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- PDB-6p1c: Transcription antitermination factor Q21, SeMet-derivative -

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Basic information

Entry
Database: PDB / ID: 6p1c
TitleTranscription antitermination factor Q21, SeMet-derivative
ComponentsQ protein
KeywordsGENE REGULATION / RNA polymerase / DNA Binding / transcription / Q-dependent antitermination / Q antitermination factor
Function / homologyBacteriophage 933W, GpQ / Phage antitermination protein Q / negative regulation of termination of DNA-templated transcription / DNA binding / Q protein
Function and homology information
Biological speciesPhage 21 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.005 Å
AuthorsYin, Z. / Ebright, R.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)GM041376 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2019
Title: Structural basis of Q-dependent antitermination.
Authors: Zhou Yin / Jason T Kaelber / Richard H Ebright /
Abstract: Lambdoid bacteriophage Q protein mediates the switch from middle to late bacteriophage gene expression by enabling RNA polymerase (RNAP) to read through transcription terminators preceding ...Lambdoid bacteriophage Q protein mediates the switch from middle to late bacteriophage gene expression by enabling RNA polymerase (RNAP) to read through transcription terminators preceding bacteriophage late genes. Q loads onto RNAP engaged in promoter-proximal pausing at a Q binding element (QBE) and adjacent sigma-dependent pause element (SDPE) to yield a Q-loading complex, and Q subsequently translocates with RNAP as a pausing-deficient, termination-deficient Q-loaded complex. Here, we report high-resolution structures of 4 states on the pathway of antitermination by Q from bacteriophage 21 (Q21): Q21, the Q21-QBE complex, the Q21-loading complex, and the Q21-loaded complex. The results show that Q21 forms a torus, a "nozzle," that narrows and extends the RNAP RNA-exit channel, extruding topologically linked single-stranded RNA and preventing the formation of pause and terminator hairpins.
History
DepositionMay 19, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 25, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Q protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0792
Polymers19,0441
Non-polymers351
Water99155
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.466, 88.595, 31.186
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Q protein


Mass: 19043.953 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phage 21 (virus) / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9XJQ6
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.1 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 20% PEG 8000 100 mM HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 11573 / % possible obs: 99.7 % / Redundancy: 12.2 % / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.018 / Rrim(I) all: 0.062 / Χ2: 0.927 / Net I/σ(I): 10.7 / Num. measured all: 140779
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.0312.61.1075630.8250.3191.1531.007100
2.03-2.0712.50.965760.8790.27911.00199.8
2.07-2.1112.40.8155620.9110.2360.850.951100
2.11-2.1512.50.5945570.9550.1720.6190.91899.6
2.15-2.212.10.4715640.9630.1380.4910.889100
2.2-2.2511.80.3915730.9640.1160.4080.95399.1
2.25-2.3110.90.2885650.9720.0890.3020.88599.8
2.31-2.3713.10.2535620.9870.0710.2630.899100
2.37-2.4412.90.2125680.9870.0610.2210.852100
2.44-2.5212.80.1755780.9890.050.1820.851100
2.52-2.6112.20.1435820.9930.0420.1490.852100
2.61-2.7112.20.115600.9950.0320.1150.855100
2.71-2.84110.0765880.9950.0230.080.84299.2
2.84-2.9912.90.0685590.9960.0190.070.895100
2.99-3.1712.70.0525840.9970.0150.0540.905100
3.17-3.4212.40.045860.9980.0120.0420.931100
3.42-3.7611.40.035850.9980.0090.0310.93899
3.76-4.3112.60.035950.9980.0090.0311.066100
4.31-5.4311.40.0286050.9980.0080.0291.03298.9
5.43-5011.10.0256610.9980.0080.0261.01499

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACT3.25data extraction
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.005→44.297 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 22.3
RfactorNum. reflection% reflection
Rfree0.2359 2046 10.01 %
Rwork0.1967 --
obs0.2007 11457 95.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 155.89 Å2 / Biso mean: 42.1733 Å2 / Biso min: 9.57 Å2
Refinement stepCycle: final / Resolution: 2.005→44.297 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1190 0 1 55 1246
Biso mean--48.23 35.92 -
Num. residues----150
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0051-2.05170.27891090.2347905101468
2.0517-2.1030.29641160.24411027114382
2.103-2.15990.22161310.21291164129591
2.1599-2.22340.26671410.21241290143197
2.2234-2.29520.27111360.20841211134798
2.2952-2.37720.20111380.199212941432100
2.3772-2.47240.30051410.197112891430100
2.4724-2.58490.27991450.206312911436100
2.5849-2.72120.22811410.198312381379100
2.7212-2.89160.23021420.20381270141299
2.8916-3.11490.25351440.206613051449100
3.1149-3.42820.23571390.197812801419100
3.4282-3.9240.21521460.18021280142699
3.924-4.94280.221370.165912671404100
4.9428-44.30830.20611400.20171274141499
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.58890.57051.35764.04740.9644.3608-0.0859-0.1439-0.65020.38730.07831.24440.2289-0.58830.03480.2028-0.02390.06850.174-0.01980.34631.457813.348127.7106
24.1219-1.0362-2.73283.7271-0.29653.6583-0.2712-0.53280.72151.06370.1763-0.8424-0.35161.00880.17480.3356-0.0211-0.1850.3189-0.05260.419345.676325.507531.1081
37.4299-5.9471-3.6334.85653.02842.3602-0.2852-1.92430.60791.7626-0.61910.3607-0.0413-0.15560.63151.3409-0.43110.10350.8871-0.21390.926636.367232.967838.6179
45.13380.497-0.8812.6120.71234.9981-0.0604-0.5202-0.16030.81370.08190.14360.1791-0.21450.01740.2910.04730.03540.1842-0.0030.114240.493916.152632.0011
56.9436-1.0056-2.43694.9421-0.19473.5136-0.13770.44040.0741-0.0652-0.12530.2617-0.4302-0.0039-0.32810.1174-0.01390.00160.16640.00560.109435.663225.052224.0018
61.78550.25710.950.240.30357.0378-0.22060.22780.4155-0.230.20890.6463-1.3533-0.43430.54730.32740.054-0.04620.1970.04050.358825.847533.82123.0347
77.0106-4.4529-1.98864.2833-0.74333.3048-0.70531.07621.3083-1.00780.4438-0.9044-0.63510.73411.01440.8779-0.2273-0.06260.81630.05240.791625.951836.636312.317
82.4825-0.32750.47021.2112-0.26362.5695-0.04070.205-0.5683-0.1654-0.22370.38750.822-0.3371-0.35610.19440.0074-0.14480.1716-0.15490.277834.978212.675822.0697
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 28 )A6 - 28
2X-RAY DIFFRACTION2chain 'A' and (resid 29 through 46 )A29 - 46
3X-RAY DIFFRACTION3chain 'A' and (resid 47 through 51 )A47 - 51
4X-RAY DIFFRACTION4chain 'A' and (resid 52 through 74 )A52 - 74
5X-RAY DIFFRACTION5chain 'A' and (resid 75 through 93 )A75 - 93
6X-RAY DIFFRACTION6chain 'A' and (resid 94 through 103 )A94 - 103
7X-RAY DIFFRACTION7chain 'A' and (resid 104 through 122 )A104 - 122
8X-RAY DIFFRACTION8chain 'A' and (resid 123 through 159 )A123 - 159

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