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Open data
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Basic information
| Entry | Database: PDB / ID: 9w3e | |||||||||||||||||||||
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| Title | Cryo-EM structure of E. coli RNA polymerase in complex with PP1 | |||||||||||||||||||||
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Keywords | TRANSCRIPTION / AlphaFold 3 / transcription regulation / phage / RNA polymerase / sigma factor | |||||||||||||||||||||
| Function / homology | Function and homology informationDNA-directed RNA polymerase complex / ribonucleoside binding / DNA-directed RNA polymerase / DNA-directed RNA polymerase activity / protein dimerization activity / DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||||||||||||||
| Biological species | ![]() Pseudomonas phage vB_PaeM_PAO1_Ab17 (virus) | |||||||||||||||||||||
| Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||||||||||||||
Authors | Yuan, L. / Feng, Y. | |||||||||||||||||||||
| Funding support | China, 1items
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Citation | Journal: Cell Rep / Year: 2026Title: AlphaFold 3-powered discovery of phage proteins that inhibit bacterial transcription initiation. Authors: Linggang Yuan / Qingyang Liu / Xiaojian Xiao / Liqiao Xu / Liang Liang / Yang Guo / Yue Yao / Hui Wang / Youjun Feng / Xiaoting Hua / Yu Feng / ![]() Abstract: Many phages encode proteins that specifically inhibit host RNA polymerase activity, thereby sabotaging and, in some cases, hijacking the host transcription machinery to serve their needs. Traditional ...Many phages encode proteins that specifically inhibit host RNA polymerase activity, thereby sabotaging and, in some cases, hijacking the host transcription machinery to serve their needs. Traditional methods for identifying new phage proteins that inhibit bacterial transcription are labor intensive and require access to live phages. To overcome these limitations, we develop a highly efficient pipeline for AlphaFold 3-guided discovery of phage proteins that inhibit bacterial transcription initiation. Using this pipeline, three phage proteins are identified and characterized. Structural and biochemical analyses demonstrate that these phage proteins bind to distinct sites on RNA polymerase and inhibit transcription initiation via different mechanisms. This study showcases the power of AlphaFold 3 in discovering novel binders of large protein complexes, and the pipeline developed here could be readily adapted to screen modulators of other large targets, such as the ribosome, proteasome, and CRISPR-Cas systems. | |||||||||||||||||||||
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Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 9w3e.cif.gz | 541.5 KB | Display | PDBx/mmCIF format |
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| PDB format | pdb9w3e.ent.gz | 434 KB | Display | PDB format |
| PDBx/mmJSON format | 9w3e.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w3/9w3e ftp://data.pdbj.org/pub/pdb/validation_reports/w3/9w3e | HTTPS FTP |
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-Related structure data
| Related structure data | ![]() 65598MC ![]() 9w3dC ![]() 9w3gC M: map data used to model this data C: citing same article ( |
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| Similar structure data | Similarity search - Function & homology F&H Search |
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Links
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Assembly
| Deposited unit | ![]()
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Components
| #1: Protein | Mass: 36558.680 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: rpoA, A5U30_004529, A8502_004046, ACN81_25405, ACU57_21075, AW118_24785, AWP47_12760, B6R15_004092, B6R31_004991, BANRA_01926, BCB93_004270, BE932_15420, BER14_25075, BG944_001110, BGM66_ ...Gene: rpoA, A5U30_004529, A8502_004046, ACN81_25405, ACU57_21075, AW118_24785, AWP47_12760, B6R15_004092, B6R31_004991, BANRA_01926, BCB93_004270, BE932_15420, BER14_25075, BG944_001110, BGM66_003616, BGZ_02613, BGZ_04102, BJI68_08790, BK292_20390, BK383_24760, BR158_003767, BTB68_004379, BTQ06_10575, BvCmsKKP061_03007, BvCmsSIP010_02662, BXT93_05590, C0P57_002645, C1Q91_004927, C2121_004185, C2R31_004610, C3F40_19835, C9Z68_22520, CF22_004872, CG704_20985, CIG67_10790, CQ842_14440, CQ842_22230, CTR35_003607, CV83915_02803, D3G36_23165, D4M65_20540, D4N09_20140, D9D43_22665, D9E49_05125, D9J61_16620, DD762_23515, DIV22_15290, DNQ45_03725, DNX30_25510, DS732_24230, DTL43_21030, DU321_11970, E2865_04448, E4K51_21460, E5H86_24555, E6D34_21790, EAI46_07445, ECs4160, EIA08_23925, EIZ93_12500, EN85_004372, EPS76_07245, EPS97_20125, EWK56_24965, ExPECSC038_03663, F7F11_22755, F7N46_24040, F9413_21265, F9461_25685, F9B07_24715, FGAF848_26080, FIJ20_21225, FJQ40_18275, FKO60_25605, FOI11_019290, FOI11_03890, FPI65_20275, FPS11_25460, FVB16_04840, FZU14_21790, G3V95_19815, G3W53_20925, G4A38_21480, G4A47_20750, G5603_24555, GAI89_24860, GAJ12_24750, GFY48_21540, GKF66_21515, GNW61_16600, GNZ05_26015, GOP25_22675, GP711_23275, GP954_00975, GP975_01155, GP979_02035, GQA06_03980, GQE86_20050, GQM04_10535, GQM13_25170, GQM21_11200, GQN34_23235, GQW07_21580, GRC73_21780, GRO95_20845, GRW05_09030, GRW24_04785, GUC01_21150, H0O53_20860, H0O72_19385, HEP30_018605, HEP34_004777, HHH44_004542, HI055_004133, HIE29_005180, HJQ60_005018, HLX92_10105, HLZ50_22210, HMV95_19575, HMW38_23075, HV109_02220, HV209_14745, HVV39_09235, HVW04_17565, HVW43_18700, HVY77_02205, I6H00_20955, I6H02_11960, J0541_004390, JNP96_25275, NCTC10082_02846, NCTC10089_00509, NCTC10418_00698, NCTC10767_01523, NCTC10865_00668, NCTC10974_00559, NCTC11126_02779, NCTC11181_02745, NCTC11341_01882, NCTC13148_03434, NCTC7927_00558, NCTC7928_02508, NCTC8009_01520, NCTC8179_05950, NCTC8333_00496, NCTC8500_00344, NCTC8621_00515, NCTC8622_00499, NCTC8959_03254, NCTC8960_03077, NCTC9044_01349, NCTC9077_00611, NCTC9081_00926, NCTC9117_00762, NCTC9702_00544, NCTC9706_02744, OGM49_22300, P6223_003976, QDW62_02225, RZR61_12860, SAMEA3472112_00700, SAMEA3752557_01945, WR15_19575 Production host: ![]() #2: Protein | | Mass: 150820.875 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: rpoB, A5U30_004588, A8502_003926, ACN81_23170, ACU57_23190, B6R15_000401, B6R31_004825, BANRA_02657, BCB93_004500, BE932_19390, BG944_004751, BGM66_002187, BGZ_01825, BGZ_04900, BJI68_24530, ...Gene: rpoB, A5U30_004588, A8502_003926, ACN81_23170, ACU57_23190, B6R15_000401, B6R31_004825, BANRA_02657, BCB93_004500, BE932_19390, BG944_004751, BGM66_002187, BGZ_01825, BGZ_04900, BJI68_24530, BK292_28030, BK383_27725, BKL28_004342, BR158_004263, BTB68_004076, BTQ06_27270, BvCmsKKP061_02983, BvCmsSIP010_03567, C0P57_003017, C1Q91_004815, C2121_004048, C2R31_004867, C3F40_15465, CF22_004730, CG704_19805, CIG67_06965, CQ842_10385, CQ842_21775, CTR35_004065, CV83915_02066, D3G36_22420, D4M65_19260, D4N09_21555, D9D43_22310, D9E49_24270, D9J61_19510, DIV22_03740, DNX30_24150, DS732_01545, DTL43_13705, DU321_23430, E2865_05183, E4K51_22915, E5H86_23040, E6D34_20875, EAI46_11700, ECs4910, EIA08_23405, EIZ93_16330, EN85_004184, EPS97_19155, EWK56_25655, ExPECSC038_04328, F7F11_23820, F7N46_22875, F9413_20760, F9461_25105, F9B07_23665, FGAF848_44560, FIJ20_20105, FJQ40_20830, FKO60_24820, FOI11_015715, FOI11_24355, FPS11_24520, FVB16_05295, FZU14_22850, G3V95_20435, G3W53_22320, G4A38_22925, G4A47_22785, G5603_24105, GAI89_24240, GAJ12_23550, GFY48_22990, GKF66_20530, GNW61_19025, GNZ05_25255, GOP25_23375, GP711_23600, GP954_05260, GP965_06575, GP975_06485, GP979_07405, GQA06_03465, GQE86_18840, GQM04_07515, GQM13_25050, GQM21_14970, GQN34_23560, GQW07_19570, GRC73_22185, GRO95_18745, GRW05_10060, GRW24_04150, GUC01_23010, H0O53_14775, H0O72_20915, HEP30_021890, HEP34_004579, HHH44_004416, HI055_004310, HJQ60_004917, HLX92_23670, HLZ50_21725, HMV95_21225, HMW38_24340, HV109_22425, HV209_21195, HVV39_13135, HVW04_13835, HVY77_24375, I6H00_17170, J0541_004716, J5U05_003962, JNP96_01275, NCTC10082_02081, NCTC10089_04873, NCTC10418_07146, NCTC10764_02972, NCTC10767_00716, NCTC10865_05895, NCTC10974_05351, NCTC11112_02281, NCTC11341_02774, NCTC7927_05249, NCTC8179_05096, NCTC8333_05558, NCTC8500_05325, NCTC8621_04872, NCTC8959_04064, NCTC8960_02340, NCTC9001_04473, NCTC9044_02304, NCTC9075_06427, NCTC9081_06476, NCTC9117_05904, NCTC9706_02003, OGM49_00575, P6223_004406, QDW62_24495, RZR61_19915, SAMEA3472112_05166, SAMEA3752557_04843, WR15_01485 Production host: ![]() #3: Protein | | Mass: 155366.781 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: rpoC, ACN81_23175, ACU57_23185, B6R15_000400, B6R31_004826, BANRA_02658, BANRA_05060, BCB93_004501, BG944_004752, BGM66_002186, BGZ_01824, BGZ_04901, BJI68_24535, BK292_28025, BK383_27720, ...Gene: rpoC, ACN81_23175, ACU57_23185, B6R15_000400, B6R31_004826, BANRA_02658, BANRA_05060, BCB93_004501, BG944_004752, BGM66_002186, BGZ_01824, BGZ_04901, BJI68_24535, BK292_28025, BK383_27720, BKL28_004343, BTB68_004077, BTQ06_27265, BvCmsKKP061_02982, BvCmsSIP010_03566, BXT93_12730, C0P57_003018, C1Q91_004816, CF22_004731, CIG67_06970, CQ842_10380, CQ842_21770, CTR35_004066, CV83915_02065, D4M65_19255, D9D43_22315, DD762_22280, DIV22_03745, DTL43_13700, DU321_23425, E2865_05184, E4K51_22920, E5H86_23045, E6D34_20880, EAI46_11695, ECs4911, EIZ93_16335, EN85_004185, EPS97_19150, F7F11_23815, F7N46_22880, F9413_20765, F9461_25110, F9B07_23670, FGAF848_44550, FIJ20_20110, FJQ40_20835, FOI11_015710, FOI11_24350, FPS11_24525, FVB16_05290, FWK02_01680, FZU14_22855, G3V95_20430, G4A38_22920, G4A47_22780, GAI89_24245, GAJ12_23555, GNW61_19030, GOP25_23380, GP954_05255, GP965_06570, GP975_06480, GP979_07400, GQA06_03470, GQM04_07520, GQM13_25045, GQM21_14965, GRW05_10055, GRW24_04145, GUC01_23005, H0O72_20910, HEP30_021895, HEP34_004580, HHH44_004417, HI055_004311, HJQ60_004916, HLZ50_21730, HMV95_21230, HV109_22420, HV209_21190, HVW43_14980, I6H00_17165, I6H02_15720, J0541_004717, J5U05_003963, JNP96_01280, NCTC10082_02080, NCTC10429_00081, NCTC10865_05894, NCTC10974_05350, NCTC11181_01964, NCTC13148_04414, NCTC7927_05248, NCTC8333_05557, NCTC8500_05324, NCTC8960_02339, NCTC9044_02305, NCTC9045_05541, NCTC9077_05932, NCTC9706_02002, P6223_004407, RZR61_19920, SAMEA3472112_05167, SAMEA3752557_04844, WR15_01490 Production host: ![]() #4: Protein | | Mass: 13974.707 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas phage vB_PaeM_PAO1_Ab17 (virus)Production host: ![]() #5: Protein | | Mass: 10249.547 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: rpoZ, A5U30_004148, ACN81_07055, ACU57_08210, AW118_10810, AWP47_16050, B6R15_003237, B6R31_002878, BANRA_02310, BANRA_04690, BCB93_002408, BE932_17435, BER14_16095, BG944_002252, BGM66_003986, ...Gene: rpoZ, A5U30_004148, ACN81_07055, ACU57_08210, AW118_10810, AWP47_16050, B6R15_003237, B6R31_002878, BANRA_02310, BANRA_04690, BCB93_002408, BE932_17435, BER14_16095, BG944_002252, BGM66_003986, BGZ_02214, BGZ_04512, BJI68_21645, BK292_27460, BK383_09585, BKL28_001536, BR158_002512, BTB68_002430, BTQ06_17920, BvCmsKKP061_02010, BvCmsSIP010_04544, BXT93_06150, C0P57_002947, C1Q91_001894, C2121_003335, C2M16_17105, C2R31_004094, C3F40_17525, C9Z68_15355, CF22_002039, CG704_10080, CIG67_24930, CQ842_12520, CQ842_18710, CTR35_001090, CV83915_02433, D3C88_28115, D3G36_09320, D4M65_21000, D4N09_11435, D9D43_20755, D9E49_10255, D9J61_13945, DD762_15130, DIV22_25200, DNQ45_15780, DNX30_23515, DS732_26345, DTL43_17875, DU321_24340, E2865_05030, E4K51_22275, E5H86_15705, E6D34_14240, EAI46_01840, ECs4524, EIA08_13140, EIMP300_11010, EIZ93_18370, EN85_002956, EPS76_07085, EPS97_14185, EWK56_19170, ExPECSC038_00846, F7F11_13860, F7N46_06720, F9413_20095, F9461_04565, F9B07_09920, FGAF848_22320, FIJ20_14920, FJQ40_21575, FKO60_20865, FOI11_017480, FOI11_05700, FPI65_22445, FPS11_15600, FVB16_16120, FWK02_33875, FZU14_11370, G3V95_06620, G3W53_09695, G4A38_07455, G4A47_06855, G5603_14085, GAI89_21090, GAJ12_11155, GFY48_10985, GKF66_06160, GNW61_14945, GNZ05_16450, GOP25_14490, GP711_13960, GP965_26105, GP975_06850, GP979_20345, GQE86_16840, GQM04_17590, GQM13_19325, GQM21_23705, GQN34_13425, GQW07_20690, GRC73_07290, GRO95_19885, GRW05_19000, GRW24_24035, GUC01_19190, H0O72_08780, HEP30_004255, HEP34_000545, HHH44_001968, HI055_001969, HIE29_002327, HJQ60_004422, HLX92_21100, HLZ50_07700, HMV95_20745, HMW38_12410, HV109_00280, HV209_24645, HVV39_11020, HVW04_15785, HVW43_16805, HVY77_00270, I6H00_19090, I6H02_13725, J0541_001532, J5U05_003683, JNP96_00560, NCTC10082_02470, NCTC10089_00122, NCTC10429_00579, NCTC10764_03466, NCTC10767_01139, NCTC10974_00114, NCTC11112_01617, NCTC11126_01727, NCTC11181_02381, NCTC11341_02352, NCTC13148_03955, NCTC7922_04533, NCTC7927_00174, NCTC7928_03021, NCTC8009_00942, NCTC8179_05509, NCTC8333_00095, NCTC8500_05773, NCTC8621_00157, NCTC8622_01081, NCTC8959_03642, NCTC8960_02710, NCTC8985_04508, NCTC9001_03765, NCTC9045_00155, NCTC9073_06404, NCTC9075_00220, NCTC9077_00123, NCTC9081_00466, NCTC9702_00091, NCTC9706_02361, NCTC9962_01055, OGM49_24110, P6223_003124, QDW62_00285, RZR61_11660, SAMEA3472112_02301, SAMEA3752557_01157, WR15_15985 Production host: ![]() Has protein modification | 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 |
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Sample preparation
| Component | Name: E. coli RNA polymerase in complex with phage protein / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT | ||||||||||||
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| Molecular weight | Experimental value: NO | ||||||||||||
| Source (natural) |
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| Source (recombinant) | Organism: ![]() | ||||||||||||
| Buffer solution | pH: 7.5 | ||||||||||||
| Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||
| Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
| Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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| Microscopy | Model: TFS 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: 1000 nm |
| Image recording | Electron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) |
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Processing
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| CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
| 3D reconstruction | Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 43424 / Symmetry type: POINT | ||||||||||||||||||||||||
| Refinement | Highest resolution: 3.6 Å Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS) | ||||||||||||||||||||||||
| Refine LS restraints |
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Movie
Controller
About Yorodumi





Pseudomonas phage vB_PaeM_PAO1_Ab17 (virus)
China, 1items
Citation




PDBj




FIELD EMISSION GUN