coli (E. coli) / References: UniProt: A0A037Y8L6
#62: 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) / Strain: MRE600 / Gene: rplP, b3313, JW3275 / Production host: Escherichia coli (E. coli) / References: UniProt: P0ADY7
#63: 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) / Strain: MRE600 / Gene: rplQ, EAXG_02993 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1X3LC97
#64: 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) / Strain: MRE600 / Gene: rplR / Production host: Escherichia coli (E. coli) / References: UniProt: D7Z9H1
#65: 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) / Strain: MRE600 / Gene: rplS / Production host: Escherichia coli (E. coli) / References: UniProt: D7ZKU3
#66: 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) / Strain: MRE600 / Gene: rplT / Production host: Escherichia coli (E. coli) / References: UniProt: B7MAS6

-
DNA chain , 2 types, 2 molecules 56

#6: DNA chain	NT DNA Mass: 11042.110 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#7: DNA chain	T DNA Mass: 10956.012 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
RNA chain , 5 types, 6 molecules 7ABDad

#8: RNA chain	mRNA with 27 nt long spacer Mass: 13830.813 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#10: RNA chain	E-site and P-site tRNA (fMet) Mass: 24496.617 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: MRE600 / Production host: Escherichia coli (E. coli) / References: GenBank: 1384458579
#18: 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) / Strain: MRE600 / Production host: Escherichia coli (E. coli) / References: GenBank: 1732209707
#41: 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) / Strain: MRE600 / Production host: Escherichia coli (E. coli) / References: GenBank: 937521852
#44: 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) / Strain: MRE600 / 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) / Strain: MRE600 / Gene: rpoB, Z5560, ECs4910 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A8V4, 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) / Strain: MRE600 / Gene: rpoA / Production host: Escherichia coli (E. coli) References: UniProt: A0A073G207, 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) / Strain: MRE600 / Gene: rpoC, BvCmsKKP036_03580 / Production host: Escherichia coli (E. coli) References: UniProt: A0A4S1NBU2, 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) / Strain: MRE600 / Gene: rpoZ, Z5075, ECs4524 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A802, DNA-directed RNA polymerase

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Transcription termination/antitermination protein ... , 2 types, 2 molecules ABAG

#12: Protein	Transcription termination/antitermination protein NusG Mass: 20560.523 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: MRE600 / Gene: nusG, V415_18420 / Production host: Escherichia coli (E. coli) / References: UniProt: V8K3D7
#16: Protein	Transcription termination/antitermination protein NusA Mass: 54932.684 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: MRE600 / Gene: nusA / Production host: Escherichia coli (E. coli) / References: UniProt: U9XV73

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

#17: 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) / Strain: MRE600 / Gene: rpsR / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0E2KXL3
#19: 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) / Strain: MRE600 / Gene: rpsT / Production host: Escherichia coli (E. coli) / References: UniProt: D7ZAS2
#20: 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) / Strain: MRE600 / Gene: rpsU / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0E2L2J1
#21: 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) / Strain: MRE600 / Gene: rpsB / Production host: Escherichia coli (E. coli) / References: UniProt: D7ZK99
#22: 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) / Strain: MRE600 / Gene: EAXG_00304 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1X3LHG1
#23: 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) / Strain: MRE600 / Gene: rpsC / Production host: Escherichia coli (E. coli) / References: UniProt: B7MCS9
#24: 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) / Strain: MRE600 / Gene: rpsD / Production host: Escherichia coli (E. coli) / References: UniProt: D7Z9H7
#25: 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) / Strain: MRE600 / Gene: rpsE / Production host: Escherichia coli (E. coli) / References: UniProt: D7Z9H2
#26: 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) / Strain: MRE600 / Gene: rpsF, b4200, JW4158 / Production host: Escherichia coli (E. coli) / References: UniProt: P02358
#27: Protein	30S ribosomal protein S7 Mass: 20055.156 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: MRE600 / Gene: rpsG, GHR40_06850 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A5Q2GFB5
#28: 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) / Strain: MRE600 / Gene: rpsH / Production host: Escherichia coli (E. coli) / References: UniProt: D7Z9G9
#29: 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) / Strain: MRE600 / Gene: rpsI / Production host: Escherichia coli (E. coli) / References: UniProt: D7ZES9
#30: 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) / Strain: MRE600 / Gene: rpsJ / Production host: Escherichia coli (E. coli) / References: UniProt: D7Z9F4
#31: 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) / Strain: MRE600 / Gene: rpsK / Production host: Escherichia coli (E. coli) / References: UniProt: B7MCR3
#32: 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) / Strain: MRE600 / Gene: rpsL / Production host: Escherichia coli (E. coli) / References: UniProt: D7ZAN0
#33: 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) / Strain: MRE600 / Gene: rpsN / Production host: Escherichia coli (E. coli) / References: UniProt: D7Z9G8
#34: 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) / Strain: MRE600 / Gene: rpsO / Production host: Escherichia coli (E. coli) / References: UniProt: D7ZEL4
#35: 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) / Strain: MRE600 / Gene: rpsP / Production host: Escherichia coli (E. coli) / References: UniProt: B7MIU7
#36: 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) / Strain: MRE600 / Gene: rpsQ / Production host: Escherichia coli (E. coli) / References: UniProt: D7Z9G4
#37: 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) / Strain: MRE600 / Gene: rpsS / Production host: Escherichia coli (E. coli) / References: UniProt: D7Z9F9
#38: 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) / Strain: MRE600 / Gene: rpsM / Production host: Escherichia coli (E. coli) / References: UniProt: H4UQ02

-
Non-polymers , 2 types, 3 molecules

#67: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#68: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

-
Details

Has ligand of interest	N
Has protein modification	Y

-
Experiment

Experiment	Method: ELECTRON MICROSCOPY
EM experiment	Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component	Name: Cryo-EM structure of an Escherichia coli coupled transcription-translation complex B2 (TTC-B2) containing an mRNA with a 27 nt long spacer, transcription factors NusA and NusG, and fMet-tRNAs at P-site and E-site Type: COMPLEX / Entity ID: #1-#66 / Source: RECOMBINANT
Molecular weight	Experimental value: NO
Source (natural)	Organism: Escherichia coli (E. coli)
Source (recombinant)	Organism: Escherichia coli (E. coli)
Buffer solution	pH: 7.6
Specimen	Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Vitrification	Cryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment	Model: Titan Krios / Image courtesy: FEI Company
Microscopy	Model: FEI TITAN KRIOS
Electron gun	Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lens	Mode: BRIGHT FIELD
Image recording	Electron dose: 45 e/Å² / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correction	Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstruction	Resolution: 4.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 11509 / Symmetry type: POINT

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50S ribosomal protein ... , 32 types, 32 molecules 012349YZbcefghijklmnopqrstuvwxyz

-
DNA chain , 2 types, 2 molecules 56

-
RNA chain , 5 types, 6 molecules 7ABDad

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

-
Transcription termination/antitermination protein ... , 2 types, 2 molecules ABAG

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

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Non-polymers , 2 types, 3 molecules

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Details

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Experimental details

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Experiment

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Sample preparation

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Electron microscopy imaging

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Processing

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About Yorodumi

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+50S ribosomal protein ... , 32 types, 32 molecules 012349YZbcefghijklmnopqrstuvwxyz

-DNA chain , 2 types, 2 molecules 56

-RNA chain , 5 types, 6 molecules 7ABDad

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

-Transcription termination/antitermination protein ... , 2 types, 2 molecules ABAG

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

-Non-polymers , 2 types, 3 molecules

-Details

-Experimental details

-Experiment

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-Electron microscopy imaging

-Processing

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50S ribosomal protein ... , 32 types, 32 molecules 012349YZbcefghijklmnopqrstuvwxyz

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DNA chain , 2 types, 2 molecules 56

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RNA chain , 5 types, 6 molecules 7ABDad

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

-
Transcription termination/antitermination protein ... , 2 types, 2 molecules ABAG

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

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Non-polymers , 2 types, 3 molecules

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Details

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Experimental details

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Experiment

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Sample preparation

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