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- PDB-6p1a: Transcription antitermination factor Q21 in complex with Q21-bind... -

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Basic information

Entry
Database: PDB / ID: 6p1a
TitleTranscription antitermination factor Q21 in complex with Q21-binding-element DNA
Components
  • DNA (5'-D(*CP*TP*TP*GP*CP*TP*CP*AP*TP*TP*TP*GP*CP*TP*CP*AP*AP*TP*GP*AP*G)-3')
  • DNA (5'-D(P*CP*TP*CP*AP*TP*TP*GP*AP*GP*CP*AP*AP*AP*TP*GP*AP*GP*CP*AP*AP*G)-3')
  • Q 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 / DNA / DNA (> 10) / Q protein
Function and homology information
Biological speciesPhage 21 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.837 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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
C: Q protein
D: DNA (5'-D(P*CP*TP*CP*AP*TP*TP*GP*AP*GP*CP*AP*AP*AP*TP*GP*AP*GP*CP*AP*AP*G)-3')
E: DNA (5'-D(*CP*TP*TP*GP*CP*TP*CP*AP*TP*TP*TP*GP*CP*TP*CP*AP*AP*TP*GP*AP*G)-3')
F: DNA (5'-D(P*CP*TP*CP*AP*TP*TP*GP*AP*GP*CP*AP*AP*AP*TP*GP*AP*GP*CP*AP*AP*G)-3')
G: DNA (5'-D(*CP*TP*TP*GP*CP*TP*CP*AP*TP*TP*TP*GP*CP*TP*CP*AP*AP*TP*GP*AP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,03212
Polymers81,7757
Non-polymers2575
Water0
1
A: Q protein
B: Q protein
D: DNA (5'-D(P*CP*TP*CP*AP*TP*TP*GP*AP*GP*CP*AP*AP*AP*TP*GP*AP*GP*CP*AP*AP*G)-3')
E: DNA (5'-D(*CP*TP*TP*GP*CP*TP*CP*AP*TP*TP*TP*GP*CP*TP*CP*AP*AP*TP*GP*AP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,4448
Polymers50,2224
Non-polymers2224
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6680 Å2
ΔGint-27 kcal/mol
Surface area22580 Å2
MethodPISA
2
C: Q protein
F: DNA (5'-D(P*CP*TP*CP*AP*TP*TP*GP*AP*GP*CP*AP*AP*AP*TP*GP*AP*GP*CP*AP*AP*G)-3')
G: DNA (5'-D(*CP*TP*TP*GP*CP*TP*CP*AP*TP*TP*TP*GP*CP*TP*CP*AP*AP*TP*GP*AP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5894
Polymers31,5533
Non-polymers351
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3780 Å2
ΔGint-28 kcal/mol
Surface area15970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.573, 263.224, 56.770
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
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...
31(chain C and (resid 7 through 13 or resid 15...
12chain D
22chain F
13chain E
23(chain G and ((resid 1 and (name O5 or name...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ASNASNHISHIS(chain A and (resid 7 through 13 or resid 15...AA7 - 137 - 13
121TRPTRPLYSLYS(chain A and (resid 7 through 13 or resid 15...AA15 - 3415 - 34
131ARGARGARGARG(chain A and (resid 7 through 13 or resid 15...AA3535
141GLUGLUGLUGLU(chain A and (resid 7 through 13 or resid 15...AA5 - 1565 - 156
151GLUGLUGLUGLU(chain A and (resid 7 through 13 or resid 15...AA5 - 1565 - 156
161GLUGLUGLUGLU(chain A and (resid 7 through 13 or resid 15...AA5 - 1565 - 156
171GLUGLUGLUGLU(chain A and (resid 7 through 13 or resid 15...AA5 - 1565 - 156
211ASNASNHISHIS(chain B and (resid 7 through 13 or resid 15...BB7 - 137 - 13
221TRPTRPLYSLYS(chain B and (resid 7 through 13 or resid 15...BB15 - 3415 - 34
231ARGARGARGARG(chain B and (resid 7 through 13 or resid 15...BB3535
241ASNASNLYSLYS(chain B and (resid 7 through 13 or resid 15...BB7 - 1537 - 153
251ASNASNLYSLYS(chain B and (resid 7 through 13 or resid 15...BB7 - 1537 - 153
261ASNASNLYSLYS(chain B and (resid 7 through 13 or resid 15...BB7 - 1537 - 153
271ASNASNLYSLYS(chain B and (resid 7 through 13 or resid 15...BB7 - 1537 - 153
311ASNASNHISHIS(chain C and (resid 7 through 13 or resid 15...CC7 - 137 - 13
321TRPTRPALAALA(chain C and (resid 7 through 13 or resid 15...CC15 - 9815 - 98
331TYRTYRTYRTYR(chain C and (resid 7 through 13 or resid 15...CC100100
341LEULEUGLUGLU(chain C and (resid 7 through 13 or resid 15...CC6 - 1566 - 156
351LYSLYSLYSLYS(chain C and (resid 7 through 13 or resid 15...CC153153
361LEULEUGLUGLU(chain C and (resid 7 through 13 or resid 15...CC6 - 1566 - 156
371LEULEUGLUGLU(chain C and (resid 7 through 13 or resid 15...CC6 - 1566 - 156
381LEULEUGLUGLU(chain C and (resid 7 through 13 or resid 15...CC6 - 1566 - 156
391LEULEUGLUGLU(chain C and (resid 7 through 13 or resid 15...CC6 - 1566 - 156
112DCDCDGDGchain DDD1 - 211 - 21
212DCDCDGDGchain FFF1 - 211 - 21
113DCDCDGDGchain EEE1 - 211 - 21
213DCDCDCDC(chain G and ((resid 1 and (name O5 or name...GG11
223DCDCDGDG(chain G and ((resid 1 and (name O5 or name...GG1 - 211 - 21
233DCDCDGDG(chain G and ((resid 1 and (name O5 or name...GG1 - 211 - 21
243DCDCDGDG(chain G and ((resid 1 and (name O5 or name...GG1 - 211 - 21
253DCDCDGDG(chain G and ((resid 1 and (name O5 or name...GG1 - 211 - 21
263DCDCDGDG(chain G and ((resid 1 and (name O5 or name...GG1 - 211 - 21
273DCDCDGDG(chain G and ((resid 1 and (name O5 or name...GG1 - 211 - 21
283DCDCDGDG(chain G and ((resid 1 and (name O5 or name...GG1 - 211 - 21
293DCDCDGDG(chain G and ((resid 1 and (name O5 or name...GG1 - 211 - 21
2103DCDCDGDG(chain G and ((resid 1 and (name O5 or name...GG1 - 211 - 21
2113DCDCDGDG(chain G and ((resid 1 and (name O5 or name...GG1 - 211 - 21
2123DCDCDGDG(chain G and ((resid 1 and (name O5 or name...GG1 - 211 - 21
2133DCDCDGDG(chain G and ((resid 1 and (name O5 or name...GG1 - 211 - 21
2143DCDCDGDG(chain G and ((resid 1 and (name O5 or name...GG1 - 211 - 21
2153DCDCDGDG(chain G and ((resid 1 and (name O5 or name...GG1 - 211 - 21

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Q protein / Transcription antitermination factor Q21


Mass: 18668.789 Da / Num. of mol.: 3
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: DNA chain DNA (5'-D(P*CP*TP*CP*AP*TP*TP*GP*AP*GP*CP*AP*AP*AP*TP*GP*AP*GP*CP*AP*AP*G)-3') / Q21-binding element DNA / nontemplate strand


Mass: 6480.225 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Phage 21 (virus)
#3: DNA chain DNA (5'-D(*CP*TP*TP*GP*CP*TP*CP*AP*TP*TP*TP*GP*CP*TP*CP*AP*AP*TP*GP*AP*G)-3') / Q21-binding element DNA / template strand


Mass: 6404.145 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Phage 21 (virus)
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl

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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: 3.18 Å3/Da / Density % sol: 61.3 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M Sodium chloride, 0.1 M BIS-TRIS pH 6.5, 25% PEG 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.97 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.837→50 Å / Num. obs: 25517 / % possible obs: 99.6 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.033 / Rrim(I) all: 0.084 / Χ2: 0.864 / Net I/σ(I): 9.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.85-2.95.90.91912470.6460.4091.0090.99499.8
2.9-2.955.80.78212060.680.3520.860.93598.9
2.95-3.015.50.63212600.7740.2910.6980.98697.8
3.01-3.075.80.5712220.7970.2560.6270.95599.2
3.07-3.146.30.47412740.9120.2030.5170.965100
3.14-3.216.40.34212490.9560.1460.3730.92299.4
3.21-3.296.40.23912420.9470.1060.2620.959100
3.29-3.386.40.21212570.9520.0960.2330.94299.4
3.38-3.486.50.1612630.9540.0690.1750.879100
3.48-3.596.50.14612700.9340.0620.160.92899.7
3.59-3.726.50.12112500.9320.0520.1320.83599.8
3.72-3.876.60.10912880.9660.0450.1180.79100
3.87-4.046.70.08912740.9720.0360.0960.78499.8
4.04-4.266.70.07612690.9810.0310.0820.76799.8
4.26-4.526.60.06412830.9790.0270.0690.82499.8
4.52-4.876.40.05512890.9850.0240.060.75299.9
4.87-5.365.80.04813060.9860.0210.0530.77999.7
5.36-6.146.20.04713030.9860.020.0510.7699.8
6.14-7.736.90.04313370.9960.0170.0470.76699.7
7.73-506.50.03414280.9670.0150.0380.84999.1

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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: 6P1B

6p1b


Resolution: 2.837→47.808 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.26
RfactorNum. reflection% reflection
Rfree0.2749 1999 8.73 %
Rwork0.2314 --
obs0.2353 22885 89.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 207.24 Å2 / Biso mean: 62.5374 Å2 / Biso min: 6.93 Å2
Refinement stepCycle: final / Resolution: 2.837→47.808 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3603 1719 32 0 5354
Biso mean--54.82 --
Num. residues----534
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2020X-RAY DIFFRACTION13.457TORSIONAL
12B2020X-RAY DIFFRACTION13.457TORSIONAL
13C2020X-RAY DIFFRACTION13.457TORSIONAL
21D414X-RAY DIFFRACTION13.457TORSIONAL
22F414X-RAY DIFFRACTION13.457TORSIONAL
31E412X-RAY DIFFRACTION13.457TORSIONAL
32G412X-RAY DIFFRACTION13.457TORSIONAL
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 (%)
2.8372-2.90820.3611650.297568775243
2.9082-2.98680.3157800.295682990950
2.9868-3.07470.33511060.29541116122269
3.0747-3.17390.33761470.30111534168192
3.1739-3.28730.29241530.27491587174098
3.2873-3.41890.34281540.24361617177199
3.4189-3.57440.26751590.230916511810100
3.5744-3.76280.28411580.222216551813100
3.7628-3.99850.25911590.220416521811100
3.9985-4.3070.2591600.207716791839100
4.307-4.74010.23481610.194116821843100
4.7401-5.42520.21221590.20116671826100
5.4252-6.83190.27771660.241917191885100
6.8319-47.81490.28461720.23411811198399

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