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- PDB-9m7z: Cryo-EM structure of gp79 bound RNAP core enzyme -

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Basic information

Entry
Database: PDB / ID: 9m7z
TitleCryo-EM structure of gp79 bound RNAP core enzyme
Components
  • DNA-directed RNA polymerase subunit alpha
  • DNA-directed RNA polymerase subunit beta
  • DNA-directed RNA polymerase subunit beta'
  • DNA-directed RNA polymerase subunit omega
  • gp79
KeywordsTRANSCRIPTION / phage / transcription regulation / sigma factor / gp79 / gp36
Function / homology
Function and homology information


DNA-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
Similarity search - Function
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 ...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, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 3 superfamily / RPB6/omega subunit-like superfamily / 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 Rpb1, clamp domain superfamily / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit / 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 / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase, N-terminal / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase Rpb2, domain 2 / RNA polymerase I subunit A N-terminus / 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
Similarity search - Domain/homology
Uncharacterized protein / DNA-directed RNA polymerase subunit beta' / DNA-directed RNA polymerase subunit beta / DNA-directed RNA polymerase subunit omega / DNA-directed RNA polymerase subunit alpha
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Escherichia phage phiEco32 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.5 Å
AuthorsXu, L. / Feng, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nucleic Acids Res / Year: 2025
Title: A phage transcription factor displaces the host σ factor and stabilizes its own σ factor.
Authors: Liqiao Xu / Liang Liang / Linggang Yuan / Yue Yao / Xiaoting Hua / Yu Feng /
Abstract: Phages are the most abundant self-replicating entities on earth, and understanding their transcriptional regulation can provide insights into bacterial gene expression mechanisms. The bacterial RNA ...Phages are the most abundant self-replicating entities on earth, and understanding their transcriptional regulation can provide insights into bacterial gene expression mechanisms. The bacterial RNA polymerase core enzyme interacts with various σ factors to recognize and unwind promoter DNA. Gp79, a protein from Escherichia coli phage phiEco32, inhibits host σ70-mediated transcription while simultaneously activating transcription through its own σ factor, gp36. The underlying mechanism of this unusual dual regulatory role has remained unclear. In this study, we present cryo-EM structures of E. coli RNA polymerase (RNAP) in complex with gp79, and of RNAP in complex with gp79, gp36, and a cognate promoter. Structural and biochemical analyses reveal the basis for σ displacement by gp79 and promoter recognition by gp36. Our findings show that the N-terminus of gp79 invades the RNA channel, effectively displacing σ4. Upon encountering gp36, the N-terminus of gp79 adopts a new conformation, binds to gp36, and stabilizes the RNAP-promoter open complex. These findings advance our understanding of phage transcriptional regulation and suggest potential applications for synthetic biology.
History
DepositionMar 11, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 3, 2025Provider: repository / Type: Initial release

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Structure visualization

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MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA-directed RNA polymerase subunit beta
B: DNA-directed RNA polymerase subunit beta'
C: DNA-directed RNA polymerase subunit alpha
D: DNA-directed RNA polymerase subunit alpha
E: DNA-directed RNA polymerase subunit omega
G: gp79


Theoretical massNumber of molelcules
Total (without water)399,1166
Polymers399,1166
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

#1: 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
#2: 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
#3: 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
#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
#5: Protein gp79


Mass: 9561.070 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia phage phiEco32 (virus) / Gene: phi32_79 / Production host: Escherichia coli (E. coli) / References: UniProt: B0FIP1
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: RNAP-gp79 complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Escherichia phage phiEco32 (virus)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
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: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
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 softwareName: PHENIX / Version: 1.20.1_4487: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 5.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 54549 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00315156
ELECTRON MICROSCOPYf_angle_d0.44421066
ELECTRON MICROSCOPYf_dihedral_angle_d5.1823072
ELECTRON MICROSCOPYf_chiral_restr0.0432847
ELECTRON MICROSCOPYf_plane_restr0.0023072

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Yorodumi

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  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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