[English] 日本語
Yorodumi
- PDB-8u5t: Structure of Mango II variant aptamer bound to T01-6A-B -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8u5t
TitleStructure of Mango II variant aptamer bound to T01-6A-B
ComponentsMango II variant
KeywordsRNA / aptamer / fluorescence / turn-on / fluorogenic / fluorophore / G-quartet / G-quadruplex
Function / homology: / : / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsPassalacqua, L.F.M. / 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: To Be Published
Title: Structure of Mango II variant aptamer bound to T01-6A-B
Authors: Passalacqua, L.F.M. / Ferre-D'Amare, A.R.
History
DepositionSep 12, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Mango II variant
B: Mango II variant
C: Mango II variant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,57215
Polymers35,6683
Non-polymers2,90412
Water1,35175
1
A: Mango II variant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,8866
Polymers11,8891
Non-polymers9965
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Mango II variant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,8635
Polymers11,8891
Non-polymers9734
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Mango II variant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,8234
Polymers11,8891
Non-polymers9343
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.849, 181.111, 105.908
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-103-

K

21A-232-

HOH

-
Components

#1: RNA chain Mango II variant


Mass: 11889.210 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-VLR / 3-{2,16-dioxo-20-[(3aS,4R,6aS)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]-6,9,12-trioxa-3,15-diazaicosan-1-yl}-2-{(E)-[6-(4-methoxyphenyl)-1-methylquinolin-4(1H)-ylidene]methyl}-1,3-benzothiazol-3-ium


Mass: 856.084 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C45H55N6O7S2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 2.48 Å3/Da / Density % sol: 50.34 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: Magnesium chloride hexahydrate, MOPS, Tacsimate, hexamine cobalt (III) chloride, and 1-propanol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 11, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→45.28 Å / Num. obs: 18555 / % possible obs: 99.57 % / Redundancy: 12.8 % / Biso Wilson estimate: 54.44 Å2 / CC1/2: 0.999 / Net I/σ(I): 9.55
Reflection shellResolution: 2.2→2.279 Å / Num. unique obs: 1812 / CC1/2: 0.752

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158phasing
PHENIX1.19.2_4158refinement
DIALS3.8data reduction
DIALS3.8data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→45.28 Å / SU ML: 0.4171 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.2623
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2331 1851 10 %
Rwork0.1882 16654 -
obs0.1901 18505 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.76 Å2
Refinement stepCycle: LAST / Resolution: 2.2→45.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2359 127 75 2561
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00552784
X-RAY DIFFRACTIONf_angle_d1.22424327
X-RAY DIFFRACTIONf_chiral_restr0.0492535
X-RAY DIFFRACTIONf_plane_restr0.0087119
X-RAY DIFFRACTIONf_dihedral_angle_d19.07431308
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.260.44141380.39151237X-RAY DIFFRACTION98.5
2.26-2.330.39821400.37521252X-RAY DIFFRACTION99.22
2.33-2.40.37771350.32911245X-RAY DIFFRACTION99.71
2.4-2.490.31281430.28511281X-RAY DIFFRACTION99.72
2.49-2.590.30151410.26581273X-RAY DIFFRACTION99.86
2.59-2.70.33921400.27911253X-RAY DIFFRACTION99.93
2.7-2.850.3611410.29651278X-RAY DIFFRACTION100
2.85-3.020.31511420.23721272X-RAY DIFFRACTION99.86
3.03-3.260.21571430.16881286X-RAY DIFFRACTION99.79
3.26-3.590.21131420.15351285X-RAY DIFFRACTION99.72
3.59-4.10.21491440.15481286X-RAY DIFFRACTION99.24
4.11-5.170.16461470.13511323X-RAY DIFFRACTION99.93
5.17-45.280.1711550.13651383X-RAY DIFFRACTION99.35
Refinement TLS params.Method: refined / Origin x: -16.5170492825 Å / Origin y: 25.1498481218 Å / Origin z: -3.25205055172 Å
111213212223313233
T0.416827362618 Å2-0.01970496512 Å20.0726457747783 Å2-0.332252360865 Å20.0075251169053 Å2--0.375283030108 Å2
L1.0889303389 °2-0.507373568407 °20.1992852148 °2-1.04897819318 °2-0.225594771926 °2--0.787289125448 °2
S-0.0836795714169 Å °-0.171487346924 Å °-0.200912095043 Å °0.155145535692 Å °0.0360956843925 Å °-0.0277260619833 Å °0.151700702033 Å °-0.0617133917771 Å °0.0311378478964 Å °
Refinement TLS groupSelection details: all

+
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