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- PDB-9w3g: Cryo-EM structure of E. coli RNA polymerase in complex with VP1 -

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Basic information

Entry
Database: PDB / ID: 9w3g
TitleCryo-EM structure of E. coli RNA polymerase in complex with VP1
Components
  • (DNA-directed RNA polymerase subunit ...) x 4
  • Phage protein
  • RNA polymerase sigma factor RpoD
KeywordsTRANSCRIPTION / AlphaFold 3 / transcription regulation / phage / RNA polymerase / sigma factor
Function / homology
Function and homology information


sigma factor antagonist complex / regulation of DNA-templated transcription initiation / sigma factor activity / cytosolic DNA-directed RNA polymerase complex / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed RNA polymerase / DNA-directed RNA polymerase activity / response to heat ...sigma factor antagonist complex / regulation of DNA-templated transcription initiation / sigma factor activity / cytosolic DNA-directed RNA polymerase complex / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed RNA polymerase / DNA-directed RNA polymerase activity / response to heat / protein dimerization activity / transcription cis-regulatory region binding / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / cytoplasm / cytosol
Similarity search - Function
RNA polymerase sigma factor 70, non-essential domain / Sigma-70, non-essential region / RNA polymerase sigma factor 70, region 1.1 / Sigma-70 factor, region 1.1 superfamily / Sigma-70 factor, region 1.1 / Sigma-70 factors family signature 1. / RNA polymerase sigma factor RpoD, C-terminal / RNA polymerase sigma factor RpoD / : / RNA polymerase sigma-70 region 1.2 ...RNA polymerase sigma factor 70, non-essential domain / Sigma-70, non-essential region / RNA polymerase sigma factor 70, region 1.1 / Sigma-70 factor, region 1.1 superfamily / Sigma-70 factor, region 1.1 / Sigma-70 factors family signature 1. / RNA polymerase sigma factor RpoD, C-terminal / RNA polymerase sigma factor RpoD / : / RNA polymerase sigma-70 region 1.2 / Sigma-70 factor, region 1.2 / RNA polymerase sigma-70 region 3 / Sigma-70 region 3 / Sigma-70 factors family signature 2. / RNA polymerase sigma-70 / RNA polymerase sigma-70 region 4 / Sigma-70, region 4 / RNA polymerase sigma-70 region 2 / RNA polymerase sigma-70 like domain / Sigma-70 region 2 / RNA polymerase sigma factor, region 2 / RNA polymerase sigma factor, region 3/4-like / DNA-directed RNA polymerase, omega subunit / DNA-directed RNA polymerase, subunit beta-prime, bacterial type / DNA-directed RNA polymerase, beta subunit, external 1 domain superfamily / DNA-directed RNA polymerase, beta subunit, external 1 domain / RNA polymerase beta subunit external 1 domain / RNA polymerase, alpha subunit, C-terminal / Bacterial RNA polymerase, alpha chain C terminal domain / DNA-directed RNA polymerase beta subunit, bacterial-type / DNA-directed RNA polymerase, alpha subunit / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb6 / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RNA polymerase Rpb1, domain 3 superfamily / RPB6/omega subunit-like superfamily / RNA polymerase Rpb1, clamp domain superfamily / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / DNA-directed RNA polymerase, insert domain / DNA-directed RNA polymerase, RpoA/D/Rpb3-type / RNA polymerase Rpb3/RpoA insert domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerases D / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb2, domain 2 / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase, RBP11-like subunit / RNA polymerase, beta subunit, conserved site / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3 / RNA polymerase Rpb2, OB-fold / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3 / RNA polymerases beta chain signature. / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain / DNA-directed RNA polymerase, subunit 2 / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily / RNA polymerase Rpb2, domain 6 / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
DNA-directed RNA polymerase subunit beta' / DNA-directed RNA polymerase subunit beta / DNA-directed RNA polymerase subunit omega / DNA-directed RNA polymerase subunit alpha / RNA polymerase sigma factor RpoD
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Vibrio phage vB_VpaP_M3 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsYuan, L. / Feng, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Cell Rep / Year: 2026
Title: 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.
History
DepositionJul 29, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 29, 2026Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA-directed RNA polymerase subunit alpha
B: DNA-directed RNA polymerase subunit alpha
C: DNA-directed RNA polymerase subunit beta
D: DNA-directed RNA polymerase subunit beta'
E: DNA-directed RNA polymerase subunit omega
F: RNA polymerase sigma factor RpoD
G: Phage protein


Theoretical massNumber of molelcules
Total (without water)468,0807
Polymers468,0807
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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DNA-directed RNA polymerase subunit ... , 4 types, 5 molecules ABCDE

#1: Protein DNA-directed RNA polymerase subunit alpha / RNAP subunit alpha / RNA polymerase subunit alpha / Transcriptase subunit alpha


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, 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: Escherichia coli (E. coli) / References: UniProt: C3SR67, DNA-directed RNA polymerase
#2: Protein DNA-directed RNA polymerase subunit beta / RNAP subunit beta / RNA polymerase subunit beta / Transcriptase subunit beta


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, 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: Escherichia coli (E. coli) / References: UniProt: C3SIA7, DNA-directed RNA polymerase
#3: Protein DNA-directed RNA polymerase subunit beta' / RNAP subunit beta' / RNA polymerase subunit beta' / Transcriptase subunit beta'


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, 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: Escherichia coli (E. coli) / References: UniProt: C3SIA2, DNA-directed RNA polymerase
#4: Protein DNA-directed RNA polymerase subunit omega / RNAP omega subunit / RNA polymerase omega subunit / Transcriptase subunit omega


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, 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: Escherichia coli (E. coli) / References: UniProt: C3SM87, DNA-directed RNA polymerase

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Protein , 2 types, 2 molecules FG

#5: Protein RNA polymerase sigma factor RpoD / Sigma-70


Mass: 70352.242 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: rpoD, alt, b3067, JW3039 / Production host: Escherichia coli (E. coli) / References: UniProt: P00579
#6: Protein Phage protein


Mass: 8173.253 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio phage vB_VpaP_M3 (virus) / Production host: Escherichia coli (E. coli)

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Details

Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: E. coli RNA polymerase in complex with phage protein / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Escherichia coli (E. coli)562
31Vibrio phage vB_VpaP_M3 (virus)2950470
41Escherichia coli (strain K12) (bacteria)83333
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1RELIONparticle selection
2PHENIX1.20.1_4487model refinement
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 244153 / Symmetry type: POINT
RefinementHighest resolution: 3.3 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00625919
ELECTRON MICROSCOPYf_angle_d0.81434977
ELECTRON MICROSCOPYf_dihedral_angle_d4.6583567
ELECTRON MICROSCOPYf_chiral_restr0.0473966
ELECTRON MICROSCOPYf_plane_restr0.0074592

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