6XDR

Escherichia coli transcription-translation complex B (TTC-B) containing an 27 nt long mRNA spacer, NusG, and fMet-tRNAs at E-site and P-site


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis of transcription-translation coupling.

Wang, C.Molodtsov, V.Firlar, E.Kaelber, J.T.Blaha, G.Su, M.Ebright, R.H.

(2020) Science 369: 1359-1365

  • DOI: 10.1126/science.abb5317
  • Primary Citation of Related Structures:  
    6X7F, 6X7K, 6X6T, 6X9Q, 6XDR, 6XDQ, 6XGF, 6XIJ, 6XII, 6VU3

  • PubMed 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 ribosome-translating mRNA. Coupling is modulated by the transc ...

    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 ribosome-translating mRNA. Coupling is modulated by the transcription factors NusG (which is thought to bridge RNAP and the ribosome) and NusA. Here, we report cryo-electron microscopy structures of Escherichia coli transcription-translation complexes (TTCs) containing different-length mRNA spacers between RNAP and the ribosome active-center P site. Structures of TTCs containing short spacers show a state incompatible with NusG bridging and NusA binding (TTC-A, previously termed "expressome"). Structures of TTCs containing longer spacers reveal a new state compatible with NusG bridging and NusA binding (TTC-B) and reveal how NusG bridges and NusA binds. We propose that TTC-B mediates NusG- and NusA-dependent transcription-translation coupling.


    Organizational Affiliation

    Waksman Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA. minsu@umich.edu ebright@waksman.rutgers.edu.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L21 0103Escherichia coliMutation(s): 0 
Gene Names: rplU
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Entity ID: 2
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50S ribosomal protein L22 1110Escherichia coliMutation(s): 0 
Gene Names: rplV
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Entity ID: 3
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50S ribosomal protein L23 2100Escherichia coliMutation(s): 0 
Gene Names: rplW
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Entity ID: 4
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50S ribosomal protein L24 3104Escherichia coliMutation(s): 0 
Gene Names: rplX
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L25 494Escherichia coliMutation(s): 0 
Gene Names: rplY
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L10 9165Escherichia coliMutation(s): 0 
Gene Names: rplJ
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta AA1342Escherichia coliMutation(s): 0 
Gene Names: rpoBZ5560ECs4910
EC: 2.7.7.6
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription termination/antitermination protein NusG AB181Escherichia coliMutation(s): 0 
Gene Names: nusGV415_18420
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Entity ID: 13
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DNA-directed RNA polymerase subunit alpha ACAD329Escherichia coliMutation(s): 0 
Gene Names: rpoA
EC: 2.7.7.6
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Entity ID: 14
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DNA-directed RNA polymerase subunit beta' AE1407Escherichia coliMutation(s): 1 
Gene Names: rpoCBvCmsKKP036_03580G5696_22040
EC: 2.7.7.6
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Entity ID: 15
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DNA-directed RNA polymerase subunit omega AF91Escherichia coliMutation(s): 0 
Gene Names: rpoZZ5075ECs4524
EC: 2.7.7.6
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Entity ID: 16
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30S ribosomal protein S18 C75Escherichia coliMutation(s): 0 
Gene Names: rpsR
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Entity ID: 18
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30S ribosomal protein S20 E87Escherichia coliMutation(s): 0 
Gene Names: rpsT
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Entity ID: 19
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30S ribosomal protein S21 F71Escherichia coliMutation(s): 0 
Gene Names: rpsU
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Entity ID: 20
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30S ribosomal protein S2 G241Escherichia coliMutation(s): 0 
Gene Names: rpsB
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Entity ID: 21
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30S ribosomal protein S1 H557Escherichia coliMutation(s): 0 
Gene Names: ECCG_01333
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Entity ID: 22
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30S ribosomal protein S3 I233Escherichia coliMutation(s): 0 
Gene Names: rpsC
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Entity ID: 23
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30S ribosomal protein S4 J206Escherichia coliMutation(s): 0 
Gene Names: rpsD
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Entity ID: 24
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30S ribosomal protein S5 K167Escherichia coliMutation(s): 0 
Gene Names: rpsE
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Entity ID: 25
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30S ribosomal protein S6 L135Escherichia coliMutation(s): 0 
Gene Names: rpsFb4200JW4158
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Entity ID: 26
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30S ribosomal protein S7 M179Escherichia coliMutation(s): 0 
Gene Names: rpsGGHR40_06850NCTC12650_00665
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Entity ID: 27
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30S ribosomal protein S8 N130Escherichia coliMutation(s): 0 
Gene Names: rpsH
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Entity ID: 28
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30S ribosomal protein S9 O130Escherichia coliMutation(s): 0 
Gene Names: rpsI
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Entity ID: 29
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30S ribosomal protein S10 P103Escherichia coliMutation(s): 0 
Gene Names: rpsJ
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Entity ID: 30
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30S ribosomal protein S11 Q129Escherichia coliMutation(s): 0 
Gene Names: rpsK
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Entity ID: 31
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30S ribosomal protein S12 R124Escherichia coliMutation(s): 0 
Gene Names: rpsL
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Entity ID: 32
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30S ribosomal protein S14 S101Escherichia coliMutation(s): 0 
Gene Names: rpsN
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Entity ID: 33
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30S ribosomal protein S15 T89Escherichia coliMutation(s): 0 
Gene Names: rpsO
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Entity ID: 34
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30S ribosomal protein S16 U82Escherichia coliMutation(s): 0 
Gene Names: rpsP
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Entity ID: 35
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30S ribosomal protein S17 V84Escherichia coliMutation(s): 0 
Gene Names: rpsQ
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Entity ID: 36
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30S ribosomal protein S19 W92Escherichia coliMutation(s): 0 
Gene Names: rpsS
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Entity ID: 37
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30S ribosomal protein S13 X118Escherichia coliMutation(s): 0 
Gene Names: rpsM
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Entity ID: 38
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50S ribosomal protein L11 Y142Escherichia coliMutation(s): 0 
Gene Names: rplK
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Entity ID: 39
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50S ribosomal protein L7/L12 Z121Escherichia coliMutation(s): 0 
Gene Names: rplLECDEC2C_4837
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Entity ID: 41
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50S ribosomal protein L27 b85Escherichia coliMutation(s): 0 
Gene Names: rpmAb3185JW3152
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Entity ID: 42
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50S ribosomal protein L28 c78Escherichia coliMutation(s): 0 
Gene Names: rpmB
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Entity ID: 44
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50S ribosomal protein L29 e63Escherichia coliMutation(s): 0 
Gene Names: rpmC
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Entity ID: 45
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50S ribosomal protein L30 f59Escherichia coliMutation(s): 0 
Gene Names: rpmD
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Entity ID: 46
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50S ribosomal protein L31 g70Escherichia coliMutation(s): 0 
Gene Names: rpmE
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Entity ID: 47
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50S ribosomal protein L2 h273Escherichia coliMutation(s): 0 
Gene Names: rplBb3317JW3279
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Entity ID: 48
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50S ribosomal protein L32 i57Escherichia coliMutation(s): 0 
Gene Names: rpmF
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Entity ID: 49
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50S ribosomal protein L3 j209Escherichia coliMutation(s): 0 
Gene Names: rplCb3320JW3282
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Entity ID: 50
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50S ribosomal protein L33 k55Escherichia coliMutation(s): 0 
Gene Names: rpmG
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Entity ID: 51
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50S ribosomal protein L4 l201Escherichia coliMutation(s): 0 
Gene Names: rplD
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Entity ID: 52
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50S ribosomal protein L34 m46Escherichia coliMutation(s): 0 
Gene Names: rpmH
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Entity ID: 53
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50S ribosomal protein L5 n179Escherichia coliMutation(s): 0 
Gene Names: rplE
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Entity ID: 54
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50S ribosomal protein L35 o65Escherichia coliMutation(s): 0 
Gene Names: rpmI
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Entity ID: 55
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50S ribosomal protein L6 p177Escherichia coliMutation(s): 0 
Gene Names: rplF
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Entity ID: 56
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50S ribosomal protein L36 q38Escherichia coliMutation(s): 0 
Gene Names: rpmJ
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Entity ID: 57
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50S ribosomal protein L9 r149Escherichia coliMutation(s): 0 
Gene Names: rplI
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Entity ID: 58
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50S ribosomal protein L13 s142Escherichia coliMutation(s): 0 
Gene Names: rplM
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Entity ID: 59
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50S ribosomal protein L14 t123Escherichia coliMutation(s): 0 
Gene Names: rplN
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Entity ID: 60
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50S ribosomal protein L15 u144Escherichia coliMutation(s): 0 
Gene Names: 
rplOA8C65_19395A9R57_24660ACU57_21045AM464_09135AUQ13_22145BANRA_01932BANRA_03684BHS87_18545BJJ90_02210BMA87_18510BON75_18850BON98_13310BUE81_25610BvCms2454_01416BvCmsHHP001_00334BvCmsHHP019_04131BvCmsHHP056_02703BvCmsKSP026_02554BvCmsSINP011_02480BW690_10710BZL31_22885C5F72_02595C5F73_02860C5N07_23575C9E25_20065C9Z39_20710CA593_09735CG692_20270CI693_13520CI694_01990CIG45_22410D0X26_24495D2185_22985D3821_17755D3O91_20305D3Y67_24390D4638_19455D4718_17880D9C99_17930D9D20_21995D9D44_22490D9G29_15635D9G69_20945D9H68_17710D9J52_19090D9Z28_15390DAH37_14685DBQ99_03415DJ503_19770DL326_22310DNC98_19095DT034_22410DTL43_21000E2119_19640E2134_21880E2135_06185E4A44_21305E4K51_21490E4K55_21420E4K60_18985E4K61_20025E5P22_10480E5P28_20875EA213_19860EAI42_04990EAI52_16365EC1094V2_354EC3234A_55c00230EC3426_04459ECTO6_00449ED307_17010EEP23_17135EG808_17075EI021_21030EI028_20740EI032_18995EI041_20035EIZ93_12470EL75_0396EL79_0415EL80_0407ELT20_19170EPT01_19765ERS085365_03907ERS085416_03881ERS139211_03685ERS150873_04051EXX71_21335EYD11_02080F1E19_19655F9040_18095FRV13_20015FV293_22465FWK02_06270G5632_17770G5688_20025GHR40_07050GKF39_20550GKF74_18130GKF86_20070GKF89_18470GP671_20580GP689_20785GP954_00945GP979_02005GQE33_22230GQE34_14255GQE64_20420GQM17_19915GRW05_09060GRW27_21285GRW42_19350GRW57_03540GRW80_20585GRW81_21150NCTC10963_00456NCTC11022_03475NCTC11126_02772NCTC12650_00710NCTC13216_01351NCTC9045_00567NCTC9062_02686NCTC9117_00757NCTC9706_02738PGD_00585RK56_021420SAMEA3472047_03862SAMEA3472080_04748SAMEA3484427_04887SAMEA3484429_04875SAMEA3752559_00346SAMEA3753300_02227

Find proteins for A0A037Y8L6 (Escherichia coli)
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Entity ID: 61
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L16 v136Escherichia coliMutation(s): 0 
Gene Names: rplPb3313JW3275
Find proteins for P0ADY7 (Escherichia coli (strain K12))
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Entity ID: 62
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L17 w127Escherichia coliMutation(s): 0 
Gene Names: rplQECCG_03701
Find proteins for D6I1Y5 (Escherichia coli B088)
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Entity ID: 63
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L18 x117Escherichia coliMutation(s): 0 
Gene Names: rplR
Find proteins for D7Z9H1 (Escherichia coli MS 69-1)
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Entity ID: 64
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L19 y115Escherichia coliMutation(s): 0 
Gene Names: rplS
Find proteins for D7ZKU3 (Escherichia coli MS 69-1)
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Entity ID: 65
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L20 z118Escherichia coliMutation(s): 0 
Gene Names: rplT
Find proteins for B7MAS6 (Escherichia coli O45:K1 (strain S88 / ExPEC))
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Entity ID: 6
MoleculeChainsLengthOrganismImage
NT DNA536synthetic construct
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Entity ID: 7
MoleculeChainsLengthOrganismImage
T DNA636synthetic construct
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Entity ID: 8
MoleculeChainsLengthOrganismImage
mRNA with 27 nt long spacer744synthetic construct
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Entity ID: 10
MoleculeChainsLengthOrganismImage
E-site and P-site tRNA (fMet)A, B76Escherichia coli
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Entity ID: 17
MoleculeChainsLengthOrganismImage
16S rRNAD1542Escherichia coli
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Entity ID: 40
MoleculeChainsLengthOrganismImage
23S rRNAa2904Escherichia coli
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Entity ID: 43
MoleculeChainsLengthOrganismImage
5S rRNAd120Escherichia coli
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
AE
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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AE
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States--

Revision History 

  • Version 1.0: 2020-09-02
    Type: Initial release
  • Version 1.1: 2020-09-16
    Changes: Database references
  • Version 1.2: 2020-09-23
    Changes: Database references