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- PDB-6xt7: Tel25 Hybrid Four-quartet G-quadruplex with K+ -

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Basic information

Entry
Database: PDB / ID: 6xt7
TitleTel25 Hybrid Four-quartet G-quadruplex with K+
ComponentsDNA (25-MER)
KeywordsDNA / G-quadruplex / Hybrid / Four-quartets / lateral loops / propeller loop
Function / homology: / SPERMINE / DNA / DNA (> 10)
Function and homology information
Biological speciesTetrahymena thermophila (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 Å
AuthorsYatsunyk, L.A. / McCarthy, S.E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)1R15CA208676-01A1 United States
Citation
Journal: Nucleic Acids Res. / Year: 2022
Title: The first crystal structures of hybrid and parallel four-tetrad intramolecular G-quadruplexes.
Authors: Beseiso, D. / Chen, E.V. / McCarthy, S.E. / Martin, K.N. / Gallagher, E.P. / Miao, J. / Yatsunyk, L.A.
#1: Journal: Nucleic Acids Res. / Year: 2021
Title: Water spines and networks in G-quadruplex structures.
Authors: Li, K. / Yatsunyk, L. / Neidle, S.
History
DepositionJul 17, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 2.0Apr 21, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / entity / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_nonpoly_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_validate_close_contact / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_symm_contact / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns / software / struct_conn
Item: _entity.pdbx_number_of_molecules / _pdbx_refine_tls.L[1][1] ..._entity.pdbx_number_of_molecules / _pdbx_refine_tls.L[1][1] / _pdbx_refine_tls.L[1][2] / _pdbx_refine_tls.L[1][3] / _pdbx_refine_tls.L[2][2] / _pdbx_refine_tls.L[2][3] / _pdbx_refine_tls.L[3][3] / _pdbx_refine_tls.S[1][1] / _pdbx_refine_tls.S[1][2] / _pdbx_refine_tls.S[1][3] / _pdbx_refine_tls.S[2][1] / _pdbx_refine_tls.S[2][2] / _pdbx_refine_tls.S[2][3] / _pdbx_refine_tls.S[3][1] / _pdbx_refine_tls.S[3][2] / _pdbx_refine_tls.S[3][3] / _pdbx_refine_tls.T[1][1] / _pdbx_refine_tls.T[1][2] / _pdbx_refine_tls.T[1][3] / _pdbx_refine_tls.T[2][2] / _pdbx_refine_tls.T[2][3] / _pdbx_refine_tls.T[3][3] / _pdbx_refine_tls.origin_x / _pdbx_refine_tls.origin_y / _pdbx_refine_tls.origin_z / _pdbx_refine_tls_group.beg_auth_asym_id / _pdbx_refine_tls_group.beg_auth_seq_id / _pdbx_refine_tls_group.beg_label_asym_id / _pdbx_refine_tls_group.end_auth_asym_id / _pdbx_refine_tls_group.end_auth_seq_id / _pdbx_refine_tls_group.end_label_asym_id / _pdbx_struct_assembly_prop.value / _refine.B_iso_mean / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_number_reflns_R_work / _refine.ls_number_reflns_obs / _refine.ls_percent_reflns_obs / _refine.overall_SU_ML / _refine.pdbx_overall_phase_error / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_ls_restr.dev_ideal / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.number_reflns_R_work / _refine_ls_shell.percent_reflns_obs / _reflns.B_iso_Wilson_estimate / _software.version
Description: Model completeness
Details: The structure of G-quadruplex was not modified. One of the two spermine molecules has been shifted by one atom to create a more appropriate (and better fitting) hydrogen bond network with ...Details: The structure of G-quadruplex was not modified. One of the two spermine molecules has been shifted by one atom to create a more appropriate (and better fitting) hydrogen bond network with nearby nucleotides and waters. The coordination sphere of one Mg atom was completed with the sixth water ligand (previously only five oxygen atoms were coordinated). Finally, 92 water molecules have been added into clear densities bringing the total water count to 379.
Provider: author / Type: Coordinate replacement
Revision 2.1Dec 28, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)32,96024
Polymers31,9404
Non-polymers1,02020
Water6,828379
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis, Determined purity and homogeneity of the samples. The sample exists as a monomer, but on the gel three bands were obvious and the crystallized samples clearly ...Evidence: native gel electrophoresis, Determined purity and homogeneity of the samples. The sample exists as a monomer, but on the gel three bands were obvious and the crystallized samples clearly represents only one of those bands. We have also conducted circular dichroism spectroscopy to obtain conformation information - parallel vs anti-parallel - as well as CD thermal melting studies to obtain stability information.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3590 Å2
ΔGint-53 kcal/mol
Surface area14990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.998, 92.916, 50.081
Angle α, β, γ (deg.)90.000, 99.621, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: DNA chain
DNA (25-MER)


Mass: 7985.084 Da / Num. of mol.: 4 / Source method: obtained synthetically
Details: Residues 1007 to 1010 on chain B are split into alternate conformations.
Source: (synth.) Tetrahymena thermophila (eukaryote)
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-SPM / SPERMINE


Mass: 202.340 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H26N4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 379 / 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: 2.21 Å3/Da / Density % sol: 44.4 %
Description: Long rods with a line down the middle. Somewhat opaque.
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop
Details: 39% 2-methyl-2,4-pentanediol, 0.165 M potassium chloride, 0.02 M magnesium chloride, 0.04 M sodium cacodylate pH 6.5, 0.012 M spermine tetrahydrochloride
PH range: 6.5-7.2 / Temp details: Crystals grown at room temperature.

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Data collection

DiffractionMean temperature: 196 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 13, 2020
RadiationMonochromator: Cryogenically-cooled single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.56→93.06 Å / Num. obs: 37569 / % possible obs: 98 % / Redundancy: 6.6 % / Biso Wilson estimate: 27.14 Å2 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.03 / Rrim(I) all: 0.082 / Net I/σ(I): 15.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) all% possible all
1.56-1.656.30.787253510.385196.1
4.94-93.066.50.05944.312490.0250.06699.7

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Processing

Software
NameVersionClassification
PHENIX1.18_3845refinement
XDSdata scaling
XDSdata reduction
Cootmodel building
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JRN

1jrn


Resolution: 1.56→49.38 Å / SU ML: 0.1486 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 25.689
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.1825 1996 5.32 %Random selection
Rwork0.1536 35517 --
obs0.1552 37513 97.12 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.73 Å2
Refinement stepCycle: LAST / Resolution: 1.56→49.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2124 46 379 2549
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122509
X-RAY DIFFRACTIONf_angle_d1.36033882
X-RAY DIFFRACTIONf_chiral_restr0.0655412
X-RAY DIFFRACTIONf_plane_restr0.0132104
X-RAY DIFFRACTIONf_dihedral_angle_d32.881049
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.56-1.60.32841300.32022309X-RAY DIFFRACTION89.41
1.6-1.640.32841390.2652475X-RAY DIFFRACTION95.44
1.64-1.690.25131420.23812518X-RAY DIFFRACTION96.03
1.69-1.740.22641430.22052526X-RAY DIFFRACTION96.25
1.74-1.80.27261400.21842488X-RAY DIFFRACTION96.8
1.8-1.880.23341450.19162570X-RAY DIFFRACTION97.45
1.88-1.960.20861410.19212524X-RAY DIFFRACTION97.91
1.96-2.070.24851430.18892548X-RAY DIFFRACTION97.75
2.07-2.190.21051440.18712557X-RAY DIFFRACTION98.33
2.19-2.360.23711430.18652576X-RAY DIFFRACTION98.34
2.36-2.60.22671460.18212583X-RAY DIFFRACTION98.81
2.6-2.980.22261470.17822624X-RAY DIFFRACTION98.82
2.98-3.750.14721440.12612577X-RAY DIFFRACTION98.84
3.75-49.380.12891490.11142642X-RAY DIFFRACTION99.39
Refinement TLS params.Method: refined / Origin x: -8.58246456259 Å / Origin y: -27.3649458929 Å / Origin z: -10.9788063564 Å
111213212223313233
T0.379801285228 Å2-0.0042538176447 Å2-0.0626242470628 Å2-0.172025751446 Å2-0.0147347132192 Å2--0.295310059325 Å2
L0.453038825109 °2-0.134002577761 °2-0.157093106679 °2-2.55595028574 °2-0.648765281821 °2--0.505450098075 °2
S-0.0108713098377 Å °0.0415270943039 Å °-0.0157411521495 Å °-0.0157438050123 Å °0.0307619183475 Å °0.0978131951635 Å °-0.0636744421607 Å °0.0482215745817 Å °-0.0235004856202 Å °
Refinement TLS groupSelection details: all

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