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- PDB-9p3a: T-Motif1-Motif2 right-left hybrid parallel G-quadruplex in comple... -

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Basic information

Entry
Database: PDB / ID: 9p3a
TitleT-Motif1-Motif2 right-left hybrid parallel G-quadruplex in complex with N-methylmesoporphyrin IX
ComponentsDNA (26-MER)
KeywordsDNA / G-quadruplex / right-left hybrid G-quadruplex / parallel / N-methylmesoporphyrin IX
Function / homology: / N-METHYLMESOPORPHYRIN / DNA / DNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 Å
AuthorsXing, E.R. / Seth, P.C. / Yatsunyk, L.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)1R15CA253134 United States
CitationJournal: To Be Published
Title: Preservation of left-handed fold and interaction with N-methylmesoporphyrin IX by two-block sequences with left-hand folding potential
Authors: Xing, E.R. / Yatsunyk, L.A.
History
DepositionJun 13, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (26-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,8476
Polymers8,5681
Non-polymers1,2795
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint-1 kcal/mol
Surface area4980 Å2
Unit cell
Length a, b, c (Å)21.572, 57.042, 57.641
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2

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Components

#1: DNA chain DNA (26-MER)


Mass: 8568.457 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Chemical ChemComp-MMP / N-METHYLMESOPORPHYRIN


Mass: 580.716 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C35H40N4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.56 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 008 M potassium chloride, 0.02 M magnesium chloride hexahydrate, 0.04 M sodium cacodylate trihydrate pH 6.0, 45% MPD, 12 mM spermine

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Data collection

DiffractionMean temperature: 196 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97911 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 24, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 2.34→57.64 Å / Num. obs: 3310 / % possible obs: 99.3 % / Redundancy: 6 % / Biso Wilson estimate: 77.34 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.075 / Net I/σ(I): 14.2
Reflection shellResolution: 2.34→2.42 Å / Rmerge(I) obs: 2.279 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 320 / CC1/2: 0.469

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
Coot0.9.5model building
XDSdata reduction
XDSdata scaling
PHENIX1.21.2_5419phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.34→40.54 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2569 165 5.11 %
Rwork0.2075 --
obs0.2101 3232 97.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.34→40.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 569 77 0 646
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012720
X-RAY DIFFRACTIONf_angle_d1.611114
X-RAY DIFFRACTIONf_dihedral_angle_d34.755310
X-RAY DIFFRACTIONf_chiral_restr0.063107
X-RAY DIFFRACTIONf_plane_restr0.01235
LS refinement shellResolution: 2.34→40.54 Å
RfactorNum. reflection% reflection
Rfree0.2569 165 -
Rwork0.2075 3067 -
obs--98 %
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)
12.03811.8927.22930.5251.17724.94761.0735-0.2253-2.7054-0.86371.1034-0.93640.68540.9047-1.53711.00410.09240.14430.6381-0.14921.10.9067-18.21891.9835
27.99115.14561.58489.98853.79469.17960.3276-0.27810.38670.2926-0.67840.8672-0.3176-0.29740.44060.82780.05110.05360.5958-0.02790.7048-5.4732-14.94839.6641
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 27 )

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