8ABZ

RNA polymerase at U-rich pause bound to non-regulatory RNA - pause prone, closed clamp state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural insights into RNA-mediated transcription regulation in bacteria.

Dey, S.Batisse, C.Shukla, J.Webster, M.W.Takacs, M.Saint-Andre, C.Weixlbaumer, A.

(2022) Mol Cell 82: 3885

  • DOI: https://doi.org/10.1016/j.molcel.2022.09.020
  • Primary Citation of Related Structures:  
    8ABY, 8ABZ, 8AC0, 8AC1, 8AC2, 8ACP, 8AD1

  • PubMed Abstract: 

    RNA can regulate its own synthesis without auxiliary proteins. For example, U-rich RNA sequences signal RNA polymerase (RNAP) to pause transcription and are required for transcript release at intrinsic terminators in all kingdoms of life. In contrast, the regulatory RNA putL suppresses pausing and termination in cis. However, how nascent RNA modulates its own synthesis remains largely unknown. We present cryo-EM reconstructions of RNAP captured during transcription of putL variants or an unrelated sequence at a U-rich pause site. Our results suggest how putL suppresses pausing and promotes its synthesis. We demonstrate that transcribing a U-rich sequence, a ubiquitous trigger of intrinsic termination, promotes widening of the RNAP nucleic-acid-binding channel. Widening destabilizes RNAP interactions with DNA and RNA to facilitate transcript dissociation reminiscent of intrinsic transcription termination. Surprisingly, RNAP remains bound to DNA after transcript release. Our results provide the structural framework to understand RNA-mediated intrinsic transcription termination.


  • Organizational Affiliation

    Department of Integrated Structural Biology, IGBMC, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67400 Illkirch, France; Université de Strasbourg, IGBMC UMR 7104-UMR-S 1258, 67400 Illkirch, France; CNRS, UMR 7104, 67400 Illkirch, France; Inserm, UMR-S 1258, 67400 Illkirch, France.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit alpha
A, B
329Escherichia coli K-12Mutation(s): 0 
Gene Names: rpoApezphssezb3295JW3257
EC: 2.7.7.6
UniProt
Find proteins for P0A7Z4 (Escherichia coli (strain K12))
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Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7Z4
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta1,342Escherichia coli K-12Mutation(s): 0 
Gene Names: rpoBgroNnitBrifronstlstvtabDb3987JW3950
EC: 2.7.7.6
UniProt
Find proteins for P0A8V2 (Escherichia coli (strain K12))
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UniProt GroupP0A8V2
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta'1,406Escherichia coli K-12Mutation(s): 0 
Gene Names: 
rpoCA6592_25550A9X72_23915AAG43_004319ABE90_012715ACN68_05320ACN81_23175ACU57_23185AM464_13270APX88_03320AT335_003682AT845_003984AW119_26060B6R12_002490B6R15_000400B6R31_004826B6R48_004921B6R87_004892BANRA_00556BANRA_02658BANRA_05060BEA19_22935BF481_004768BG944_004752BGZ_01811BGZ_04901BHS81_23830BJI68_24535BJJ90_25120BK292_28025BK383_27720BMC79_004282BMT49_21005BMT50_08090BMT91_03285BN17_39521BO068_004210BOH76_00535BON63_20110BON64_17760BON65_15085BON66_14380BON67_10880BON68_25620BON69_07675BON70_00395BON71_08940BON72_17275BON73_00245BON74_15225BON75_02240BON76_16220BON77_22675BON78_03480BON79_17585BON80_22860BON81_01110BON83_01620BON87_25670BON89_14770BON91_27070BON92_00590BON93_00705BON94_22185BON95_12860BON96_11000BON97_20250BON98_22915BTQ06_27265BvCmsF30A_00478BvCmsHHP019_04451BvCmsHHP056_02607BvCmsKKP061_02982BvCmsKSNP073_02854BvCmsNSP072_02893BVL39_05360BXT93_12730BZL69_05725C2U48_12715C5N07_24540C5Y87_25310C9114_22905C9160_23380C9E67_28655CA593_06020CCS08_08140CDC27_21560CDL36_24870CG831_003924CIG67_06970CO706_19510CR538_24210CR539_01675CV83915_02065CWS33_24550CXJ73_004162CY655_25300D0X26_26125D3822_07080D3Y67_18045D9D43_22315D9D77_23620D9E34_21770D9H94_18950D9J03_21580DAH17_22710DAH18_24925DAH19_24515DAH20_24815DAH21_23320DAH23_25900DAH24_26040DAH25_26075DAH26_25940DAH27_25270DAH28_23885DAH29_24350DAH30_23845DAH31_24375DAH33_24565DAH34_21555DAH35_26340DAH36_23725DAH37_22570DAH38_23230DAH40_23335DAH42_24295DAH43_24880DAH45_24825DAH46_24660DAH47_25135DAH48_24925DAH49_24835DAH50_22035DD762_22280DEN87_24580DEN88_24360DEN89_26510DEN90_25535DEN91_25230DEN92_24665DEN93_24980DEN94_24465DEN95_25125DEN96_23600DEN97_23710DEN98_23795DEN99_23135DEO00_23170DEO01_23750DEO02_23980DEO03_22675DEO04_24305DEO05_24175DEO06_24620DEO07_24855DEO08_24290DEO09_24370DEO10_24290DEO11_23940DEO12_25050DEO13_24310DEO14_24495DEO15_24970DEO17_24875DEO18_23920DEO19_24555DEO20_25020DIV22_03745DN627_23155DRW19_23990DTL43_13700DTL90_24530DTM16_24360DU321_23425DXT69_22805DXT70_21465DXT71_22310DXT73_22940E0I42_21900E2112_20360E2113_19800E2117_21880E2119_22340E2121_20400E2122_20800E2127_20900E2128_03185E2129_21295E2131_19275E2132_20135E2133_18885E2134_22790E2135_19330E3O05_23740E4K51_22920E4T14_19265E5M02_21775E5P22_12650E5P23_19725E5P24_19615E5P25_23055E5P26_18290E5P27_19155E5P28_08825E5P29_14400E5P30_23670E5P31_18530E5P32_02825E5P33_07130E5P34_19120E5P35_02265E5P36_06040E5P37_21450E5P39_19425E5P40_03200E5P41_16050E5P42_04855E5P43_16470E5P44_18160E5P45_17320E5P46_15010E5P47_19430E5P48_14465E5P49_19235E5P50_22485E5P51_03205E5P52_19925E5S34_21385E5S35_21950E5S36_22335E5S38_21405E5S39_21135E5S42_21540E5S43_20990E5S44_22255E5S45_22685E5S47_23025E5S48_22965E5S51_21950E5S52_22260E5S53_21960E5S54_23760E5S55_21995E5S56_22725E5S57_22160E5S58_21685E5S61_22375E5S62_23450EAI46_11695EAN77_22650EAX79_24760EBP16_21385EC1094V2_4282ECs4911ED648_18905EHD79_23525EHH55_00715EI021_22070EIZ93_16335EL79_4407EL80_4314ELT15_18455ELT17_21010ELT18_21900ELT20_20720ELT21_20545ELT23_22660ELT27_20990ELT29_22075ELT38_22790ELT41_20490ELT57_22290ELU85_23590ELU87_21975ELU90_21605ELU99_23055ELV08_18690ELV09_17955ELV21_16085ELV26_23220ELV28_22250ELX48_22415ELX57_20105ELX61_20545ELX65_19750ELX66_22520ELX67_21035ELX69_20060ELX72_20720ELX74_23585ELX76_21250ELX78_21735ELX82_21250ELX84_22555ELX85_02100ELX86_18600ELX87_22155ELX90_21365ELX91_23125ELX96_15665ELX98_18555ELY02_19945ELY05_18165ELY18_20340ELY22_19955ELY30_22450ELY31_22565ELY32_24365ELY35_18500ELY36_23180ELY39_21195ELY41_16445ELY48_22270ELY49_19025ERS139208_04657EVY14_16840EYV17_20985EYV18_01360F0L67_26015F2N31_22415F3N40_21595F7F11_23815F9B07_23670F9V24_17840F9X20_05965FDM60_19485FFF58_24430FJQ51_21480FOI11_015710FOI11_24350FQF29_20795FV293_23430FVB16_05290FWK02_01680FY127_17750G3813_004460G4A38_22920G5632_19555GAJ26_24175GF147_25310GF699_23055GFY34_22475GIB53_18270GJ11_25200GKF89_20995GNZ05_25260GP662_20930GP946_22700GP954_05255GP979_07400GQA06_03470GQE64_22340GQF59_23130GQM04_07520GQM09_18365GQM13_25045GQW68_22045GRW05_10055GRW57_01390GRW81_21775GSY44_21840GUB08_21175GUC01_23005H0O72_20910HHH44_004417HI055_004311HJQ60_004916HJS37_004852HJU54_004824HKA49_004956HL563_20665HLZ50_21730HMU48_21580HMV95_21230HNC36_22380HNC59_22525HNC66_25345HNC99_22045HV109_22420HV209_21190HVW19_23415HVW43_14980HVX16_24445HVX31_19105HVZ30_19815HVZ71_23865HX136_23635I6H00_17165I6H01_14335I6H02_15720IH768_05165IH772_15235IT029_004865J0541_004717J4S20_004535J5U05_003963JE86ST02C_45250JE86ST05C_45350JFD_05094JNP96_01280NCTC10082_02080NCTC10090_02779NCTC10429_00081NCTC10865_05894NCTC10974_05350NCTC11181_01964NCTC12950_05213NCTC13127_06163NCTC13148_04414NCTC13216_02108NCTC7927_05248NCTC8008_04280NCTC8333_05557NCTC8500_05324NCTC8960_02339NCTC9036_04648NCTC9037_04781NCTC9044_02305NCTC9045_05541NCTC9077_05932NCTC9111_04954NCTC9706_02002NCTC9777_01117ND22_004792PGD_00622RG28_25345SAMEA3472044_04873SAMEA3472056_05309SAMEA3472067_05183SAMEA3472080_04815SAMEA3472147_04120SAMEA3751407_05007SAMEA3752557_04844SAMEA3753106_04232WP2S18E08_45640WP4S18E07_42680WR15_01490

EC: 2.7.7.6
UniProt
Find proteins for P0A8T7 (Escherichia coli (strain K12))
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UniProt GroupP0A8T7
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit omega91Escherichia coli K-12Mutation(s): 0 
Gene Names: rpoZb3649JW3624
EC: 2.7.7.6
UniProt
Find proteins for P0A800 (Escherichia coli (strain K12))
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Go to UniProtKB:  P0A800
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UniProt GroupP0A800
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Entity ID: 5
MoleculeChains LengthOrganismImage
Non-template DNAF [auth N]295Escherichia coli K-12
Sequence Annotations
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Entity ID: 6
MoleculeChains LengthOrganismImage
Non-regulatory RNAG [auth R]122Escherichia coli
Sequence Annotations
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Entity ID: 7
MoleculeChains LengthOrganismImage
Template DNAH [auth T]295Escherichia coli K-12
Sequence Annotations
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20
RECONSTRUCTIONcryoSPARC3.3

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)European Union679734
French Infrastructure for Integrated Structural Biology (FRISBI)FranceANR-10-INBS-05
Agence Nationale de la Recherche (ANR)FranceANR-10-LABX-0030-INRT
Agence Nationale de la Recherche (ANR)FranceANR-10-IDEX-0002-02

Revision History  (Full details and data files)

  • Version 1.0: 2022-10-19
    Type: Initial release
  • Version 1.1: 2022-11-02
    Changes: Database references
  • Version 1.2: 2024-07-24
    Changes: Data collection, Refinement description