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PDB ID Mentions in PubMed Central Article count: 3

Citations in PubMed

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PDB ID Mentions in PubMed Central

Data mentions are occurrences of PDB IDs in the full text articles from the PubMedCentral Open Access Subset of currently about 1 million articles. For each article, the sentences containing the PDB ID are listed. Article titles can be filtered by keywords and sorted by year.

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Transcription inhibition by the depsipeptide antibiotic salinamide A.

(2014) Elife 3

PubMed: 24843001 | PubMedCentral: PMC4029172 | DOI: 10.7554/eLife.02451

Weixlbaumer A , Leon K , Landick R , Darst SA , 2013 , Crystal structures of bacterial RNA Polymerase paused elongation complexes , http://www.pdb.org/pdb/explore/explore.do?structureId=4gzy , Publicl... available at RCSB Protein Data Bank.

( B ) Superimposition of bridge helices of E. coli RNAP-Sal (black), E. coli RNAP (green; unbent BH-H N and BH-H C ), T. thermophilus RNAP (cyan; PDB 1IW7), T. thermophilus RPo (yellow; PDB 4G7H), T. thermophilus transcription elongation complex (pink; PDB 2O5J), and paused T. thermophilus transcription elongation complex (violet; PDB 4GZY).

Publication Year: 2014


RNA polymerase pausing and nascent-RNA structure formation are linked through clamp-domain movement.

(2014) Nat Struct Mol Biol 21

PubMed: 25108353 | PubMedCentral: PMC4156911 | DOI: 10.1038/nsmb.2867

For this purpose, we designed double cysteine variant RNAPs that were predicted to form disulfide bonds between the lid and flap domains in either the closed-clamp conformation (β′258i... -β1044C; based on Tth RNAP EC, pdb 2o5i) 35 or the open-clamp conformation (β′258iC-β843C; based on Tth RNAP ePEC, pdb 4gzy) 16 ( Figs. 3a,b ).

The open-clamp conformation was modeled from pdb 4gzy 16 .

Right, model of open-clamp, duplex-stabilized PEC containing E. coli RNAP (based on PDB 4gzy 16 ) with arrows indicating clamp and flap movement upon duplex formation.

Publication Year: 2014


PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4496699

Structure PDB code Reference Source Subunit and domain α subunit NTD 1BDF X [ 7 ] A α subunit NTD 4NOI X none F α subunit CTD 1COO N , 3K4G X [ 5 , 8 ] A α subunit CTD ... DOQ N [ 9 ] B α subunit CTD 2MAX N [ 10 ] E β subunit 2/i4 domains 3LTI X [ 11 ] A β subunit flap domain 2LY7 N none C β subunit 1/2 domains 4KBJ X [ 12 ] I β' subunit i2 domain 2AUJ X [ 13 ] B β' subunit i6 domain 2AUK X , 4IQZ X [ 13 ] A σ region 1.1 2K6X N [ 14 ] G, a σ 70 domain2 1SIG X [ 15 ] A, a σ A domains2 and 3 1KU2 X [ 16 ] B, a σ A domain4 1KU3 X [ 16 ] B, a σ A domain4–DNA (−35 element) 1KU7 X [ 16 ] B, a σ A domain4 1TTY N [ 17 ] G, a σ A domain2–DNA (−10 element) 3UGO X , 3UGP X [ 18 ] B, a σ A domain4–αCTD–DNA 3N97 X none B, a, A σ N RpoN–DNA (−24 element) 2O8K N , 2O9L N [ 19 ] D, d σ N core binding domain 2K9M N [ 20 ] D, d σ N RpoN domain 2AHQ N [ 21 ] D, d σ E domain4–DNA (−35 element) 2H27 X [ 22 ] A, c σ C domain2 2O7G X [ 23 ] I, c σ C domain4 2O8X X [ 23 ] I, c σ D domain4 3VFZ X [ 24 ] I, c δ subunit NTD 2KRC N , 4NC7 X , 4NC8 X , 2M4K N , 2KRC N [ 25 , 26 , 27 ] C ε subunit 4NJC X [ 28 ] C RNAP Core enzyme 1HQM X [ 29 , 30 ] B Core enzyme (Δω subunit) 2GHO X [ 31 ] B Holoenzyme 1L9U X , 1IW7 X , 2A6E X , 2CW0 X [ 32 , 33 , 34 ] B Holoenzyme 4YG2 X , 4LJZ X , 4MEY X [ 35 , 36 , 37 ] A Holoenzyme–DNA (−41 ~ −7) 1L9Z X [ 38 ] B Holoenzyme–DNA (−12 ~ +12) 4G7H X , 4G7O X [ 39 ] B de novo initiation complex 4Q4Z X , 4OIO X [ 40 , 41 ] B Initially transcribing complex 4Q5S X [ 40 ] B Elongation complex 2O5I X , 2O5J X [ 42 , 43 ] B Paused elongation complex 4GZY X , 4GZZ X [ 44 ] B Backtracked elongation complex 4WQS X [ 45 ] B A: Escherichia coli ; B: Thermus aquatics/Thermus thermophilus ; C: Bacillus subtilis/Bacilus stearothermophilus ; D: Aquifex aeolicus ; E: Helicobacter pylori ; F: Campylobacter jejuni ; G: Thermotoga maritime ; I: Mycobacterium tuberculosis ; a: group I σ factor; c: extracytoplasmic function (ECF) σ factor; d: σ N /σ 54 factor; X : X-ray crystallography method; N : NMR method.

The structure of an elemental-paused elongation complex using Thermus RNAP and DNA/RNA scaffolds derived from the E. coli his-pause sequence showed a unique RNAP conformation including an open-clamp and kinked bridge helix that may inhibit processive RNA extension (PDB: 4GZY, 4GZZ) [ 44 ].

Publication Year: 2015