7UWE

CryoEM Structure of E. coli Transcription-Coupled Ribonucleotide Excision Repair (TC-RER) complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 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

RNA polymerase drives ribonucleotide excision DNA repair in E. coli.

Hao, Z.Gowder, M.Proshkin, S.Bharati, B.K.Epshtein, V.Svetlov, V.Shamovsky, I.Nudler, E.

(2023) Cell 186: 2425

  • DOI: https://doi.org/10.1016/j.cell.2023.04.029
  • Primary Citation of Related Structures:  
    7UWE, 7UWH

  • PubMed Abstract: 

    Ribonuclease HII (RNaseHII) is the principal enzyme that removes misincorporated ribonucleoside monophosphates (rNMPs) from genomic DNA. Here, we present structural, biochemical, and genetic evidence demonstrating that ribonucleotide excision repair (RER) is directly coupled to transcription. Affinity pull-downs and mass-spectrometry-assisted mapping of in cellulo inter-protein cross-linking reveal the majority of RNaseHII molecules interacting with RNA polymerase (RNAP) in E. coli. Cryoelectron microscopy structures of RNaseHII bound to RNAP during elongation, with and without the target rNMP substrate, show specific protein-protein interactions that define the transcription-coupled RER (TC-RER) complex in engaged and unengaged states. The weakening of RNAP-RNaseHII interactions compromises RER in vivo. The structure-functional data support a model where RNaseHII scans DNA in one dimension in search for rNMPs while "riding" the RNAP. We further demonstrate that TC-RER accounts for a significant fraction of repair events, thereby establishing RNAP as a surveillance "vehicle" for detecting the most frequently occurring replication errors.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit alphaD [auth G],
E [auth H]
329Escherichia coliMutation(s): 0 
Gene Names: rpoApezphssezb3295JW3257
EC: 2.7.7.6
UniProt
Find proteins for P0A7Z4 (Escherichia coli (strain K12))
Explore P0A7Z4 
Go to UniProtKB:  P0A7Z4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7Z4
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit betaF [auth I]1,342Escherichia coliMutation(s): 0 
Gene Names: rpoBZ5560ECs4910
EC: 2.7.7.6
UniProt
Find proteins for P0A8V2 (Escherichia coli (strain K12))
Explore P0A8V2 
Go to UniProtKB:  P0A8V2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A8V2
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta'G [auth J]1,407Escherichia coliMutation(s): 0 
Gene Names: rpoCtabBb3988JW3951
EC: 2.7.7.6
UniProt
Find proteins for P0A8T7 (Escherichia coli (strain K12))
Explore P0A8T7 
Go to UniProtKB:  P0A8T7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A8T7
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit omegaH [auth K]91Escherichia coliMutation(s): 0 
Gene Names: rpoZZ5075ECs4524
EC: 2.7.7.6
UniProt
Find proteins for P0A800 (Escherichia coli (strain K12))
Explore P0A800 
Go to UniProtKB:  P0A800
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A800
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Ribonuclease HIII [auth C]198Escherichia coliMutation(s): 0 
Gene Names: 
rnhBABE90_006955ACN68_08240ACN81_28465ACU57_18505AT845_002192AWP93_20140BANRA_00657BANRA_01142BANRA_03354BG944_001858BHS81_00720BJI68_15710BJJ90_21290BK292_13740BMT50_03940BO068_002873BOH76_17645BON63_15375BON64_03455BON67_09920BON69_16465BON70_27225BON71_14810BON73_05390BON74_02650BON77_22000BON80_16390BON89_11100BON93_03865BON95_12960BTQ06_06560BvCmsF30A_01255BvCmsKSNP073_05569BvCmsNSP072_03655BVL39_02115C5N07_08650C5Y87_12645C9114_06955CA593_02795CG831_000806CIG67_16650CO706_23125CV83915_01391CWS33_09690D0X26_09345D3Y67_16475D9H94_14105DAH17_03135DAH18_22235DAH20_13890DAH22_03575DAH27_18705DAH28_17945DAH29_14760DAH30_10540DAH31_15680DAH32_15180DAH34_04115DAH35_21445DAH36_21020DAH37_16260DAH41_15695DEN87_21140DEN89_20355DEN90_18695DEN91_15555DEN92_14745DEN93_18240DEN94_16175DEN95_12235DEN96_06260DEN97_04355DEN98_04360DEN99_03185DEO00_05260DEO01_06085DEO02_09465DEO03_16395DEO04_22160DEO05_22030DEO06_22675DEO07_22500DEO08_20735DEO09_21885DEO10_22145DEO11_22040DEO12_12305DEO13_08570DEO14_11170DEO15_08350DEO18_03480DEO19_04140DEO20_19790DIV22_06340DN627_10175DRW19_04855DXT69_01400DXT70_17000E0I42_19050E2113_05780E2117_05455E2119_15650E2122_04525E2131_12130E2135_11705E4K51_05720E5M02_17430E5P23_04780E5P24_16135E5P25_12930E5P26_03445E5P27_14095E5P28_14045E5P29_07870E5P30_07200E5P35_01175E5P36_00585E5P51_07020E5S34_18450E5S35_00100E5S36_11195E5S37_18845E5S39_17415E5S42_18175E5S43_01730E5S44_09555E5S45_04795E5S47_12390E5S48_12785E5S51_08350E5S54_18395E5S56_11640EAI46_03575EAX79_05490EC1094V2_3668EC3234A_2c01650EC95NR1_04369EHD79_10665EHH55_16915EI021_19915EIZ93_07855EKI52_10365EL79_3691EL80_3638ELT41_02045ELV08_10210ELX85_10375EYV17_16515EYV18_21815F0L67_09075F2N31_00095F9V24_09570FDM60_08750FOI11_012770FOI11_22910FQ007_15880FTV90_09235FV293_02825FWK02_16565G9448_10045GIB53_10190GKF86_01260GKF89_14710GP650_06585GP662_15385GP954_09955GP979_14795GQA06_14505GQE64_01325GQF59_21085GRW05_07765GRW57_08780GRW81_09880GUC01_17950HHH44_003649HKA49_001638HV209_01610HVW19_15045HX136_20530I6H02_18720IH772_14505J0541_003901J4S20_003213J5U05_002998JE86ST02C_01770JE86ST05C_01800JFD_01269JNP96_05105NCTC10418_06054NCTC11181_01347NCTC11341_03667NCTC13216_02729NCTC8008_03658NCTC8179_01396NCTC8500_04527NCTC8960_01547NCTC9036_04009NCTC9037_04174NCTC9045_04695NCTC9073_03377NCTC9111_04250NCTC9117_05034NCTC9706_01322ND22_002535PGD_03824RG28_03840SAMEA3472067_01428SAMEA3751407_04799WP2S18E08_37600

EC: 3.1.26.4
UniProt
Find proteins for P10442 (Escherichia coli (strain K12))
Explore P10442 
Go to UniProtKB:  P10442
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP10442
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains LengthOrganismImage
DNA (29-MER)29Escherichia coli
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (29-MER)29Escherichia coli
Sequence Annotations
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 3
MoleculeChains LengthOrganismImage
RNA (18-MER)C [auth R]18Escherichia coli
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 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 StatesGM126891
Howard Hughes Medical Institute (HHMI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-31
    Type: Initial release
  • Version 1.1: 2023-06-07
    Changes: Database references
  • Version 1.2: 2024-06-12
    Changes: Data collection