[English] 日本語
Yorodumi
- PDB-8fb3: PreQ1-1 (type-1) riboswitch with stacked metabolites and a C10-G3... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8fb3
TitlePreQ1-1 (type-1) riboswitch with stacked metabolites and a C10-G34 base pair in the expression platform
ComponentsRNA (34-MER) Riboswitch
KeywordsRNA / riboswitch / Shine-Dalgarno sequence / pseudoknot / A-amino kissing motif / quintuple-base transition motif
Function / homology7-DEAZA-7-AMINOMETHYL-GUANINE / RNA / RNA (> 10)
Function and homology information
Biological speciesCarnobacterium antarcticum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsWedekind, J.E. / Schroeder, G.M. / Jenkins, J.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM063162 United States
Citation
Journal: Nucleic Acids Res. / Year: 2023
Title: A riboswitch separated from its ribosome-binding site still regulates translation.
Authors: Schroeder, G.M. / Akinyemi, O. / Malik, J. / Focht, C.M. / Pritchett, E.M. / Baker, C.D. / McSally, J.P. / Jenkins, J.L. / Mathews, D.H. / Wedekind, J.E.
#1: Journal: Nat Commun / Year: 2022
Title: A small RNA that cooperatively senses two stacked metabolites in one pocket for gene control.
Authors: Schroeder, G.M. / Cavender, C.E. / Blau, M.E. / Jenkins, J.L. / Mathews, D.H. / Wedekind, J.E.
#2: Journal: Methods Mol Biol / Year: 2023
Title: Isothermal Titration Calorimetry Analysis of a Cooperative Riboswitch Using an Interdependent-Sites Binding Model.
Authors: Cavender, C.E. / Schroeder, G.M. / Mathews, D.H. / Wedekind, J.E.
History
DepositionNov 29, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RNA (34-MER) Riboswitch
B: RNA (34-MER) Riboswitch
C: RNA (34-MER) Riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,70012
Polymers32,5523
Non-polymers1,1489
Water1086
1
A: RNA (34-MER) Riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2585
Polymers10,8511
Non-polymers4074
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RNA (34-MER) Riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2093
Polymers10,8511
Non-polymers3582
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: RNA (34-MER) Riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2334
Polymers10,8511
Non-polymers3833
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.867, 67.612, 50.589
Angle α, β, γ (deg.)90.00, 100.53, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: RNA chain RNA (34-MER) Riboswitch


Mass: 10850.541 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Carnobacterium antarcticum (bacteria)
#2: Chemical
ChemComp-PRF / 7-DEAZA-7-AMINOMETHYL-GUANINE


Mass: 179.179 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C7H9N5O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 41.43 % / Description: rod
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 30% PEG 8000, 0.2 M ammonium acetate, 0.01 M magnesium acetate tetrahydrate, and 0.05 M sodium cacodylate pH 6.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 21, 2022
Details: Flat Si Rh coated M0, Kirkpatrick-Baez flat bent Si M1 & M2
RadiationMonochromator: Liquid nitrogen-cooled double crystal Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 3→35.2 Å / Num. obs: 5588 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Rpim(I) all: 0.051 / Net I/σ(I): 7.6
Reflection shellResolution: 3→3.2 Å / Redundancy: 5.3 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 871 / Rpim(I) all: 0.339 / % possible all: 92.2

-
Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487)refinement
XDSdata reduction
Aimlessdata scaling
PHENIX(1.20.1_4487)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→35.16 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 34.75 / Stereochemistry target values: ML
Details: NCS restraints were applied throughout except for the last cycle of refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.2651 548 10 %random
Rwork0.2245 ---
obs0.2286 5478 97.32 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 111.8 Å2
Refinement stepCycle: LAST / Resolution: 3→35.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2071 3 6 2080
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022309
X-RAY DIFFRACTIONf_angle_d0.7263576
X-RAY DIFFRACTIONf_dihedral_angle_d15.6851121
X-RAY DIFFRACTIONf_chiral_restr0.028469
X-RAY DIFFRACTIONf_plane_restr0.003100
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.30.34421300.29061174X-RAY DIFFRACTION94
3.3-3.780.2861380.28251233X-RAY DIFFRACTION98
3.78-4.760.24911390.25911247X-RAY DIFFRACTION99
4.76-35.160.2531410.18181276X-RAY DIFFRACTION99
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)
16.18031.9792-4.47134.8658-3.30464.0670.12410.01621.16281.9731-0.46271.8484-1.9469-0.02270.42741.3792-0.14250.43610.6008-0.03151.4234-19.3574-14.2561-17.1237
21.3827-1.7241.4082.4398-1.8321.46181.65820.14530.08243.1371-1.9859-0.4876-2.06681.2640.81061.1634-0.4495-0.07181.02880.17781.7697-7.1562-0.1712-20.1589
35.92843.35880.33683.9783-0.97825.71750.8656-0.5242.80251.82080.10451.7093-0.0634-1.3016-0.54031.76090.34270.11420.7728-0.0151.5901-16.14874.096-23.2131
47.7281-7.733.44062.05982.88027.52952.10621.47411.11862.8743-3.78291.6219-1.936-3.23660.95681.44970.04860.49981.6235-0.0471.4633-21.2354-7.7871-27.1958
59.4821-0.06373.08872.02672.54321.2994-0.00331.62070.36351.6983-0.3139-2.2036-0.913-0.6785-0.15590.8710.05530.24250.93030.30671.1738-11.0455-15.9547-21.4785
64.8525-3.5159-1.5892.03479.43032.113-0.6955-1.91180.1965.0087-1.21591.33470.45670.13371.88822.1739-0.4067-0.06141.24440.23771.4599-15.5908-18.8555-10.3692
72.15650.6531-4.162.0847-1.0582.02441.6035-1.80440.6481.0885-0.5119-2.0114-1.78411.8059-1.14681.0446-0.0758-0.1861.14650.11611.5474-4.0698-8.7381-19.775
82.03091.68922.03972.00642.02932.0268-0.7494-0.073-3.1617-1.13761.62152.5331-0.05540.2321-0.77631.11880.1851-0.01241.1821-0.2491.66019.09-7.9151-44.5662
92.1706-6.165-4.81259.9111-0.70992.1767-0.6124-2.1372-1.37870.01320.81570.2796-0.73860.88940.14521.05440.32960.02411.20620.00590.92525.54831.0027-31.8321
101.92152.8105-3.33265.5024-2.01617.1508-0.59250.76681.94080.6759-1.57481.8379-0.6206-2.09461.59340.79650.29510.13461.0183-0.20451.3516-4.0387.0909-32.9725
116.0387-2.15293.38652.03314.79527.58-0.56341.0020.83140.1062-0.78932.19032.3674-0.50040.77331.1512-0.03280.06550.8979-0.04581.3103-0.17880.8761-46.0604
128.0615-1.56970.98766.8589-1.212.06930.1665-0.03050.17730.05640.0227-0.85741.17062.2459-0.26451.0110.2028-0.06631.3338-0.11790.769713.4590.9385-41.1713
133.8644-3.7494-0.68712.03490.80126.77460.0407-1.88440.8919-0.3476-0.0659-2.43961.25142.164-0.19550.78860.4297-0.07061.9958-0.08581.176112.3281.6725-31.771
149.7887-2.9508-3.40612.1727-3.54968.19960.5479-0.18253.7469-0.7436-0.43890.009-0.9263-0.49830.46130.83140.0455-0.14780.9236-0.06051.346-0.176310.8983-40.4568
151.43980.76011.64524.5270.03521.94190.5202-0.873-0.2683-0.3497-0.5767-0.19970.41380.14730.44421.46890.48350.36931.3769-0.01591.075811.6546-6.4359-2.4741
162.45591.769-1.00164.39720.40192.9274-0.56541.71730.3688-3.04080.75471.4431-0.15480.457-0.48121.6925-0.191-0.27451.4227-0.0370.797617.58286.8209-14.5117
176.74053.8186-2.59432.0308-0.04954.52120.68940.8242-0.4307-0.2584-0.9273-2.3995-0.07931.33250.03270.9920.03640.00821.1878-0.1221.048227.19287.3038-10.0238
189.79742.78125.20446.42340.42969.36930.40770.3655-0.2557-0.43580.1603-0.69121.56540.0828-0.3351.13320.0544-0.00411.0155-0.12140.92616.41714.1544-0.7891
196.65530.25350.80669.3342-6.22975.6244-0.6497-1.12540.034-0.38852.29441.37852.5008-1.9737-1.66311.29070.0102-0.12621.3543-0.06920.79693.9683-3.6517-6.6284
209.41192.7032-1.82645.94951.97031.9837-0.2894-0.28280.6149-1.9849-2.8614-0.08224.21112.13722.35021.3510.1774-0.54982.5427-0.18120.9788.4569-2.5486-15.459
217.0103-0.47862.15735.30072.16688.235-0.20080.5854-0.8889-1.10750.37680.8572-2.02250.50620.04531.07110.033-0.21770.83990.24171.341519.105812.2662-6.8296
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 5 )
2X-RAY DIFFRACTION2chain 'A' and (resid 6 through 9 )
3X-RAY DIFFRACTION3chain 'A' and (resid 10 through 13 )
4X-RAY DIFFRACTION4chain 'A' and (resid 14 through 17 )
5X-RAY DIFFRACTION5chain 'A' and (resid 18 through 21 )
6X-RAY DIFFRACTION6chain 'A' and (resid 22 through 26 )
7X-RAY DIFFRACTION7chain 'A' and (resid 27 through 30 )
8X-RAY DIFFRACTION8chain 'B' and (resid 1 through 4 )
9X-RAY DIFFRACTION9chain 'B' and (resid 5 through 8 )
10X-RAY DIFFRACTION10chain 'B' and (resid 9 through 12 )
11X-RAY DIFFRACTION11chain 'B' and (resid 13 through 16 )
12X-RAY DIFFRACTION12chain 'B' and (resid 17 through 21 )
13X-RAY DIFFRACTION13chain 'B' and (resid 22 through 30 )
14X-RAY DIFFRACTION14chain 'B' and (resid 31 through 34 )
15X-RAY DIFFRACTION15chain 'C' and (resid 1 through 4 )
16X-RAY DIFFRACTION16chain 'C' and (resid 5 through 9 )
17X-RAY DIFFRACTION17chain 'C' and (resid 10 through 13 )
18X-RAY DIFFRACTION18chain 'C' and (resid 14 through 19 )
19X-RAY DIFFRACTION19chain 'C' and (resid 20 through 24 )
20X-RAY DIFFRACTION20chain 'C' and (resid 25 through 28 )
21X-RAY DIFFRACTION21chain 'C' and (resid 29 through 34 )

+
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://pdbjlvh1.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