[English] 日本語
Yorodumi
- PDB-9c46: Right-left hybrid parallel G-quadruplex from SLC2A1 promoter -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9c46
TitleRight-left hybrid parallel G-quadruplex from SLC2A1 promoter
ComponentsDNA (25-MER)
KeywordsDNA / G-quadruplex / right-left-handed / parallel
Function / homology: / DNA / DNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å
AuthorsXing, E.R. / Yatsunyk, L.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)1R15CA253134 United States
CitationJournal: Nucleic Acids Res. / Year: 2025
Title: Interaction of N-methylmesoporphyrin IX with a hybrid left-/right-handed G-quadruplex motif from the promoter of the SLC2A1 gene.
Authors: Seth, P. / Xing, E. / Hendrickson, A.D. / Li, K. / Monsen, R. / Chaires, J.B. / Neidle, S. / Yatsunyk, L.A.
History
DepositionJun 3, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2025Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.year / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA (25-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,2677
Polymers7,9691
Non-polymers2986
Water181
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.137, 31.491, 31.500
Angle α, β, γ (deg.)90.000, 104.308, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-104-

K

-
Components

#1: DNA chain DNA (25-MER)


Mass: 7969.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / 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-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.98 Å3/Da / Density % sol: 38 % / Description: Long needles
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.08 M NaCl 0.04 M Na Cacodylate pH 6.0 45% MPD

-
Data collection

DiffractionMean temperature: 196 K / Ambient temp details: Liquid Nitrogen / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.920105 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 9, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.920105 Å / Relative weight: 1
ReflectionResolution: 2.388→30.523 Å / Num. obs: 2469 / % possible obs: 98.7 % / Redundancy: 3.3 % / Biso Wilson estimate: 45.06 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.103 / Net I/σ(I): 8.4
Reflection shellResolution: 2.388→2.429 Å / Redundancy: 3.4 % / Rmerge(I) obs: 1.383 / Num. unique obs: 120 / CC1/2: 0.541 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
Coot0.8.9.2model building
autoPROCdata reduction
autoPROCdata scaling
PHENIX1.19.2_4158phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.39→25.1 Å / SU ML: 0.286 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.1266
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2543 138 5.69 %
Rwork0.2334 2287 -
obs0.2345 2425 96.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 68.36 Å2
Refinement stepCycle: LAST / Resolution: 2.39→25.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 530 13 1 544
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041603
X-RAY DIFFRACTIONf_angle_d0.6677935
X-RAY DIFFRACTIONf_chiral_restr0.0378100
X-RAY DIFFRACTIONf_plane_restr0.00425
X-RAY DIFFRACTIONf_dihedral_angle_d37.5747247
LS refinement shellResolution: 2.39→25.1 Å
RfactorNum. reflection% reflection
Rfree0.2543 138 -
Rwork0.2334 2287 -
obs--96.96 %
Refinement TLS params.Method: refined / Origin x: -7.37227320646 Å / Origin y: -15.0394758857 Å / Origin z: 0.611787987161 Å
111213212223313233
T0.2284134256 Å2-0.0521103425253 Å20.0471139562059 Å2-0.900066468933 Å20.0154507151063 Å2--0.340858555908 Å2
L1.23251467589 °2-1.28246840956 °20.0400834848819 °2-1.39754277912 °2-0.566125852934 °2--8.16722262439 °2
S-0.0477047884491 Å °-0.104063762583 Å °-0.328723971275 Å °0.00855466207353 Å °0.350679306336 Å °0.993918256943 Å °0.823465165572 Å °-3.17232058668 Å °0.512628463825 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