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- PDB-6jny: Crystal structure of bacteriophage 21 Q protein -

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Basic information

Entry
Database: PDB / ID: 6jny
TitleCrystal structure of bacteriophage 21 Q protein
ComponentsAntiterminator Q protein
KeywordsTRANSCRIPTION / RNA polymerase / Antitermination
Function / homologyBacteriophage 933W, GpQ / Phage antitermination protein Q / negative regulation of termination of DNA-templated transcription / DNA binding / Antiterminator Q protein
Function and homology information
Biological speciesEnterobacteria phage SfI (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.451 Å
AuthorsFeng, Y. / Shi, J.
CitationJournal: Nat Commun / Year: 2019
Title: Structural basis of Q-dependent transcription antitermination.
Authors: Jing Shi / Xiang Gao / Tongguan Tian / Zhaoyang Yu / Bo Gao / Aijia Wen / Linlin You / Shenghai Chang / Xing Zhang / Yu Zhang / Yu Feng /
Abstract: Bacteriophage Q protein engages σ-dependent paused RNA polymerase (RNAP) by binding to a DNA site embedded in late gene promoter and renders RNAP resistant to termination signals. Here, we report a ...Bacteriophage Q protein engages σ-dependent paused RNA polymerase (RNAP) by binding to a DNA site embedded in late gene promoter and renders RNAP resistant to termination signals. Here, we report a single-particle cryo-electron microscopy (cryo-EM) structure of an intact Q-engaged arrested complex. The structure reveals key interactions responsible for σ-dependent pause, Q engagement, and Q-mediated transcription antitermination. The structure shows that two Q protomers (Q and Q) bind to a direct-repeat DNA site and contact distinct elements of the RNA exit channel. Notably, Q forms a narrow ring inside the RNA exit channel and renders RNAP resistant to termination signals by prohibiting RNA hairpin formation in the RNA exit channel. Because the RNA exit channel is conserved among all multisubunit RNAPs, it is likely to serve as an important contact site for regulators that modify the elongation properties of RNAP in other organisms, as well.
History
DepositionMar 18, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 12, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 22, 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: Antiterminator Q protein
B: Antiterminator Q protein


Theoretical massNumber of molelcules
Total (without water)37,4262
Polymers37,4262
Non-polymers00
Water3,297183
1
A: Antiterminator Q protein


Theoretical massNumber of molelcules
Total (without water)18,7131
Polymers18,7131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Antiterminator Q protein


Theoretical massNumber of molelcules
Total (without water)18,7131
Polymers18,7131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.902, 77.827, 68.692
Angle α, β, γ (deg.)90.000, 98.590, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Antiterminator Q protein


Mass: 18712.908 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage SfI (virus) / Production host: Escherichia coli (E. coli) / References: UniProt: M1FPN0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 2.32 Å3/Da / Density % sol: 47.06 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / Details: 0.2M KF and 14% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. obs: 57774 / % possible obs: 95.5 % / Redundancy: 6.9 % / Biso Wilson estimate: 18.15 Å2 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.03 / Rrim(I) all: 0.079 / Χ2: 0.819 / Net I/σ(I): 18
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.45-1.486.50.45525810.9290.190.4950.76285.4
1.48-1.570.36328410.960.1480.3920.78293.6
1.5-1.5370.32229080.9640.1310.3480.78896.6
1.53-1.5670.27828870.9660.1130.30.77994.9
1.56-1.670.23129220.980.0940.250.79398.1
1.6-1.636.90.20128620.980.0820.2170.80695.5
1.63-1.676.90.17329430.9850.0710.1870.82797.5
1.67-1.726.80.1529120.9860.0620.1620.82595.7
1.72-1.776.50.13228500.9890.0550.1430.84595.6
1.77-1.836.90.11627750.9910.0470.1250.84290.6
1.83-1.897.20.10829530.9920.0430.1170.82799.5
1.89-1.977.30.09429410.9940.0380.1010.85196.9
1.97-2.067.10.08729490.9940.0350.0940.87497.2
2.06-2.1770.0829980.9950.0320.0860.88699.1
2.17-2.36.90.07629340.9950.0310.0820.88797.7
2.3-2.486.60.07228630.9950.030.0780.87194.5
2.48-2.737.10.06928860.9960.0270.0740.85694.3
2.73-3.127.30.06829840.9960.0270.0730.82598.8
3.12-3.947.10.06529890.9960.0260.070.78598.6
3.94-506.70.06427960.9950.0270.070.64689.9

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OR7

1or7


Resolution: 1.451→31.214 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 23.81
RfactorNum. reflection% reflection
Rfree0.2273 1971 3.48 %
Rwork0.211 --
obs0.2116 56680 93.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 55.27 Å2 / Biso mean: 23.8356 Å2 / Biso min: 11.06 Å2
Refinement stepCycle: final / Resolution: 1.451→31.214 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2275 0 0 183 2458
Biso mean---29.81 -
Num. residues----280
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052324
X-RAY DIFFRACTIONf_angle_d0.7353119
X-RAY DIFFRACTIONf_chiral_restr0.057326
X-RAY DIFFRACTIONf_plane_restr0.004390
X-RAY DIFFRACTIONf_dihedral_angle_d10.821875
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 (%)
1.4511-1.48740.2671200.24623348346880
1.4874-1.52760.26751370.23183710384790
1.5276-1.57260.24921350.22343816395191
1.5726-1.62330.23141440.22073925406994
1.6233-1.68130.22051430.22173927407096
1.6813-1.74860.27151400.21393939407994
1.7486-1.82820.22081380.21723822396091
1.8282-1.92460.2571470.22184047419498
1.9246-2.04510.23651450.22084063420898
2.0451-2.2030.21821460.20764063420998
2.203-2.42460.24841460.21234072421898
2.4246-2.77530.2241410.2113904404593
2.7753-3.49580.23751480.2134146429499
3.4958-31.2210.19631410.19723927406892

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