7ADD | pdb_00007add

Transcription termination intermediate complex IIIa

• PDB DOI: https://doi.org/10.2210/pdb7ADD/pdb
• NAKB: 7ADD
• EM Map EMD-11724: EMDB EMDataResource

• Classification: TRANSCRIPTION
• Organism(s): Escherichia coli, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-09-14 Released: 2020-11-25 
• Deposition Author(s): Said, N., Hilal, T., Loll, B., Wahl, C.M.
• Funding Organization(s): German Research Foundation (DFG), National Institutes of Health/National Center for Complementary and Integrative Health (NIH/NCCIH)

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Steps toward translocation-independent RNA polymerase inactivation by terminator ATPase rho.

Said, N., Hilal, T., Sunday, N.D., Khatri, A., Burger, J., Mielke, T., Belogurov, G.A., Loll, B., Sen, R., Artsimovitch, I., Wahl, M.C.

(2021) Science 371

• PubMed: 33243850 
• DOI: https://doi.org/10.1126/science.abd1673
• Primary Citation of Related Structures:  
  6Z9P, 6Z9Q, 6Z9R, 6Z9S, 6Z9T, 7ADB, 7ADC, 7ADD, 7ADE


• PubMed Abstract: 
  

  Factor-dependent transcription termination mechanisms are poorly understood. We determined a series of cryo-electron microscopy structures portraying the hexameric adenosine triphosphatase (ATPase) ρ on a pathway to terminating NusA/NusG-modified elongation complexes. An open ρ ring contacts NusA, NusG, and multiple regions of RNA polymerase, trapping and locally unwinding proximal upstream DNA. NusA wedges into the ρ ring, initially sequestering RNA. Upon deflection of distal upstream DNA over the RNA polymerase zinc-binding domain, NusA rotates underneath one capping ρ subunit, which subsequently captures RNA. After detachment of NusG and clamp opening, RNA polymerase loses its grip on the RNA:DNA hybrid and is inactivated. Our structural and functional analyses suggest that ρ, and other termination factors across life, may use analogous strategies to allosterically trap transcription complexes in a moribund state.

---

Organizational Affiliation: 

Laboratory of Structural Biochemistry, Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 12-mer - A6B1C1D1E1F1G1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 12-mer - A6B2C1D1E1F1 Local Symmetry: Helical - H  (Explore in 3D)
Local Stoichiometry: Homo 6-mer - A6 

Local Symmetry: Helical - H  (Explore in 3D)
Local Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 793.4 kDa 
• Atom Count: 51,610 
• Modelled Residue Count: 6,419 
• Deposited Residue Count: 6,717 
• Unique protein chains: 6
• Unique nucleic acid chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription termination factor Rho	A [auth f], B [auth a], C [auth b], D [auth c], E [auth d], F [auth e]	419	Escherichia coli	Mutation(s): 0  Gene Names: rho, AC789_1c41660, ACN002_3874, EL75_4398, EL79_4648, EL80_4555 EC: 3.6.4
UniProt
Find proteins for P0AG30 (Escherichia coli (strain K12)) Explore P0AG30  Go to UniProtKB:  P0AG30

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription termination/antitermination protein NusA	G [auth A]	497	Escherichia coli	Mutation(s): 0  Gene Names:  nusA, A6581_13525, A8C65_02280, A9819_18195, A9R57_12710, A9X72_02950, AC789_1c35390, ACN002_3262, ACN68_12470, ACN81_18560, ACU57_14555, ACU90_11675, AJ318_05130, AM270_15620, AM464_08470, AM465_07745, AMK83_06450, AML35_13995, ARC77_12295, AU473_05845, AUQ13_02965, AW059_15285, AWB10_02965, AWE53_007755, AWF59_011800, AWG78_015835, AZZ83_001443, B6V57_17910, B7C53_06460, B9N33_16970, BANRA_01789, BANRA_03826, BB545_09890, BFD68_02465, BHF03_08610, BHF46_07205, BHS87_17855, BIQ87_17925, BIU72_05295, BIZ41_14490, BJJ90_02880, BK373_10285, BK375_17175, BK383_15855, BMT91_09130, BN17_31141, BOH76_04800, BON63_14350, BON65_19800, BON66_12095, BON69_26670, BON71_25285, BON72_14050, BON75_23260, BON76_05640, BON94_12450, BON95_22130, BON96_06470, BTQ04_16590, BTQ06_11760, BUE81_19575, BvCms12BK_01027, BvCms2454_04844, BvCms28BK_03352, BvCms35BK_01521, BvCmsC61A_01481, BvCmsHHP001_01224, BvCmsHHP019_03131, BvCmsHHP056_02506, BvCmsKKP036_00266, BvCmsKKP061_00866, BvCmsKSNP073_02140, BvCmsKSNP081_00264, BvCmsKSNP120_03552, BvCmsKSP011_02072, BvCmsKSP024_00305, BvCmsKSP026_00480, BvCmsKSP045_01628, BvCmsKSP058_01862, BvCmsKSP067_01442, BvCmsKSP076_01608, BvCmsNSNP036_02129, BvCmsNSP006_04618, BvCmsNSP007_02229, BvCmsNSP047_04140, BvCmsOUP014_03610, BvCmsSINP011_04480, BvCmsSINP022_03541, BvCmsSIP019_00385, BvCmsSIP044_00115, BW690_05715, BWI89_22180, BWP17_10040, BXT93_11865, BZL31_05810, C2U48_17660, C4K41_03670, C5N07_18180, C5P44_00540, C7B06_16690, C7B07_10710, C9098_07900, C9114_15345, C9162_04220, C9E25_11380, C9E67_03485, C9Z23_02315, C9Z28_00495, C9Z29_07080, C9Z37_14770, C9Z39_14385, C9Z69_11065, C9Z70_06875, C9Z78_03425, CCZ14_12145, CCZ17_15255, CF006_16780, CG692_07185, CI693_03560, CI694_20950, CIG45_16160, CMR93_08950, CO706_14520, COD46_10645, CR538_03185, CR539_21135, CRD98_04825, CRM83_23610, CRT43_19205, CT146_02945, CUB99_16245, CVH05_10890, D2184_10395, D2185_00555, D3821_08435, D3C88_08620, D3O91_07735, D3Y67_18400, D4M06_11115, D6X76_04225, D7K63_12110, D7Y10_03480, D9D20_06165, D9D31_09845, D9D33_00520, D9E34_10725, D9E35_01735, D9E49_09485, D9F17_07090, D9G42_16790, D9H53_01085, D9H68_07450, D9H70_01530, D9I18_07065, D9I87_04950, D9I88_16540, D9I97_11390, D9J11_01020, D9J44_07740, D9J46_20540, D9J78_05020, D9K54_17930, D9L99_02550, DAH26_17205, DAH30_12985, DAH34_01870, DAH37_04365, DAH43_16670, DD762_19130, DEN89_09295, DEN97_16025, DEO04_19495, DEO19_06320, DJ487_12875, DJ503_10865, DL455_12590, DL545_03770, DMI04_04160, DMZ50_12310, DN627_01240, DN700_04485, DNB37_13595, DNR41_11075, DOY56_12135, DP258_01950, DQF57_03505, DQO13_01185, DS732_23585, DS966_19180, DTL43_04185, DTL90_07460, DTM10_07095, DU333_16810, DW236_11975, DXT69_05630, DXT71_00550, DXT73_13270, DXX80_009480, E0I42_14230, E0L04_19775, E2119_05760, E2127_02465, E2128_02605, E2129_05650, E2134_15705, E2135_07970, E5P22_12885, E5P28_13020, E5P37_13245, E5S42_11905, E5S47_02870, E5S61_05815, EA223_04935, EA250_06525, EA834_14925, EAI42_15045, EAI52_10000, EAX79_13120, EB509_07090, EB510_12295, EC1094V2_475, EC3234A_53c00480, EC382_14545, ECs4050, ECTO124_00620, ECTO6_00587, ED225_04160, ED607_10315, ED611_04170, ED648_02805, EF173_16895, EGT48_12340, EI021_03955, EI028_15160, EI032_08695, EIA21_02770, EIZ93_15765, EL75_0516, EL79_0538, EL80_0529, ELT20_05155, ELT23_06875, ELT33_08795, ELT34_10430, ELT48_07010, ELU82_09405, ELU96_15075, ELV05_02165, ELV13_06455, ELV24_06465, ELX79_02850, ELX83_01985, ELY05_03160, ELY23_12925, ELY24_06185, ELY50_10980, EO241_09470, EPS76_01475, EPS94_08345, EPT01_00525, EQ825_16425, ERS085365_00562, ERS085374_01906, ERS085379_00395, ERS085383_00719, ERS085386_00510, ERS085404_02209, ERS085406_02909, ERS085416_00332, ERS139211_00573, ERS150873_04324, EWK56_02885, EXM29_19885, ExPECSC065_00153, EXX06_09580, EXX13_07225, EXX55_08945, EXX71_13290, EXX78_16840, EXX87_04480, EYD11_02755, EYX82_02345, EYX99_26665, EYY34_08675, F1E19_22155, F7F18_01095, F7G01_14090, F7G03_16260, FKO60_06130, FNJ67_03685, FORC82_0590, FQ915_16570, FQR64_03145, FQU83_04620, FRV13_20655, FV293_08485, FV438_11000, FY127_14855, FZ043_21925, HmCms184_00231, HmCmsJML079_04422, HmCmsJML146_01153, HmCmsJML204_02228, HW43_20805, MJ49_14455, MS8345_03518, NCTC10089_00629, NCTC10090_03662, NCTC10767_01660, NCTC10865_00813, NCTC10974_00712, NCTC11022_03334, NCTC11126_02933, NCTC11341_01740, NCTC13127_00931, NCTC8179_06097, NCTC8621_00649, NCTC8959_03134, NCTC9045_00717, NCTC9055_02514, NCTC9058_01244, NCTC9062_02552, NCTC9075_00900, NCTC9081_01077, NCTC9111_00998, NCTC9119_00655, NCTC9434_00566, NCTC9701_00709, NCTC9703_05100, NCTC9706_02868, NCTC9969_00791, PGD_03947, PU06_19960, RG28_20965, RK56_014720, RX35_04256, SAMEA3472044_03332, SAMEA3472047_01872, SAMEA3472055_00400, SAMEA3472056_03072, SAMEA3472080_00945, SAMEA3472090_00548, SAMEA3472108_00102, SAMEA3472114_00483, SAMEA3472147_01878, SAMEA3485101_01710, SAMEA3752553_01187, SAMEA3752557_01875, SAMEA3752559_03273, SAMEA3752620_02341, SAMEA3753064_02936, SAMEA3753097_03302, SAMEA3753164_02300, SAMEA3753290_00148, SAMEA3753300_02131, SK85_03482, SY51_18275, U12A_03405, U14A_03402, UC41_24435, UN86_15490, UN91_15505, WQ89_06750, WR15_24550
UniProt
Find proteins for P0AFF6 (Escherichia coli (strain K12)) Explore P0AFF6  Go to UniProtKB:  P0AFF6

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit alpha	H [auth U], I [auth V]	329	Escherichia coli	Mutation(s): 0  Gene Names: rpoA, pez, phs, sez, b3295, JW3257 EC: 2.7.7.6
UniProt
Find proteins for P0A7Z4 (Escherichia coli (strain K12)) Explore P0A7Z4  Go to UniProtKB:  P0A7Z4

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit omega	J [auth W]	91	Escherichia coli	Mutation(s): 0  Gene Names: rpoZ, b3649, JW3624 EC: 2.7.7.6
UniProt
Find proteins for P0A800 (Escherichia coli (strain K12)) Explore P0A800  Go to UniProtKB:  P0A800

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit beta	K [auth X]	1,342	Escherichia coli	Mutation(s): 0  Gene Names: rpoB, Z5560, ECs4910 EC: 2.7.7.6
UniProt
Find proteins for P0A8V2 (Escherichia coli (strain K12)) Explore P0A8V2  Go to UniProtKB:  P0A8V2

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit beta'	L [auth Y]	1,416	Escherichia coli	Mutation(s): 0  Gene Names:  rpoC, A6581_23995, A6592_25550, A6V01_22675, A8C65_22170, A9P13_25145, A9R57_05210, A9X72_23915, AC789_1c43830, ACN002_4075, ACN68_05320, ACN81_23175, ACU57_23185, ACU90_26200, AM270_23445, AM446_26250, AM464_13270, AMK83_15405, AML07_02735, AML35_27125, APT94_08715, APZ14_17345, ARC77_17020, AU473_00845, AUQ13_12340, AUS26_26460, AW059_24210, AWB10_24945, AWE53_003330, AWG90_024870, AZZ83_004736, B7C53_21460, B9M99_23215, BANRA_02658, BANRA_02959, BANRA_04874, BANRA_05060, BB545_03160, BE963_11280, BHF03_13085, BHF46_21990, BHS81_23830, BHS87_22295, BIQ87_22860, BIU72_18810, BIZ41_20460, BJJ90_25120, BK292_28025, BK296_22655, BK373_27210, BK375_25315, BK383_27720, BMT49_21005, BMT91_03285, BN17_39521, BOH76_00535, BON63_20110, BON65_15085, BON66_14380, BON69_07675, BON71_08940, BON72_17275, BON75_02240, BON76_16220, BON83_01620, BON87_25670, BON91_27070, BON92_00590, BON94_22185, BON95_12860, BON96_11000, BTQ04_24495, BTQ06_27265, BUE81_05360, BvCms12BK_01429, BvCms2454_04769, BvCms28BK_04518, BvCms35BK_02095, BvCmsC61A_02150, BvCmsHHP001_05236, BvCmsHHP019_04451, BvCmsHHP056_02607, BvCmsKKP061_02982, BvCmsKSNP073_02854, BvCmsKSNP081_04479, BvCmsKSNP120_03436, BvCmsKSP011_02756, BvCmsKSP024_02908, BvCmsKSP026_03362, BvCmsKSP045_04187, BvCmsKSP058_05144, BvCmsKSP067_02566, BvCmsNSNP036_01157, BvCmsNSP006_02615, BvCmsNSP007_05019, BvCmsNSP047_00271, BvCmsNSP072_02893, BvCmsOUP014_03200, BvCmsSINP011_03932, BvCmsSINP022_04155, BvCmsSIP019_00812, BvCmsSIP044_03274, BVL39_05360, BW690_26755, BWI89_17380, BWP17_22705, BXT93_12730, BZL31_04385, BZL69_05725, C2U48_12715, C5715_03850, C5N07_24540, C5P01_26050, C5P44_24170, C7235_23705, C7B02_25785, C7B06_24625, C7B07_24550, C7B08_25760, C9098_22155, C9114_22905, C9141_23610, C9160_23380, C9162_26345, C9201_22200, C9306_18300, C9E25_22085, C9E67_28655, C9Z03_20320, C9Z23_22490, C9Z28_21990, C9Z29_22175, C9Z37_20920, C9Z39_11515, C9Z43_22460, C9Z69_21605, C9Z70_22865, CA593_06020, CDC27_21560, CF006_23865, CI641_013325, CI693_09915, CI694_22465, CIG45_23820, CJU63_23545, CMR93_21720, CO706_19510, COD30_25650, COD46_23645, CR538_24210, CR539_01675, CRD98_23235, CRE06_23980, CRM83_18625, CRX46_23050, CV83915_02065, CVH05_03875, CWS33_24550, D0X26_26125, D2184_25090, D2185_24280, D2188_26590, D3821_09095, D3822_07080, D3O91_23490, D3P01_24335, D3Y67_18045, D4M06_24790, D6T60_24455, D6X76_25460, D7K63_24300, D7K66_23610, D9D20_23630, D9D31_17430, D9D43_22315, D9E34_21770, D9E35_23870, D9F17_24240, D9G48_16815, D9H53_22620, D9H68_20330, D9H70_22065, D9H94_18950, D9I18_21370, D9I87_21145, D9I88_19005, D9I97_19385, D9J03_21580, D9J11_22220, D9J44_24520, D9J60_24650, D9J78_24495, D9K48_24885, D9L89_22865, D9X97_23575, DAH18_24925, DAH26_25940, DAH30_23845, DAH34_21555, DAH37_22570, DAH43_24880, DBQ99_24540, DD762_22280, DEN89_26510, DEN97_23710, DEO04_24305, DEO19_24555, DIV22_03745, DJ487_24740, DJ503_21515, DL455_22980, DL545_23680, DLW88_24480, DM102_24810, DMI04_23195, DN627_23155, DN700_22970, DNB37_22370, DND16_22020, DOY56_23525, DP258_23435, DP277_21385, DQE83_24465, DQF57_23790, DQO13_23780, DTL43_13700, DTL90_24530, DTM10_25855, DU309_24205, DU321_23425, DW236_24545, DXT69_22805, DXT71_22310, DXT73_22940, DXX80_014100, E0I42_21900, E0K84_22885, E0L12_22045, E2112_20360, E2119_22340, E2127_20900, E2128_03185, E2129_21295, E2134_22790, E2135_19330, E4K55_23345, E5P22_12650, E5P28_08825, E5P37_21450, E5S42_21540, E5S47_23025, E5S58_21685, E5S61_22375, EA223_18745, EA410_23470, EAI42_07590, EAI46_11695, EAI52_22800, EAX79_24760, EB509_19940, EB510_23045, EB515_23245, EC1094V2_4282, EC3234A_76c00080, EC3426_00300, EC382_20005, ECs4911, ECTO6_04517, ED225_22845, ED607_18495, ED611_23935, ED648_18905, ED903_15585, ED944_23315, EEA45_21100, EEP23_09490, EF173_24455, EHH55_00715, EHJ36_22705, EI021_22070, EI028_22520, EI032_21250, EIA21_22525, EIZ93_16335, EJC75_19635, EL75_4201, EL79_4407, EL80_4314, ELT20_20720, ELT23_22660, ELU85_23590, ELV08_18690, ELV28_22250, ELY05_18165, EO241_25775, EPT01_21680, EQ820_22870, EQ823_21565, ERS085365_04275, ERS085366_03840, ERS085374_04587, ERS085379_04695, ERS085383_04736, ERS085386_04630, ERS085404_04514, ERS085416_04248, ERS139211_00022, ERS150873_04406, ERS150876_04849, EST51_23860, EVY14_16840, EXM29_02400, EXX06_24525, EXX23_22305, EXX24_23170, EXX53_21005, EXX55_24440, EXX71_22255, EXX78_24010, EXX87_24980, EYD11_21590, EYX82_16690, EYY34_19805, EYY78_22660, F1E13_23750, F1E19_21825, F7F11_23815, F7F18_24055, F7F29_25930, F7G01_23350, F7G03_24075, FAF34_028960, FNJ69_19110, FNJ83_24800, FORC82_4521, FQ915_26150, FQR64_21800, FRV13_16215, FV293_23430, FV438_22435, FWK02_01680, FY127_17750, FZ043_01140, GJ11_25200, HmCms184_03861, HmCmsJML074_03182, HmCmsJML079_04902, HmCmsJML204_03257, HMPREF3040_01778, HW43_01585, MJ49_09425, NCTC10082_02080, NCTC10090_02779, NCTC10429_00081, NCTC10865_05894, NCTC10974_05350, NCTC11181_01964, NCTC12950_05213, NCTC13127_06163, NCTC13148_04414, NCTC7927_05248, NCTC8500_05324, NCTC8960_02339, NCTC9036_04648, NCTC9044_02305, NCTC9045_05541, NCTC9050_02817, NCTC9055_01666, NCTC9058_02148, NCTC9062_03445, NCTC9077_05932, NCTC9111_04954, NCTC9119_05054, NCTC9701_04995, NCTC9706_02002, NCTC9777_01117, NCTC9969_04931, PGD_00622, PU06_15490, RG28_25345, RK56_017400, RX35_03755, SAMEA3472043_04866, SAMEA3472044_04873, SAMEA3472047_03500, SAMEA3472055_04947, SAMEA3472056_05309, SAMEA3472070_05093, SAMEA3472080_04815, SAMEA3472090_05006, SAMEA3472108_04971, SAMEA3472110_05082, SAMEA3472112_05167, SAMEA3472114_04967, SAMEA3472147_04120, SAMEA3484427_04984, SAMEA3484429_04987, SAMEA3484434_04725, SAMEA3485101_05497, SAMEA3485113_04495, SAMEA3752372_05079, SAMEA3752553_04905, SAMEA3752557_04844, SAMEA3752559_04855, SAMEA3752620_04699, SAMEA3753064_05329, SAMEA3753097_04845, SAMEA3753164_04786, SAMEA3753290_00018, SAMEA3753300_04884, SK85_04319, UC41_25650, UN86_14180, UN91_25445, WQ89_24675, WR15_01490, YDC107_2702 EC: 2.7.7.6
UniProt
Find proteins for P0A8T7 (Escherichia coli (strain K12)) Explore P0A8T7  Go to UniProtKB:  P0A8T7

Entity ID: 7
Molecule	Chains	Length	Organism	Image
ntDNA	M [auth K]	50	synthetic construct

Entity ID: 8
Molecule	Chains	Length	Organism	Image
tDNA	N [auth L]	50	synthetic construct

Entity ID: 9
Molecule	Chains	Length	Organism	Image
rut RNA	O [auth R]	99	synthetic construct

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	BA [auth e], P [auth a], S [auth b], V [auth c], Z [auth d]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
BEF	DA [auth e], R [auth a], U [auth b], X [auth c], Y [auth c]	BERYLLIUM TRIFLUORIDE ION Be F3 OGIAHMCCNXDTIE-UHFFFAOYSA-K
ZN	FA [auth Y], GA [auth Y]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	AA [auth d], CA [auth e], EA [auth Y], Q [auth a], T [auth b], W [auth c]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	2.14

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-11-25 
Deposition Author(s): Said, N., Hilal, T., Loll, B., Wahl, C.M.

---

Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	HA 2549/15-2
German Research Foundation (DFG)	Germany	RTG 2473-1
German Research Foundation (DFG)	Germany	WA 1126/11-1
National Institutes of Health/National Center for Complementary and Integrative Health (NIH/NCCIH)	United States	GM067153

Revision History  

• Version 1.0: 2020-11-25
  Type: Initial release
  
• Version 1.1: 2021-02-03
  Changes: Database references