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- PDB-8cxf: Crystal structure of an i-motif from the HRAS promoter region -

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Basic information

Entry
Database: PDB / ID: 8cxf
TitleCrystal structure of an i-motif from the HRAS promoter region
ComponentsHRAS DNA
KeywordsDNA / HRAS / i-Motif
Function / homology1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE / RNA / RNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.77 Å
AuthorsYatsunyk, L.A. / Li, K.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)1R15CA253134 United States
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2023
Title: Crystal Structure of an i-Motif from the HRAS Oncogene Promoter.
Authors: Li, K.S. / Jordan, D. / Lin, L.Y. / McCarthy, S.E. / Schneekloth Jr., J.S. / Yatsunyk, L.A.
History
DepositionMay 20, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 28, 2023Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: HRAS DNA
A: HRAS DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,6263
Polymers16,4482
Non-polymers1781
Water1,31573
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis, we performed gel on crystals and they are composed of an HRAS dimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)118.392, 31.271, 54.279
Angle α, β, γ (deg.)90.000, 92.930, 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

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Components

#1: RNA chain HRAS DNA


Mass: 8224.110 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Chemical ChemComp-PG5 / 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE


Mass: 178.226 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C8H18O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.99 Å3/Da / Density % sol: 55.7 % / Description: rectangular prism
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.05 M MES, 17% w/v PEG 4000, X M Spermine Tetrahydrochloride (ADD SPERMINE CONCENTRATION)

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Data collection

DiffractionMean temperature: 196 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9196 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 8, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9196 Å / Relative weight: 1
ReflectionResolution: 1.77→41.01 Å / Num. obs: 19101 / % possible obs: 95.91 % / Redundancy: 9.6 % / Biso Wilson estimate: 38.58 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.02 / Rrim(I) all: 0.062 / Net I/σ(I): 16.6
Reflection shellResolution: 1.77→1.8 Å / Redundancy: 6.1 % / Rmerge(I) obs: 1.462 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 784 / CC1/2: 0.725 / Rpim(I) all: 0.625 / Rrim(I) all: 1.596 / % possible all: 68.5

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.18.2_3874phasing
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.77→41.01 Å / SU ML: 0.2511 / Cross valid method: FREE R-VALUE / σ(F): 0.28 / Phase error: 40.5211
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.237 1763 10.04 %
Rwork0.2211 15805 -
obs0.2226 17568 88.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 58.95 Å2
Refinement stepCycle: LAST / Resolution: 1.77→41.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1044 12 73 1129
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00841175
X-RAY DIFFRACTIONf_angle_d0.94281800
X-RAY DIFFRACTIONf_chiral_restr0.0404206
X-RAY DIFFRACTIONf_plane_restr0.005652
X-RAY DIFFRACTIONf_dihedral_angle_d31.9012508
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.77-1.810.5453950.4858790X-RAY DIFFRACTION58.69
1.81-1.870.3949990.4446939X-RAY DIFFRACTION69.52
1.87-1.930.42281330.40211085X-RAY DIFFRACTION79.87
1.93-20.34481250.35291192X-RAY DIFFRACTION87.45
2-2.080.33681430.34671191X-RAY DIFFRACTION87.19
2.08-2.170.34141330.30121246X-RAY DIFFRACTION90.25
2.17-2.290.26871370.28231233X-RAY DIFFRACTION90.97
2.29-2.430.33561480.27021303X-RAY DIFFRACTION94.77
2.43-2.620.3091430.25131325X-RAY DIFFRACTION96.39
2.62-2.880.32451560.271346X-RAY DIFFRACTION98.04
2.88-3.290.28771470.25311328X-RAY DIFFRACTION96.47
3.3-4.150.23711440.20571390X-RAY DIFFRACTION98.21
4.15-41.010.1381600.15261437X-RAY DIFFRACTION99.07
Refinement TLS params.Method: refined / Origin x: 58.7397517229 Å / Origin y: 12.7545310328 Å / Origin z: 14.9302910152 Å
111213212223313233
T0.511867376093 Å20.176927927317 Å20.0111738477889 Å2-0.534082072528 Å20.00187813405801 Å2--0.448883892224 Å2
L0.317393557686 °2-0.410465579177 °2-0.109094586896 °2-0.606793451947 °20.0112684460327 °2--0.254521743259 °2
S-0.613914014818 Å °-0.707467804629 Å °0.039768566303 Å °0.130915639926 Å °0.441215056995 Å °0.00859424693586 Å °-0.0225790860585 Å °0.0441830217106 Å °-0.00289965162917 Å °
Refinement TLS groupSelection details: all

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