[English] 日本語
Yorodumi
- PDB-8hze: A new fluorescent RNA aptamer bound with N -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8hze
TitleA new fluorescent RNA aptamer bound with N
ComponentsRNA (36-MER)
KeywordsRNA / Fluorescent RNA aptamer
Function / homologyGUANOSINE-5'-TRIPHOSPHATE / : / : / PHOSPHATE ION / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å
AuthorsHuang, K.Y. / Ren, A.M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat.Chem.Biol. / Year: 2024
Title: Structural basis of a small monomeric Clivia fluorogenic RNA with a large Stokes shift.
Authors: Huang, K. / Song, Q. / Fang, M. / Yao, D. / Shen, X. / Xu, X. / Chen, X. / Zhu, L. / Yang, Y. / Ren, A.
History
DepositionJan 9, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 19, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RNA (36-MER)
B: RNA (36-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,81520
Polymers22,5502
Non-polymers2,26618
Water2,720151
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.151, 45.870, 57.116
Angle α, β, γ (deg.)90.00, 115.08, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-264-

HOH

-
Components

-
RNA chain , 1 types, 2 molecules AB

#1: RNA chain RNA (36-MER)


Mass: 11274.813 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others)
Production host: in vitro transcription vector pT7-TP(deltai) (others)

-
Non-polymers , 6 types, 169 molecules

#2: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-NI4 / (5~{Z})-5-[[4-[2-hydroxyethyl(methyl)amino]phenyl]methylidene]-3-methyl-2-[(~{E})-2-phenylethenyl]imidazol-4-one


Mass: 361.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H23N3O2 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.92 Å3/Da / Density % sol: 35.85 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.05 M magnesium chloride, 0.1 M HEPES pH 7.5, 30% polyethylene glycol monomethyl ether 550, 0.6% 1,6-diaminohexane

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97892 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97892 Å / Relative weight: 1
ReflectionResolution: 1.59→50 Å / Num. obs: 23824 / % possible obs: 99.6 % / Redundancy: 6.7 % / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.041 / Rrim(I) all: 0.107 / Χ2: 1.818 / Net I/σ(I): 6.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.6-1.666.90.58123700.890.9710.2370.6280.689100
1.66-1.726.90.42423750.9280.9810.1730.4590.838100
1.72-1.86.70.33923720.9450.9860.140.3671.024100
1.8-1.96.30.2823660.9610.990.1190.3051.30399.4
1.9-2.026.90.22724110.9760.9940.0930.2451.603100
2.02-2.176.90.19323650.9780.9940.0790.2091.889100
2.17-2.396.50.16523620.9790.9950.0690.1792.2199
2.39-2.746.90.13523910.9860.9970.0550.1462.54399.8
2.74-3.456.60.123880.9880.9970.0430.1093.05599
3.45-506.70.07824240.9950.9990.0330.0853.03398.6

-
Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
HKL-3000data scaling
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.59→38.19 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 26.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2337 1154 4.85 %
Rwork0.1995 --
obs0.2011 23804 99.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.59→38.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1564 74 151 1789
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041812
X-RAY DIFFRACTIONf_angle_d0.9652806
X-RAY DIFFRACTIONf_dihedral_angle_d15.836874
X-RAY DIFFRACTIONf_chiral_restr0.044358
X-RAY DIFFRACTIONf_plane_restr0.00882
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.59-1.660.30091500.26672722X-RAY DIFFRACTION97
1.66-1.750.27981630.24512806X-RAY DIFFRACTION100
1.75-1.860.26971600.22992820X-RAY DIFFRACTION100
1.86-2.010.26771370.22912857X-RAY DIFFRACTION100
2.01-2.210.27641130.23492864X-RAY DIFFRACTION100
2.21-2.530.26621550.2392833X-RAY DIFFRACTION99
2.53-3.180.26381560.23152857X-RAY DIFFRACTION100
3.18-38.190.17681200.1562891X-RAY DIFFRACTION98

+
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