7ADC

Transcription termination intermediate complex 3 delta NusG


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


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

  • 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.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription termination factor Rho419Escherichia coliMutation(s): 0 
Gene Names: rhoAC789_1c41660ACN002_3874EL75_4398EL79_4648EL80_4555
EC: 3.6.4
UniProt
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UniProt GroupP0AG30
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription termination/antitermination protein NusAG [auth A]497Escherichia coliMutation(s): 0 
Gene Names: 
nusAA6581_13525A8C65_02280A9819_18195A9R57_12710A9X72_02950AC789_1c35390ACN002_3262ACN68_12470ACN81_18560ACU57_14555ACU90_11675AJ318_05130AM270_15620AM464_08470AM465_07745AMK83_06450AML35_13995ARC77_12295AU473_05845AUQ13_02965AW059_15285AWB10_02965AWE53_007755AWF59_011800AWG78_015835AZZ83_001443B6V57_17910B7C53_06460B9N33_16970BANRA_01789BANRA_03826BB545_09890BFD68_02465BHF03_08610BHF46_07205BHS87_17855BIQ87_17925BIU72_05295BIZ41_14490BJJ90_02880BK373_10285BK375_17175BK383_15855BMT91_09130BN17_31141BOH76_04800BON63_14350BON65_19800BON66_12095BON69_26670BON71_25285BON72_14050BON75_23260BON76_05640BON94_12450BON95_22130BON96_06470BTQ04_16590BTQ06_11760BUE81_19575BvCms12BK_01027BvCms2454_04844BvCms28BK_03352BvCms35BK_01521BvCmsC61A_01481BvCmsHHP001_01224BvCmsHHP019_03131BvCmsHHP056_02506BvCmsKKP036_00266BvCmsKKP061_00866BvCmsKSNP073_02140BvCmsKSNP081_00264BvCmsKSNP120_03552BvCmsKSP011_02072BvCmsKSP024_00305BvCmsKSP026_00480BvCmsKSP045_01628BvCmsKSP058_01862BvCmsKSP067_01442BvCmsKSP076_01608BvCmsNSNP036_02129BvCmsNSP006_04618BvCmsNSP007_02229BvCmsNSP047_04140BvCmsOUP014_03610BvCmsSINP011_04480BvCmsSINP022_03541BvCmsSIP019_00385BvCmsSIP044_00115BW690_05715BWI89_22180BWP17_10040BXT93_11865BZL31_05810C2U48_17660C4K41_03670C5N07_18180C5P44_00540C7B06_16690C7B07_10710C9098_07900C9114_15345C9162_04220C9E25_11380C9E67_03485C9Z23_02315C9Z28_00495C9Z29_07080C9Z37_14770C9Z39_14385C9Z69_11065C9Z70_06875C9Z78_03425CCZ14_12145CCZ17_15255CF006_16780CG692_07185CI693_03560CI694_20950CIG45_16160CMR93_08950CO706_14520COD46_10645CR538_03185CR539_21135CRD98_04825CRM83_23610CRT43_19205CT146_02945CUB99_16245CVH05_10890D2184_10395D2185_00555D3821_08435D3C88_08620D3O91_07735D3Y67_18400D4M06_11115D6X76_04225D7K63_12110D7Y10_03480D9D20_06165D9D31_09845D9D33_00520D9E34_10725D9E35_01735D9E49_09485D9F17_07090D9G42_16790D9H53_01085D9H68_07450D9H70_01530D9I18_07065D9I87_04950D9I88_16540D9I97_11390D9J11_01020D9J44_07740D9J46_20540D9J78_05020D9K54_17930D9L99_02550DAH26_17205DAH30_12985DAH34_01870DAH37_04365DAH43_16670DD762_19130DEN89_09295DEN97_16025DEO04_19495DEO19_06320DJ487_12875DJ503_10865DL455_12590DL545_03770DMI04_04160DMZ50_12310DN627_01240DN700_04485DNB37_13595DNR41_11075DOY56_12135DP258_01950DQF57_03505DQO13_01185DS732_23585DS966_19180DTL43_04185DTL90_07460DTM10_07095DU333_16810DW236_11975DXT69_05630DXT71_00550DXT73_13270DXX80_009480E0I42_14230E0L04_19775E2119_05760E2127_02465E2128_02605E2129_05650E2134_15705E2135_07970E5P22_12885E5P28_13020E5P37_13245E5S42_11905E5S47_02870E5S61_05815EA223_04935EA250_06525EA834_14925EAI42_15045EAI52_10000EAX79_13120EB509_07090EB510_12295EC1094V2_475EC3234A_53c00480EC382_14545ECs4050ECTO124_00620ECTO6_00587ED225_04160ED607_10315ED611_04170ED648_02805EF173_16895EGT48_12340EI021_03955EI028_15160EI032_08695EIA21_02770EIZ93_15765EL75_0516EL79_0538EL80_0529ELT20_05155ELT23_06875ELT33_08795ELT34_10430ELT48_07010ELU82_09405ELU96_15075ELV05_02165ELV13_06455ELV24_06465ELX79_02850ELX83_01985ELY05_03160ELY23_12925ELY24_06185ELY50_10980EO241_09470EPS76_01475EPS94_08345EPT01_00525EQ825_16425ERS085365_00562ERS085374_01906ERS085379_00395ERS085383_00719ERS085386_00510ERS085404_02209ERS085406_02909ERS085416_00332ERS139211_00573ERS150873_04324EWK56_02885EXM29_19885ExPECSC065_00153EXX06_09580EXX13_07225EXX55_08945EXX71_13290EXX78_16840EXX87_04480EYD11_02755EYX82_02345EYX99_26665EYY34_08675F1E19_22155F7F18_01095F7G01_14090F7G03_16260FKO60_06130FNJ67_03685FORC82_0590FQ915_16570FQR64_03145FQU83_04620FRV13_20655FV293_08485FV438_11000FY127_14855FZ043_21925HmCms184_00231HmCmsJML079_04422HmCmsJML146_01153HmCmsJML204_02228HW43_20805MJ49_14455MS8345_03518NCTC10089_00629NCTC10090_03662NCTC10767_01660NCTC10865_00813NCTC10974_00712NCTC11022_03334NCTC11126_02933NCTC11341_01740NCTC13127_00931NCTC8179_06097NCTC8621_00649NCTC8959_03134NCTC9045_00717NCTC9055_02514NCTC9058_01244NCTC9062_02552NCTC9075_00900NCTC9081_01077NCTC9111_00998NCTC9119_00655NCTC9434_00566NCTC9701_00709NCTC9703_05100NCTC9706_02868NCTC9969_00791PGD_03947PU06_19960RG28_20965RK56_014720RX35_04256SAMEA3472044_03332SAMEA3472047_01872SAMEA3472055_00400SAMEA3472056_03072SAMEA3472080_00945SAMEA3472090_00548SAMEA3472108_00102SAMEA3472114_00483SAMEA3472147_01878SAMEA3485101_01710SAMEA3752553_01187SAMEA3752557_01875SAMEA3752559_03273SAMEA3752620_02341SAMEA3753064_02936SAMEA3753097_03302SAMEA3753164_02300SAMEA3753290_00148SAMEA3753300_02131SK85_03482SY51_18275U12A_03405U14A_03402UC41_24435UN86_15490UN91_15505WQ89_06750WR15_24550

UniProt
Find proteins for P0AFF6 (Escherichia coli (strain K12))
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UniProt GroupP0AFF6
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit alphaH [auth U],
I [auth V]
329Escherichia coliMutation(s): 0 
Gene Names: rpoApezphssezb3295JW3257
EC: 2.7.7.6
UniProt
Find proteins for P0A7Z4 (Escherichia coli (strain K12))
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UniProt GroupP0A7Z4
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit omegaJ [auth W]91Escherichia coliMutation(s): 0 
Gene Names: rpoZb3649JW3624
EC: 2.7.7.6
UniProt
Find proteins for P0A800 (Escherichia coli (strain K12))
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UniProt GroupP0A800
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit betaK [auth X]1,342Escherichia coliMutation(s): 0 
Gene Names: rpoBZ5560ECs4910
EC: 2.7.7.6
UniProt
Find proteins for P0A8V2 (Escherichia coli (strain K12))
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UniProt GroupP0A8V2
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta'L [auth Y]1,416Escherichia coliMutation(s): 0 
Gene Names: 
rpoCA6581_23995A6592_25550A6V01_22675A8C65_22170A9P13_25145A9R57_05210A9X72_23915AC789_1c43830ACN002_4075ACN68_05320ACN81_23175ACU57_23185ACU90_26200AM270_23445AM446_26250AM464_13270AMK83_15405AML07_02735AML35_27125APT94_08715APZ14_17345ARC77_17020AU473_00845AUQ13_12340AUS26_26460AW059_24210AWB10_24945AWE53_003330AWG90_024870AZZ83_004736B7C53_21460B9M99_23215BANRA_02658BANRA_02959BANRA_04874BANRA_05060BB545_03160BE963_11280BHF03_13085BHF46_21990BHS81_23830BHS87_22295BIQ87_22860BIU72_18810BIZ41_20460BJJ90_25120BK292_28025BK296_22655BK373_27210BK375_25315BK383_27720BMT49_21005BMT91_03285BN17_39521BOH76_00535BON63_20110BON65_15085BON66_14380BON69_07675BON71_08940BON72_17275BON75_02240BON76_16220BON83_01620BON87_25670BON91_27070BON92_00590BON94_22185BON95_12860BON96_11000BTQ04_24495BTQ06_27265BUE81_05360BvCms12BK_01429BvCms2454_04769BvCms28BK_04518BvCms35BK_02095BvCmsC61A_02150BvCmsHHP001_05236BvCmsHHP019_04451BvCmsHHP056_02607BvCmsKKP061_02982BvCmsKSNP073_02854BvCmsKSNP081_04479BvCmsKSNP120_03436BvCmsKSP011_02756BvCmsKSP024_02908BvCmsKSP026_03362BvCmsKSP045_04187BvCmsKSP058_05144BvCmsKSP067_02566BvCmsNSNP036_01157BvCmsNSP006_02615BvCmsNSP007_05019BvCmsNSP047_00271BvCmsNSP072_02893BvCmsOUP014_03200BvCmsSINP011_03932BvCmsSINP022_04155BvCmsSIP019_00812BvCmsSIP044_03274BVL39_05360BW690_26755BWI89_17380BWP17_22705BXT93_12730BZL31_04385BZL69_05725C2U48_12715C5715_03850C5N07_24540C5P01_26050C5P44_24170C7235_23705C7B02_25785C7B06_24625C7B07_24550C7B08_25760C9098_22155C9114_22905C9141_23610C9160_23380C9162_26345C9201_22200C9306_18300C9E25_22085C9E67_28655C9Z03_20320C9Z23_22490C9Z28_21990C9Z29_22175C9Z37_20920C9Z39_11515C9Z43_22460C9Z69_21605C9Z70_22865CA593_06020CDC27_21560CF006_23865CI641_013325CI693_09915CI694_22465CIG45_23820CJU63_23545CMR93_21720CO706_19510COD30_25650COD46_23645CR538_24210CR539_01675CRD98_23235CRE06_23980CRM83_18625CRX46_23050CV83915_02065CVH05_03875CWS33_24550D0X26_26125D2184_25090D2185_24280D2188_26590D3821_09095D3822_07080D3O91_23490D3P01_24335D3Y67_18045D4M06_24790D6T60_24455D6X76_25460D7K63_24300D7K66_23610D9D20_23630D9D31_17430D9D43_22315D9E34_21770D9E35_23870D9F17_24240D9G48_16815D9H53_22620D9H68_20330D9H70_22065D9H94_18950D9I18_21370D9I87_21145D9I88_19005D9I97_19385D9J03_21580D9J11_22220D9J44_24520D9J60_24650D9J78_24495D9K48_24885D9L89_22865D9X97_23575DAH18_24925DAH26_25940DAH30_23845DAH34_21555DAH37_22570DAH43_24880DBQ99_24540DD762_22280DEN89_26510DEN97_23710DEO04_24305DEO19_24555DIV22_03745DJ487_24740DJ503_21515DL455_22980DL545_23680DLW88_24480DM102_24810DMI04_23195DN627_23155DN700_22970DNB37_22370DND16_22020DOY56_23525DP258_23435DP277_21385DQE83_24465DQF57_23790DQO13_23780DTL43_13700DTL90_24530DTM10_25855DU309_24205DU321_23425DW236_24545DXT69_22805DXT71_22310DXT73_22940DXX80_014100E0I42_21900E0K84_22885E0L12_22045E2112_20360E2119_22340E2127_20900E2128_03185E2129_21295E2134_22790E2135_19330E4K55_23345E5P22_12650E5P28_08825E5P37_21450E5S42_21540E5S47_23025E5S58_21685E5S61_22375EA223_18745EA410_23470EAI42_07590EAI46_11695EAI52_22800EAX79_24760EB509_19940EB510_23045EB515_23245EC1094V2_4282EC3234A_76c00080EC3426_00300EC382_20005ECs4911ECTO6_04517ED225_22845ED607_18495ED611_23935ED648_18905ED903_15585ED944_23315EEA45_21100EEP23_09490EF173_24455EHH55_00715EHJ36_22705EI021_22070EI028_22520EI032_21250EIA21_22525EIZ93_16335EJC75_19635EL75_4201EL79_4407EL80_4314ELT20_20720ELT23_22660ELU85_23590ELV08_18690ELV28_22250ELY05_18165EO241_25775EPT01_21680EQ820_22870EQ823_21565ERS085365_04275ERS085366_03840ERS085374_04587ERS085379_04695ERS085383_04736ERS085386_04630ERS085404_04514ERS085416_04248ERS139211_00022ERS150873_04406ERS150876_04849EST51_23860EVY14_16840EXM29_02400EXX06_24525EXX23_22305EXX24_23170EXX53_21005EXX55_24440EXX71_22255EXX78_24010EXX87_24980EYD11_21590EYX82_16690EYY34_19805EYY78_22660F1E13_23750F1E19_21825F7F11_23815F7F18_24055F7F29_25930F7G01_23350F7G03_24075FAF34_028960FNJ69_19110FNJ83_24800FORC82_4521FQ915_26150FQR64_21800FRV13_16215FV293_23430FV438_22435FWK02_01680FY127_17750FZ043_01140GJ11_25200HmCms184_03861HmCmsJML074_03182HmCmsJML079_04902HmCmsJML204_03257HMPREF3040_01778HW43_01585MJ49_09425NCTC10082_02080NCTC10090_02779NCTC10429_00081NCTC10865_05894NCTC10974_05350NCTC11181_01964NCTC12950_05213NCTC13127_06163NCTC13148_04414NCTC7927_05248NCTC8500_05324NCTC8960_02339NCTC9036_04648NCTC9044_02305NCTC9045_05541NCTC9050_02817NCTC9055_01666NCTC9058_02148NCTC9062_03445NCTC9077_05932NCTC9111_04954NCTC9119_05054NCTC9701_04995NCTC9706_02002NCTC9777_01117NCTC9969_04931PGD_00622PU06_15490RG28_25345RK56_017400RX35_03755SAMEA3472043_04866SAMEA3472044_04873SAMEA3472047_03500SAMEA3472055_04947SAMEA3472056_05309SAMEA3472070_05093SAMEA3472080_04815SAMEA3472090_05006SAMEA3472108_04971SAMEA3472110_05082SAMEA3472112_05167SAMEA3472114_04967SAMEA3472147_04120SAMEA3484427_04984SAMEA3484429_04987SAMEA3484434_04725SAMEA3485101_05497SAMEA3485113_04495SAMEA3752372_05079SAMEA3752553_04905SAMEA3752557_04844SAMEA3752559_04855SAMEA3752620_04699SAMEA3753064_05329SAMEA3753097_04845SAMEA3753164_04786SAMEA3753290_00018SAMEA3753300_04884SK85_04319UC41_25650UN86_14180UN91_25445WQ89_24675WR15_01490YDC107_2702

EC: 2.7.7.6
UniProt
Find proteins for P0A8T7 (Escherichia coli (strain K12))
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UniProt GroupP0A8T7
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Entity ID: 7
MoleculeChains LengthOrganismImage
ntDNAM [auth K]50synthetic construct
Sequence Annotations
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Entity ID: 8
MoleculeChains LengthOrganismImage
tDNAN [auth L]50synthetic construct
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Entity ID: 9
MoleculeChains LengthOrganismImage
rut RNAO [auth R]99synthetic construct
Sequence Annotations
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Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download Ideal Coordinates CCD File 
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
Query on BEF

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DA [auth e],
R [auth a],
U [auth b],
X [auth c],
Y [auth c]
BERYLLIUM TRIFLUORIDE ION
Be F3
OGIAHMCCNXDTIE-UHFFFAOYSA-K
ZN
Query on ZN

Download Ideal Coordinates CCD File 
FA [auth Y],
GA [auth Y]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AA [auth d]
CA [auth e]
EA [auth Y]
Q [auth a]
T [auth b]
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: 4.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC2.14

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyHA 2549/15-2
German Research Foundation (DFG)GermanyRTG 2473-1
German Research Foundation (DFG)GermanyWA 1126/11-1
National Institutes of Health/National Center for Complementary and Integrative Health (NIH/NCCIH)United StatesGM067153

Revision History  (Full details and data files)

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