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- PDB-7ubl: Transcription antitermination factor Qlambda in complex with Q-la... -

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Basic information

Entry
Database: PDB / ID: 7ubl
TitleTranscription antitermination factor Qlambda in complex with Q-lambda-binding-element DNA
Components
  • Antitermination protein Q
  • DNA (5'-D(P*CP*AP*CP*CP*CP*AP*AP*TP*TP*TP*TP*AP*TP*TP*CP*AP*AP*TP*G)-3')
  • DNA (5'-D(P*CP*AP*TP*TP*GP*AP*AP*TP*AP*AP*AP*AP*TP*TP*GP*GP*GP*TP*G)-3')
KeywordsGENE REGULATION/DNA / RNA polymerase / DNA Binding / transcription / Q-dependent antitermination / Q antitermination factor / GENE REGULATION-DNA complex
Function / homology
Function and homology information


transcription antitermination / DNA-templated transcription termination / DNA binding / zinc ion binding
Similarity search - Function
Antitermination protein Q / Antitermination protein Q superfamily / Antitermination protein / Heat shock protein DnaJ, cysteine-rich domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / Antitermination protein Q
Similarity search - Component
Biological speciesEscherichia phage Lambda (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.177 Å
AuthorsYin, Z. / Ebright, R.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)GM041376 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2022
Title: In transcription antitermination by Qλ, NusA induces refolding of Qλ to form a nozzle that extends the RNA polymerase RNA-exit channel.
Authors: Zhou Yin / Jeremy G Bird / Jason T Kaelber / Bryce E Nickels / Richard H Ebright /
Abstract: Lambdoid bacteriophage Q proteins are transcription antipausing and antitermination factors that enable RNA polymerase (RNAP) to read through pause and termination sites. Q proteins load onto RNAP ...Lambdoid bacteriophage Q proteins are transcription antipausing and antitermination factors that enable RNA polymerase (RNAP) to read through pause and termination sites. Q proteins load onto RNAP engaged in promoter-proximal pausing at a Q binding element (QBE) and adjacent sigma-dependent pause element to yield a Q-loading complex, and they translocate with RNAP as a pausing-deficient, termination-deficient Q-loaded complex. In previous work, we showed that the Q protein of bacteriophage 21 (Q21) functions by forming a nozzle that narrows and extends the RNAP RNA-exit channel, preventing formation of pause and termination RNA hairpins. Here, we report atomic structures of four states on the pathway of antitermination by the Q protein of bacteriophage λ (Qλ), a Q protein that shows no sequence similarity to Q21 and that, unlike Q21, requires the transcription elongation factor NusA for efficient antipausing and antitermination. We report structures of Qλ, the Qλ-QBE complex, the NusA-free pre-engaged Qλ-loading complex, and the NusA-containing engaged Qλ-loading complex. The results show that Qλ, like Q21, forms a nozzle that narrows and extends the RNAP RNA-exit channel, preventing formation of RNA hairpins. However, the results show that Qλ has no three-dimensional structural similarity to Q21, employs a different mechanism of QBE recognition than Q21, and employs a more complex process for loading onto RNAP than Q21, involving recruitment of Qλ to form a pre-engaged loading complex, followed by NusA-facilitated refolding of Qλ to form an engaged loading complex. The results establish that Qλ and Q21 are not structural homologs and are solely functional analogs.
History
DepositionMar 15, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2022Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Antitermination protein Q
B: DNA (5'-D(P*CP*AP*CP*CP*CP*AP*AP*TP*TP*TP*TP*AP*TP*TP*CP*AP*AP*TP*G)-3')
C: DNA (5'-D(P*CP*AP*TP*TP*GP*AP*AP*TP*AP*AP*AP*AP*TP*TP*GP*GP*GP*TP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1838
Polymers27,8693
Non-polymers3145
Water2,522140
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4430 Å2
ΔGint-19 kcal/mol
Surface area14100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.102, 131.102, 49.545
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Antitermination protein Q /


Mass: 16222.834 Da / Num. of mol.: 1 / Fragment: UNP residues 62-207 / Mutation: E134K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia phage Lambda (virus) / Production host: Escherichia coli (E. coli) / References: UniProt: P03047

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DNA chain , 2 types, 2 molecules BC

#2: DNA chain DNA (5'-D(P*CP*AP*CP*CP*CP*AP*AP*TP*TP*TP*TP*AP*TP*TP*CP*AP*AP*TP*G)-3')


Mass: 5738.748 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia phage Lambda (virus)
#3: DNA chain DNA (5'-D(P*CP*AP*TP*TP*GP*AP*AP*TP*AP*AP*AP*AP*TP*TP*GP*GP*GP*TP*G)-3')


Mass: 5907.858 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia phage Lambda (virus)

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Non-polymers , 3 types, 145 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 140 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 3.82 Å3/Da / Density % sol: 67.8 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1 M HEPES, pH 7, 1 M sodium citrate

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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 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.177→46.352 Å / Num. obs: 23174 / % possible obs: 99.5 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 26.7
Reflection shellResolution: 2.177→2.22 Å / Rmerge(I) obs: 0.826 / Num. unique obs: 1143

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
DENZOdata reduction
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.177→46.352 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 23.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2285 3429 8.89 %
Rwork0.1877 35154 -
obs0.1914 23174 89.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 211.41 Å2 / Biso mean: 50.1398 Å2 / Biso min: 15.62 Å2
Refinement stepCycle: final / Resolution: 2.177→46.352 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1084 779 41 140 2044
Biso mean--57 42.43 -
Num. residues----179
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1773-2.20840.3447650.2664138
2.2084-2.24140.3171860.264690255
2.2414-2.27640.3655900.263993758
2.2764-2.31370.26571060.2248109267
2.3137-2.35360.30391160.2236124874
2.3536-2.39640.26651240.2197128579
2.3964-2.44250.26011400.2208143489
2.4425-2.49240.30371540.2335160895
2.4924-2.54660.30231530.2133152996
2.5466-2.60580.25881610.2095166199
2.6058-2.67090.22871590.21211628100
2.6709-2.74320.26731660.21641658100
2.7432-2.82390.27221550.21661593100
2.8239-2.9150.26521670.21831679100
2.915-3.01920.24181540.22621594100
3.0192-3.140.2771610.2145164199
3.14-3.28290.27211580.1898158697
3.2829-3.45590.2171610.1824162699
3.4559-3.67240.21600.17331634100
3.6724-3.95580.17631580.15361634100
3.9558-4.35360.17721540.1575164399
4.3536-4.98290.20891670.15691635100
4.9829-6.27550.2061610.1671162899
6.2755-46.3520.1731530.1575163899
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)
12.50910.2376-1.16411.25630.14193.994-0.08970.0334-0.04440.1204-0.18510.084-0.2385-0.07550.26410.21240.0250.01860.1503-0.0220.184461.95111.55628.563
20.2444-0.12271.15310.0902-0.17885.8577-0.13990.0631-0.06690.0695-0.2337-0.1196-0.14510.43840.2830.3229-0.10610.06050.35460.06360.243271.844111.0244.144
34.1376-1.65930.86793.1340.23483.2819-0.14510.1384-0.3255-0.2185-0.2773-0.0160.0545-0.10850.32210.3036-0.01240.14150.19020.02780.24261.588105.11629.936
43.4241.2483-0.44115.2141-6.18979.4913-0.3433-0.0313-0.5042-0.1201-0.3798-0.25211.12990.39620.46230.5848-0.15850.24650.43780.05020.370583.189108.1174.743
51.2051-0.2320.92270.9786-0.28032.3301-0.41760.2721-0.588-0.4166-0.0454-0.33360.46830.42230.10060.69770.05790.46480.2270.00510.507473.64393.37321.559
65.66653.4686-3.25025.4763-6.67238.40280.3588-1.0787-0.2690.4881-0.49130.13030.20880.19690.26981.0815-0.23820.49420.61770.04630.962163.80177.35335.83
72.96080.1767-1.0216.0264-3.30744.5717-0.3450.1926-0.1704-0.12140.28680.76970.6879-0.4813-0.2280.699-0.11450.4010.24390.16820.870158.4883.14533.29
80.1970.3618-0.09212.4542-1.76081.4516-0.3927-0.0557-0.5457-0.4985-0.1263-0.27480.7220.480.33310.70550.0570.38830.31070.07860.673275.19894.68920.017
90.52630.4995-0.29010.5052-0.29070.16590.0709-0.2162-0.0812-0.0168-0.0593-0.1141-0.04640.38770.26490.48360.01190.47090.67070.31420.709191.069108.1858.364
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 61:129 )A61 - 129
2X-RAY DIFFRACTION2( CHAIN A AND RESID 130:157 )A130 - 157
3X-RAY DIFFRACTION3( CHAIN A AND RESID 158:201 )A158 - 201
4X-RAY DIFFRACTION4( CHAIN B AND RESID 1:5 )B1 - 5
5X-RAY DIFFRACTION5( CHAIN B AND RESID 6:15 )B6 - 15
6X-RAY DIFFRACTION6( CHAIN B AND RESID 16:19 )B16 - 19
7X-RAY DIFFRACTION7( CHAIN C AND RESID 1:5 )C1 - 5
8X-RAY DIFFRACTION8( CHAIN C AND RESID 6:15 )C6 - 15
9X-RAY DIFFRACTION9( CHAIN C AND RESID 16:19 )C16 - 19

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