[English] 日本語
Yorodumi
- PDB-8vqv: Structure of S. odontolytica ZTP riboswitch bound to m-1-pyridiny... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8vqv
TitleStructure of S. odontolytica ZTP riboswitch bound to m-1-pyridinyl-AICA
ComponentsRNA (64-MER)
KeywordsRNA / riboswitch / drug / synthetic / aptamer
Function / homologyChem-UG4 / RNA / RNA (> 10)
Function and homology information
Biological speciesSchaalia odontolytica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.43 Å
AuthorsJones, C.P. / Ferre D'Amare, A.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI) United States
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2025
Title: Machine Learning-Augmented Molecular Dynamics Simulations (MD) Reveal Insights Into the Disconnect Between Affinity and Activation of ZTP Riboswitch Ligands.
Authors: Fullenkamp, C.R. / Mehdi, S. / Jones, C.P. / Tenney, L. / Pichling, P. / Prestwood, P.R. / Ferre-D'Amare, A.R. / Tiwary, P. / Schneekloth, J.S.
History
DepositionJan 19, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 11, 2025Provider: repository / Type: Initial release
Revision 1.1Aug 6, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title ..._citation.journal_volume / _citation.title / _citation_author.identifier_ORCID / _citation_author.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RNA (64-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0344
Polymers20,7821
Non-polymers2523
Water41423
1
A: RNA (64-MER)
hetero molecules

A: RNA (64-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0698
Polymers41,5652
Non-polymers5046
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area4550 Å2
ΔGint-68 kcal/mol
Surface area19320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.035, 41.035, 237.398
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

#1: RNA chain RNA (64-MER)


Mass: 20782.453 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schaalia odontolytica (bacteria)
Production host: in vitro transcription vector pT7-TP(deltai) (others)
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-UG4 / 5-amino-1-(pyridin-3-yl)-1H-imidazole-4-carboxamide


Mass: 203.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H9N5O / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.84 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / Details: TBD

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.10503 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 15, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.10503 Å / Relative weight: 1
ReflectionResolution: 2.43→40.44 Å / Num. obs: 14549 / % possible obs: 99.63 % / Redundancy: 12 % / CC1/2: 0.998 / Rmerge(I) obs: 0.09664 / Net I/σ(I): 16.27
Reflection shellResolution: 2.43→2.517 Å / Num. unique obs: 788 / CC1/2: 0.854

-
Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.43→40.44 Å / SU ML: 0.49 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2556 1448 9.95 %
Rwork0.2068 --
obs0.2116 14549 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.43→40.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1376 23 17 1416
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051562
X-RAY DIFFRACTIONf_angle_d1.0732440
X-RAY DIFFRACTIONf_dihedral_angle_d14.65766
X-RAY DIFFRACTIONf_chiral_restr0.041319
X-RAY DIFFRACTIONf_plane_restr0.00667
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.43-2.520.55581440.49531295X-RAY DIFFRACTION100
2.52-2.620.36471480.3791307X-RAY DIFFRACTION100
2.62-2.740.32061530.34751320X-RAY DIFFRACTION100
2.74-2.880.37661400.31281300X-RAY DIFFRACTION100
2.88-3.060.3851470.2921313X-RAY DIFFRACTION100
3.06-3.30.27221430.2121298X-RAY DIFFRACTION100
3.3-3.630.23741430.19681321X-RAY DIFFRACTION100
3.63-4.150.25071440.19941332X-RAY DIFFRACTION100
4.15-5.230.2041350.16961311X-RAY DIFFRACTION100
5.23-40.440.21510.14721304X-RAY DIFFRACTION100
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)
12.0149-0.1541-0.67233.70850.05542.77720.10790.1599-0.19060.1867-0.2908-0.2344-0.0420.33520.20940.6068-0.0125-0.13980.56530.01320.5175-24.7525-3.0186-17.6655
21.72220.04-1.08694.4784-0.07482.7813-0.0580.0592-0.65130.169-0.09630.77660.1919-0.25020.1390.54140.0738-0.10040.507-0.02440.6245-30.7307-6.9515-16.9506
30.4231-0.042-0.62690.69181.04822.4301-0.01541.69260.8024-0.2802-0.07430.2102-0.1280.11650.05420.5325-0.0197-0.08881.18880.25650.63622.2278-24.6416.6367
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 20 )
2X-RAY DIFFRACTION2chain 'A' and (resid 21 through 45 )
3X-RAY DIFFRACTION3chain 'A' and (resid 46 through 64 )

+
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