[English] 日本語
Yorodumi
- PDB-7ubk: Transcription antitermination factor Qlambda, type-II crystal -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ubk
TitleTranscription antitermination factor Qlambda, type-II crystal
ComponentsAntitermination protein Q
KeywordsGENE REGULATION / RNA polymerase / DNA Binding / transcription / Q-dependent antitermination / Q antitermination factor
Function / homology
Function and homology information


transcription antitermination / DNA-templated transcription termination / DNA binding / zinc ion binding
Similarity search - Function
Enzyme I; Chain A, domain 2 - #110 / Antitermination protein Q / Antitermination protein Q superfamily / Antitermination protein Q / Heat shock protein DnaJ, cysteine-rich domain superfamily / Enzyme I; Chain A, domain 2 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Antitermination protein Q
Similarity search - Component
Biological speciesEscherichia phage Lambda (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.97 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 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)33,03211
Polymers32,4462
Non-polymers5869
Water1,40578
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3390 Å2
ΔGint-21 kcal/mol
Surface area15210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.304, 64.317, 65.319
Angle α, β, γ (deg.)90.000, 98.350, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 61 through 85 or (resid 86...
21(chain B and (resid 61 through 118 or (resid 119...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERALAALA(chain A and (resid 61 through 85 or (resid 86...AA61 - 851 - 25
12LYSLYSLYSLYS(chain A and (resid 61 through 85 or (resid 86...AA8626
13SERSERTHRTHR(chain A and (resid 61 through 85 or (resid 86...AA61 - 2061 - 146
14SERSERTHRTHR(chain A and (resid 61 through 85 or (resid 86...AA61 - 2061 - 146
15SERSERTHRTHR(chain A and (resid 61 through 85 or (resid 86...AA61 - 2061 - 146
16SERSERTHRTHR(chain A and (resid 61 through 85 or (resid 86...AA61 - 2061 - 146
21SERSERCYSCYS(chain B and (resid 61 through 118 or (resid 119...BB61 - 1181 - 58
22ARGARGARGARG(chain B and (resid 61 through 118 or (resid 119...BB11959
23SERSERARGARG(chain B and (resid 61 through 118 or (resid 119...BB61 - 2071 - 147
24SERSERARGARG(chain B and (resid 61 through 118 or (resid 119...BB61 - 2071 - 147
25SERSERARGARG(chain B and (resid 61 through 118 or (resid 119...BB61 - 2071 - 147
26SERSERARGARG(chain B and (resid 61 through 118 or (resid 119...BB61 - 2071 - 147

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Antitermination protein Q


Mass: 16222.834 Da / Num. of mol.: 2 / 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

-
Non-polymers , 6 types, 87 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.02 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: 30% PEG600, 100 mM HEPES/sodium hydroxide, pH 7.5, 50 mM lithium sulfate, 10% glycerol

-
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 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.97→50 Å / Num. obs: 19614 / % possible obs: 98.1 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.028 / Rrim(I) all: 0.051 / Χ2: 0.862 / Net I/σ(I): 11.9 / Num. measured all: 63986
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.97-230.6059740.7380.4050.7321.13996.2
2-2.043.40.5219810.830.3290.6181.05198.4
2.04-2.083.30.4019470.8960.2590.4791.0298.4
2.08-2.123.30.3959840.8750.2520.4711.02499.5
2.12-2.173.20.2949980.9480.190.3510.95698.7
2.17-2.223.30.2289640.9610.1470.2730.95597.9
2.22-2.273.10.2069850.9630.1370.2490.93298.3
2.27-2.3430.1659340.9750.1130.2010.91194.5
2.34-2.43.40.1379920.9890.0860.1620.91799.5
2.4-2.483.40.1169860.9890.0730.1380.87598.2
2.48-2.573.30.1029720.9930.0650.1220.87999.2
2.57-2.673.20.0819900.9940.0520.0970.80498.1
2.67-2.83.10.0659570.9940.0430.0780.77596.2
2.8-2.943.30.0539790.9950.0340.0640.80498.6
2.94-3.133.40.0419960.9970.0250.0480.75398.5
3.13-3.373.40.0319970.9970.020.0370.71299.2
3.37-3.713.10.0249610.9980.0150.0280.67897
3.71-4.243.40.02210060.9980.0130.0250.68199.1
4.24-5.353.30.0199910.9980.0120.0220.68998
5.35-503.20.02410200.9970.0160.0290.72997.6

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHASERphasing
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4MO1

4mo1


Resolution: 1.97→45.588 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2277 2524 10.08 %
Rwork0.1844 22505 -
obs0.1888 17381 64.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 238.9 Å2 / Biso mean: 51.596 Å2 / Biso min: 10.56 Å2
Refinement stepCycle: final / Resolution: 1.97→45.588 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2239 0 64 78 2381
Biso mean--64.02 33.95 -
Num. residues----293
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1325X-RAY DIFFRACTION11.662TORSIONAL
12B1325X-RAY DIFFRACTION11.662TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.97-2.00770.3779440.259539720
2.0077-2.04870.2958620.239756129
2.0487-2.09320.2742700.240663532
2.0932-2.14190.3033810.242772036
2.1419-2.19550.2869850.232377841
2.1955-2.25490.27121010.221190846
2.2549-2.32120.2867990.220590547
2.3212-2.39610.22281240.2042110457
2.3961-2.48180.30141410.2037122762
2.4818-2.58110.25011490.2069129167
2.5811-2.69860.2781680.2072147875
2.6986-2.84080.23531720.2088155480
2.8408-3.01880.25082000.2048177591
3.0188-3.25180.24961990.2061181893
3.2518-3.57890.2392030.1791180893
3.5789-4.09650.20482050.1517184494
4.0965-5.16010.18182160.1441185696
5.1601-45.5880.18372050.1737184694
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)
16.85780.1671-2.76136.732-0.72077.186-0.1968-0.5350.1230.24470.0263-0.0687-0.12370.04670.09180.16030.085-0.00450.2173-0.05670.099515.4843.40231.509
22.23421.1147-1.6762.5775-1.43852.01860.0226-0.2421-0.04290.0833-0.0448-0.0019-0.0250.11550.15590.09510.0519-0.00840.15320.00050.139214.817-1.60724.284
31.3393-1.0925-0.63992.48012.18877.7111-0.0341-0.12780.16150.0008-0.07930.3228-0.3182-0.29220.04460.25560.0985-0.03960.2390.00810.2914.17721.01816.138
41.1614-0.2023-0.85891.6446-1.51552.57140.40770.1264-0.335-0.35490.23610.84130.0949-0.3181-0.37690.1570.0203-0.08310.26230.01430.34064.8436.71615.124
54.17430.5777-0.26424.9046-0.3442.5847-0.129-0.12870.1926-0.1362-0.07480.2927-0.0968-0.06550.12730.08180.0519-0.02010.1908-0.03290.165410.010.34323.278
64.82281.98852.0094.85223.33592.4084-0.22430.37510.2079-0.99690.14430.1538-0.48010.24620.07660.5911-0.01190.06440.26630.03510.202724.204-5.8410.537
73.88291.01540.93931.1519-1.06837.9911-0.12730.30980.1052-0.7987-0.14410.0114-0.10460.17310.18650.38360.09780.0660.15120.00990.166318.348-4.3546.453
86.5140.0131-3.08014.98234.20935.4764-0.4318-0.3748-0.65130.81230.161-0.09690.94570.49670.13890.24780.09340.06670.16860.05460.205620.155-18.62723.405
98.3231-3.6151-2.29724.59014.91295.68050.81630.3244-0.0011-0.86650.0258-0.63970.45540.473-0.54980.46180.19880.01730.29580.04290.307629.39-24.27216.63
102.1105-1.6512-0.2162.26170.44750.09160.27780.48660.1641-0.6201-0.318-0.62550.40220.5255-0.03491.04790.8638-0.14750.41290.09220.422834.548-31.02910.595
113.198-3.31982.59254.1772-1.62654.78360.35630.068-0.3855-0.95940.17180.64550.4994-0.1697-0.26450.2266-0.0637-0.02180.12880.01660.264818.32-17.12315.225
123.91031.5283-0.89933.9274-1.20077.2505-0.2140.4265-0.1304-0.6940.04420.3396-0.1765-0.79310.21920.62610.1234-0.25750.3669-0.17510.29577.246-6.1161.004
135.4272.9863-4.94284.4487-1.94.86350.3161.0054-1.1054-1.00450.23191.10641.6634-0.971-0.37520.80890.0278-0.23850.3556-0.00060.48139.717-15.3940.071
147.25324.99885.55374.90083.95568.2403-0.01350.6575-0.3976-0.62790.1253-0.590.20330.5973-0.19620.35340.08570.10250.2031-0.0390.215322.33-12.9237.88
159.1368-1.0633-3.24578.98234.91433.47950.1411-0.9844-0.31870.0853-0.0825-0.49960.18430.8616-0.00690.0960.01890.10410.5657-0.04760.311628.915-6.09319.877
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 61:88 )A61 - 88
2X-RAY DIFFRACTION2( CHAIN A AND RESID 89:112 )A89 - 112
3X-RAY DIFFRACTION3( CHAIN A AND RESID 113:143 )A113 - 143
4X-RAY DIFFRACTION4( CHAIN A AND RESID 144:157 )A144 - 157
5X-RAY DIFFRACTION5( CHAIN A AND RESID 158:206 )A158 - 206
6X-RAY DIFFRACTION6( CHAIN B AND RESID 61:88 )B61 - 88
7X-RAY DIFFRACTION7( CHAIN B AND RESID 89:111 )B89 - 111
8X-RAY DIFFRACTION8( CHAIN B AND RESID 112:121 )B112 - 121
9X-RAY DIFFRACTION9( CHAIN B AND RESID 122:129 )B122 - 129
10X-RAY DIFFRACTION10( CHAIN B AND RESID 130:145 )B130 - 145
11X-RAY DIFFRACTION11( CHAIN B AND RESID 146:157 )B146 - 157
12X-RAY DIFFRACTION12( CHAIN B AND RESID 158:172 )B158 - 172
13X-RAY DIFFRACTION13( CHAIN B AND RESID 173:180 )B173 - 180
14X-RAY DIFFRACTION14( CHAIN B AND RESID 181:193 )B181 - 193
15X-RAY DIFFRACTION15( CHAIN B AND RESID 194:207 )B194 - 207

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more