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Yorodumi- PDB-7uwe: CryoEM Structure of E. coli Transcription-Coupled Ribonucleotide ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7uwe | |||||||||
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Title | CryoEM Structure of E. coli Transcription-Coupled Ribonucleotide Excision Repair (TC-RER) complex | |||||||||
Components |
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Keywords | TRANSFERASE/HYDROLASE/DNA/RNA / Transcription-coupled RER / TRANSCRIPTION / TRANSFERASE-HYDROLASE-DNA-RNA complex | |||||||||
Function / homology | Function and homology information ribonuclease H2 complex / DNA replication, removal of RNA primer / ribonuclease H / submerged biofilm formation / cellular response to cell envelope stress / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / bacterial-type flagellum assembly / bacterial-type flagellum-dependent cell motility / nitrate assimilation ...ribonuclease H2 complex / DNA replication, removal of RNA primer / ribonuclease H / submerged biofilm formation / cellular response to cell envelope stress / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / bacterial-type flagellum assembly / bacterial-type flagellum-dependent cell motility / nitrate assimilation / mismatch repair / DNA-directed RNA polymerase complex / transcription elongation factor complex / regulation of DNA-templated transcription elongation / transcription antitermination / DNA-templated transcription initiation / cell motility / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / RNA-DNA hybrid ribonuclease activity / manganese ion binding / response to heat / intracellular iron ion homeostasis / protein dimerization activity / response to antibiotic / DNA-templated transcription / magnesium ion binding / DNA binding / RNA binding / zinc ion binding / membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å | |||||||||
Authors | Hao, Z.T. / Grower, M. / Bharati, B. / Proshkin, S. / Epshtein, V. / Svetlov, V. / Nudler, E. / Shamovsky, I. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Cell / Year: 2023 Title: RNA polymerase drives ribonucleotide excision DNA repair in E. coli. Authors: Zhitai Hao / Manjunath Gowder / Sergey Proshkin / Binod K Bharati / Vitaly Epshtein / Vladimir Svetlov / Ilya Shamovsky / Evgeny Nudler / 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 ...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. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7uwe.cif.gz | 622 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7uwe.ent.gz | 493 KB | Display | PDB format |
PDBx/mmJSON format | 7uwe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7uwe_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 7uwe_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 7uwe_validation.xml.gz | 95.1 KB | Display | |
Data in CIF | 7uwe_validation.cif.gz | 151.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uw/7uwe ftp://data.pdbj.org/pub/pdb/validation_reports/uw/7uwe | HTTPS FTP |
-Related structure data
Related structure data | 26830MC 7uwhC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-DNA chain , 2 types, 2 molecules AB
#1: DNA chain | Mass: 8840.689 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli) |
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#2: DNA chain | Mass: 8813.646 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli) |
-DNA-directed RNA polymerase subunit ... , 4 types, 5 molecules GHIJK
#4: Protein | Mass: 36558.680 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpoA, pez, phs, sez, b3295, JW3257 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: P0A7Z4, DNA-directed RNA polymerase #5: Protein | | Mass: 150820.875 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpoB, Z5560, ECs4910 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: P0A8V4, DNA-directed RNA polymerase #6: Protein | | Mass: 155366.781 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpoC, tabB, b3988, JW3951 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: P0A8T7, DNA-directed RNA polymerase #7: Protein | | Mass: 10249.547 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpoZ, Z5075, ECs4524 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: P0A802, DNA-directed RNA polymerase |
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-RNA chain / Protein , 2 types, 2 molecules RC
#3: RNA chain | Mass: 5859.580 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli) |
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#8: Protein | Mass: 21558.021 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) Gene: rnhB, ABE90_006955, ACN68_08240, ACN81_28465, ACU57_18505, AT845_002192, AWP93_20140, BANRA_00657, BANRA_01142, BANRA_03354, BG944_001858, BHS81_00720, BJI68_15710, BJJ90_21290, BK292_13740, ...Gene: rnhB, ABE90_006955, ACN68_08240, ACN81_28465, ACU57_18505, AT845_002192, AWP93_20140, BANRA_00657, BANRA_01142, BANRA_03354, BG944_001858, BHS81_00720, BJI68_15710, BJJ90_21290, BK292_13740, BMT50_03940, BO068_002873, BOH76_17645, BON63_15375, BON64_03455, BON67_09920, BON69_16465, BON70_27225, BON71_14810, BON73_05390, BON74_02650, BON77_22000, BON80_16390, BON89_11100, BON93_03865, BON95_12960, BTQ06_06560, BvCmsF30A_01255, BvCmsKSNP073_05569, BvCmsNSP072_03655, BVL39_02115, C5N07_08650, C5Y87_12645, C9114_06955, CA593_02795, CG831_000806, CIG67_16650, CO706_23125, CV83915_01391, CWS33_09690, D0X26_09345, D3Y67_16475, D9H94_14105, DAH17_03135, DAH18_22235, DAH20_13890, DAH22_03575, DAH27_18705, DAH28_17945, DAH29_14760, DAH30_10540, DAH31_15680, DAH32_15180, DAH34_04115, DAH35_21445, DAH36_21020, DAH37_16260, DAH41_15695, DEN87_21140, DEN89_20355, DEN90_18695, DEN91_15555, DEN92_14745, DEN93_18240, DEN94_16175, DEN95_12235, DEN96_06260, DEN97_04355, DEN98_04360, DEN99_03185, DEO00_05260, DEO01_06085, DEO02_09465, DEO03_16395, DEO04_22160, DEO05_22030, DEO06_22675, DEO07_22500, DEO08_20735, DEO09_21885, DEO10_22145, DEO11_22040, DEO12_12305, DEO13_08570, DEO14_11170, DEO15_08350, DEO18_03480, DEO19_04140, DEO20_19790, DIV22_06340, DN627_10175, DRW19_04855, DXT69_01400, DXT70_17000, E0I42_19050, E2113_05780, E2117_05455, E2119_15650, E2122_04525, E2131_12130, E2135_11705, E4K51_05720, E5M02_17430, E5P23_04780, E5P24_16135, E5P25_12930, E5P26_03445, E5P27_14095, E5P28_14045, E5P29_07870, E5P30_07200, E5P35_01175, E5P36_00585, E5P51_07020, E5S34_18450, E5S35_00100, E5S36_11195, E5S37_18845, E5S39_17415, E5S42_18175, E5S43_01730, E5S44_09555, E5S45_04795, E5S47_12390, E5S48_12785, E5S51_08350, E5S54_18395, E5S56_11640, EAI46_03575, EAX79_05490, EC1094V2_3668, EC3234A_2c01650, EC95NR1_04369, EHD79_10665, EHH55_16915, EI021_19915, EIZ93_07855, EKI52_10365, EL79_3691, EL80_3638, ELT41_02045, ELV08_10210, ELX85_10375, EYV17_16515, EYV18_21815, F0L67_09075, F2N31_00095, F9V24_09570, FDM60_08750, FOI11_012770, FOI11_22910, FQ007_15880, FTV90_09235, FV293_02825, FWK02_16565, G9448_10045, GIB53_10190, GKF86_01260, GKF89_14710, GP650_06585, GP662_15385, GP954_09955, GP979_14795, GQA06_14505, GQE64_01325, GQF59_21085, GRW05_07765, GRW57_08780, GRW81_09880, GUC01_17950, HHH44_003649, HKA49_001638, HV209_01610, HVW19_15045, HX136_20530, I6H02_18720, IH772_14505, J0541_003901, J4S20_003213, J5U05_002998, JE86ST02C_01770, JE86ST05C_01800, JFD_01269, JNP96_05105, NCTC10418_06054, NCTC11181_01347, NCTC11341_03667, NCTC13216_02729, NCTC8008_03658, NCTC8179_01396, NCTC8500_04527, NCTC8960_01547, NCTC9036_04009, NCTC9037_04174, NCTC9045_04695, NCTC9073_03377, NCTC9111_04250, NCTC9117_05034, NCTC9706_01322, ND22_002535, PGD_03824, RG28_03840, SAMEA3472067_01428, SAMEA3751407_04799, WP2S18E08_37600 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: W8T723, ribonuclease H |
-Non-polymers , 2 types, 3 molecules
#9: Chemical | ChemComp-MG / |
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#10: Chemical |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Elongation Complex(EC)-RNaseH2 complex / Type: COMPLEX / Entity ID: #1-#8 / Source: MULTIPLE SOURCES |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Source (recombinant) | Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: OTHER |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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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 / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm |
Image recording | Electron dose: 62 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
CTF correction | Type: NONE |
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3D reconstruction | Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 142145 / Symmetry type: POINT |