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- PDB-6p1b: Transcription antitermination factor Q21 -

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Basic information

Entry
Database: PDB / ID: 6p1b
TitleTranscription antitermination factor Q21
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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.942 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
Revision 1.4Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Q protein
B: Q protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,90515
Polymers37,3382
Non-polymers56713
Water2,846158
1
A: Q protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8736
Polymers18,6691
Non-polymers2045
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Q protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0329
Polymers18,6691
Non-polymers3638
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)32.233, 78.905, 68.497
Angle α, β, γ (deg.)90.000, 98.680, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 7 through 13 or resid 15...
21(chain B and (resid 7 through 13 or resid 15...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 7 through 13 or resid 15...A7 - 13
121(chain A and (resid 7 through 13 or resid 15...A15 - 47
131(chain A and (resid 7 through 13 or resid 15...A53 - 98
141(chain A and (resid 7 through 13 or resid 15...A100 - 110
151(chain A and (resid 7 through 13 or resid 15...A7 - 156
161(chain A and (resid 7 through 13 or resid 15...A7 - 156
171(chain A and (resid 7 through 13 or resid 15...A7 - 156
181(chain A and (resid 7 through 13 or resid 15...A7 - 156
191(chain A and (resid 7 through 13 or resid 15...A7 - 156
211(chain B and (resid 7 through 13 or resid 15...B7 - 13
221(chain B and (resid 7 through 13 or resid 15...B15 - 98
231(chain B and (resid 7 through 13 or resid 15...B100 - 1
241(chain B and (resid 7 through 13 or resid 15...B6 - 156
251(chain B and (resid 7 through 13 or resid 15...B154
261(chain B and (resid 7 through 13 or resid 15...B6 - 156
271(chain B and (resid 7 through 13 or resid 15...B6 - 156
281(chain B and (resid 7 through 13 or resid 15...B6 - 156
291(chain B and (resid 7 through 13 or resid 15...B6 - 156
2101(chain B and (resid 7 through 13 or resid 15...B6 - 156

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Components

#1: Protein Q protein


Mass: 18668.789 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phage 21 (virus) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9XJQ6
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 2.31 Å3/Da / Density % sol: 46.67 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 3350, 200 mM Ammonium chloride

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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: Dec 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.94→50 Å / Num. obs: 24533 / % possible obs: 97.8 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.04 / Rrim(I) all: 0.075 / Χ2: 0.809 / Net I/σ(I): 11.9 / Num. measured all: 81795
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.94-1.972.90.50611190.6990.3540.6210.78190
1.97-2.013.20.41112360.8260.2640.490.79696.1
2.01-2.053.50.39611930.860.2450.4670.77598.5
2.05-2.093.50.32912200.8910.2040.3880.84698.1
2.09-2.143.40.25312400.9350.1590.30.84398.3
2.14-2.183.30.21412070.9430.1360.2540.86798.4
2.18-2.243.30.18512230.9340.1190.2210.89997.5
2.24-2.33.10.15612270.9390.1030.1880.9395.9
2.3-2.373.40.13312130.9590.0840.1570.94299
2.37-2.443.50.1212410.9720.0750.1420.88399.1
2.44-2.533.50.10712360.970.0660.1260.84398.7
2.53-2.633.40.09412330.9770.0590.1110.88198.7
2.63-2.753.30.07912430.980.050.0940.81198.8
2.75-2.93.20.0712020.9840.0460.0840.77496.4
2.9-3.083.50.06612380.9810.0410.0780.71999.3
3.08-3.323.40.06212370.9840.0390.0730.72398.8
3.32-3.653.30.05612330.9870.0370.0680.71397.9
3.65-4.183.50.05712600.9860.0350.0670.68399.2
4.18-5.263.40.05712610.9840.0360.0680.66898.9
5.26-503.30.04812710.9910.0310.0580.82498.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6P1C

6p1c


Resolution: 1.942→39.453 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 21.86
RfactorNum. reflection% reflection
Rfree0.2255 1996 8.4 %
Rwork0.1845 --
obs0.188 23761 94.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 126.41 Å2 / Biso mean: 31.4145 Å2 / Biso min: 7.75 Å2
Refinement stepCycle: final / Resolution: 1.942→39.453 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2369 0 49 158 2576
Biso mean--52.49 33.63 -
Num. residues----296
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1317X-RAY DIFFRACTION10.888TORSIONAL
12B1317X-RAY DIFFRACTION10.888TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9418-1.99030.2616830.2291984106759
1.9903-2.04410.27291270.23051464159189
2.0441-2.10430.28761540.22481547170197
2.1043-2.17220.2471560.20651614177098
2.1722-2.24980.22511420.19791575171798
2.2498-2.33990.26571390.19331607174697
2.3399-2.44640.22071500.18431614176499
2.4464-2.57530.23261550.18581599175499
2.5753-2.73660.22611450.18151640178599
2.7366-2.94790.22951460.19441595174197
2.9479-3.24440.24691460.18511624177099
3.2444-3.71360.21831440.17521590173498
3.7136-4.67750.18531530.15111664181799
4.6775-39.46060.20411560.18091648180499
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)
12.2087-1.4625-1.13955.64423.02252.32750.07970.07220.0305-0.8922-0.1452-0.064-0.08210.0725-0.0560.20560.01860.00330.10780.0190.12837.6221-2.4234-4.5554
21.86190.1283-1.08383.4081-0.19075.36570.053-0.10170.1030.3016-0.0001-0.2125-0.01930.1399-0.01920.1436-0.0508-0.00360.08680.01430.09919.7837-5.412311.2133
32.0763-1.78751.4294.011.04823.08440.0556-0.4042-0.52970.77210.06110.80160.2904-0.45-0.03970.419-0.16470.01930.31330.10580.30684.5391-14.664419.5443
40.32280.13311.00390.74830.25153.1608-0.0818-0.667-0.72250.5011-0.07020.08610.50530.1297-0.04250.63230.0118-0.0210.33130.21450.449512.5703-19.041118.3409
51.09311.9026-0.67245.32160.66472.0893-0.0001-0.8401-0.42450.8953-0.0151-0.9253-0.01590.32360.00880.3091-0.0549-0.11260.3149-0.00010.283213.2568-3.197617.1239
61.5197-0.55660.65962.52641.93232.63610.1338-0.5033-0.23420.3223-0.10570.30820.1995-0.23870.40220.1801-0.11380.02750.24210.02740.17341.1361-9.670711.5221
71.98420.1436-1.34390.28370.55452.47630.0176-0.1275-0.3580.00940.02990.07670.45430.2999-0.02360.20180.0345-0.05260.10420.02820.233316.8271-17.0786.1839
86.65482.9641.65262.45182.15432.23170.01280.41410.17120.0198-0.16230.2902-0.1256-0.1666-0.00850.20170.1006-0.04750.19970.02150.239922.0947-31.0911-3.7615
91.68640.7720.26113.05031.79481.231-0.14890.12780.1331-0.94150.1517-0.4619-0.27310.23750.04680.33940.02710.06130.15470.02390.241726.4871-31.3675-9.8087
104.1425-1.9204-0.33362.90680.50742.3060.16920.0048-0.0798-0.2063-0.15890.19060.0658-0.22970.03810.13530.0016-0.02570.1166-0.03020.09036.4646-9.93940.3303
112.65980.8721-0.68033.14270.04674.328-0.0844-0.0526-0.22630.0342-0.03160.02890.09850.01190.06820.11320.06630.02080.1632-0.0030.083520.3203-43.001525.851
125.99150.9339-3.68095.7272-2.75633.2054-0.1620.98770.2758-0.84730.12780.1973-0.2055-0.3799-0.28260.53160.14020.01350.37690.07280.183318.6591-29.494515.2152
132.7505-0.4646-0.53274.24320.90161.8961-0.01920.68610.2348-0.4688-0.0278-0.16470.0658-0.2918-0.09890.18970.0670.00440.35350.02690.150119.815-39.503117.8967
144.0613-0.6830.30353.86790.27372.8414-0.00290.05920.3802-0.23130.13180.0211-0.23040.01330.00390.13680.06650.02240.1437-0.02580.158424.1487-31.677125.8855
153.3784-1.0484-0.52726.81315.64288.5344-0.3180.02420.0177-0.05910.36280.1463-0.35580.59470.03440.1425-0.00090.02060.2381-0.01170.256134.5518-22.715533.4425
161.39290.9785-0.20212.5627-1.05020.4693-0.1933-0.1705-0.30540.71770.3525-0.2840.36450.71810.24340.33170.1335-0.09230.2592-0.04940.329637.3896-16.477944.163
174.64151.4588-0.61442.57690.32721.8667-0.1076-0.0935-0.05960.0896-0.02840.09740.1955-0.31060.11470.12640.04420.0540.211-0.0390.127117.7437-37.916732.3708
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 6 through 15 )B6 - 15
2X-RAY DIFFRACTION2chain 'B' and (resid 16 through 28 )B16 - 28
3X-RAY DIFFRACTION3chain 'B' and (resid 29 through 41 )B29 - 41
4X-RAY DIFFRACTION4chain 'B' and (resid 42 through 46 )B42 - 46
5X-RAY DIFFRACTION5chain 'B' and (resid 47 through 59 )B47 - 59
6X-RAY DIFFRACTION6chain 'B' and (resid 60 through 74 )B60 - 74
7X-RAY DIFFRACTION7chain 'B' and (resid 75 through 103 )B75 - 103
8X-RAY DIFFRACTION8chain 'B' and (resid 104 through 111 )B104 - 111
9X-RAY DIFFRACTION9chain 'B' and (resid 112 through 122 )B112 - 122
10X-RAY DIFFRACTION10chain 'B' and (resid 123 through 156 )B123 - 156
11X-RAY DIFFRACTION11chain 'A' and (resid 7 through 33 )A7 - 33
12X-RAY DIFFRACTION12chain 'A' and (resid 34 through 45 )A34 - 45
13X-RAY DIFFRACTION13chain 'A' and (resid 46 through 74 )A46 - 74
14X-RAY DIFFRACTION14chain 'A' and (resid 75 through 93 )A75 - 93
15X-RAY DIFFRACTION15chain 'A' and (resid 94 through 112 )A94 - 112
16X-RAY DIFFRACTION16chain 'A' and (resid 113 through 122 )A113 - 122
17X-RAY DIFFRACTION17chain 'A' and (resid 123 through 156 )A123 - 156

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