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- PDB-5ua3: Crystal Structure of a DNA G-Quadruplex with a Cytosine Bulge -

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Basic information

Entry
Database: PDB / ID: 5ua3
TitleCrystal Structure of a DNA G-Quadruplex with a Cytosine Bulge
ComponentsDNA (5'-D(*GP*GP*GP*TP*TP*GP*CP*GP*GP*AP*GP*GP*GP*TP*GP*GP*GP*CP*CP*T)-3')
KeywordsDNA / G-quadruplex / G4 / cytosine bulge / DNA structure
Function / homology: / DNA / DNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8802 Å
Model detailsStructure of human telomerase RNA component DNA analogue (nucleotides 1-20 )
AuthorsMeier, M. / McDougall, M.D. / Krahn, N.J. / Moya-Torres, A. / McRae, E.K.S. / Booy, E.P. / Patel, T.R. / McKenna, S.A. / Stetefeld, J.
Funding support Canada, 3items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)342077-2012 Canada
Natural Sciences and Engineering Research Council (NSERC, Canada)345517-07 Canada
Cancer Research Society Canada
Citation
Journal: Nucleic Acids Res. / Year: 2018
Title: Structure and hydrodynamics of a DNA G-quadruplex with a cytosine bulge.
Authors: Meier, M. / Moya-Torres, A. / Krahn, N.J. / McDougall, M.D. / Orriss, G.L. / McRae, E.K.S. / Booy, E.P. / McEleney, K. / Patel, T.R. / McKenna, S.A. / Stetefeld, J.
#1: Journal: J. Biol. Chem. / Year: 2013
Title: Binding of G-quadruplexes to the N-terminal recognition domain of the RNA helicase associated with AU-rich element (RHAU).
Authors: Meier, M. / Patel, T.R. / Booy, E.P. / Marushchak, O. / Okun, N. / Deo, S. / Howard, R. / McEleney, K. / Harding, S.E. / Stetefeld, J. / McKenna, S.A.
History
DepositionDec 18, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Category: pdbx_database_related / Item: _pdbx_database_related.content_type
Revision 1.2May 9, 2018Group: Data collection / Database references / Structure summary
Category: audit_author / citation / citation_author
Item: _audit_author.name / _citation.country ..._audit_author.name / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.3May 16, 2018Group: Data collection / Database references / Category: citation
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.4Jun 13, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.5Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA (5'-D(*GP*GP*GP*TP*TP*GP*CP*GP*GP*AP*GP*GP*GP*TP*GP*GP*GP*CP*CP*T)-3')
B: DNA (5'-D(*GP*GP*GP*TP*TP*GP*CP*GP*GP*AP*GP*GP*GP*TP*GP*GP*GP*CP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,8027
Polymers12,6062
Non-polymers1955
Water1,40578
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2250 Å2
ΔGint11 kcal/mol
Surface area7060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.103, 33.100, 33.282
Angle α, β, γ (deg.)64.650, 78.640, 81.780
Int Tables number1
Space group name H-MP1

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Components

#1: DNA chain DNA (5'-D(*GP*GP*GP*TP*TP*GP*CP*GP*GP*AP*GP*GP*GP*TP*GP*GP*GP*CP*CP*T)-3')


Mass: 6303.036 Da / Num. of mol.: 2
Fragment: DNA G-quadruplex, Human telomerase RNA component (TERC) DNA analogue, nucleotides 1-20
Source method: obtained synthetically
Details: Alpha DNA, 225 Bridge CP 4023, Montreal, Quebec H3C 0J7, Canada
Source: (synth.) Homo sapiens (human)
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: K
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 78 / Source method: isolated from a natural source / Formula: H2O

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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: 2.33 Å3/Da / Density % sol: 47.11 % / Description: Stacked plates / Mosaicity: 0.71 °
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 2.5 M NaCl, 10% v/v ethanol, 0.1 M sodium cacodylate, G4R1 53-105 peptide (UniProtKB Q9H2U1/DHX36_HUMAN, amino acid residues 53-105)

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: X-stream 2000
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54187 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 7, 2015 / Details: Rigaku Osmic Confocal Max-Flux multilayer mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 1.7963→20.3024 Å / Num. obs: 9658 / % possible obs: 96 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 33.5 Å2 / Rmerge(I) obs: 0.072 / Net I/av σ(I): 16.7 / Net I/σ(I): 9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.88-20.30243.90.0699.7195.99
1.7963-1.913.50.8061.5166.23
1.88-1.973.80.6842192.72

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å19.49 Å
Translation2.5 Å19.49 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
DENZOv706data reduction
SCALEPACKv706data scaling
PHASER2.5.7phasing
PDB_EXTRACT3.22data extraction
PHASER2.5.7phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XAV

1xav


Resolution: 1.8802→19.4935 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.925 / SU B: 9.172 / SU ML: 0.1226 / SU R Cruickshank DPI: 0.1993 / Cross valid method: THROUGHOUT / ESU R: 0.1993 / ESU R Free: 0.1613 / SU Rfree Cruickshank DPI: 0.1613
Details: Resolution of the structure is 1.88 A (where average I/sigmaI in outer shell = 2.0). During refinement we included data up to 1.796 A to improve the quality of the structure and the electron density map.
RfactorNum. reflection% reflectionSelection details
Rfree0.2474 603 6.8 %RANDOM
Rwork0.2274 ---
obs0.2288 8254 95.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 108.19 Å2 / Biso mean: 39.929 Å2 / Biso min: 19.82 Å2
Baniso -1Baniso -2Baniso -3
1--0.4 Å20.76 Å2-0.85 Å2
2--0.93 Å2-0.28 Å2
3----0.57 Å2
Refinement stepCycle: final / Resolution: 1.8802→19.4935 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 838 5 78 921
Biso mean--26.4 42.55 -
Num. residues----40
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.011942
X-RAY DIFFRACTIONr_bond_other_d00.02450
X-RAY DIFFRACTIONr_angle_refined_deg1.0671.1431458
X-RAY DIFFRACTIONr_angle_other_deg2.46131066
X-RAY DIFFRACTIONr_chiral_restr0.0690.2120
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02498
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02198
LS refinement shellResolution: 1.8802→1.929 Å
RfactorNum. reflection% reflection
Rfree0.362 39 -
Rwork0.306 579 -
obs--92.24 %
Refinement TLS params.Method: refined / Origin x: 3.406 Å / Origin y: 0.487 Å / Origin z: 0.492 Å
111213212223313233
T0.0482 Å2-0.0321 Å20.0481 Å2-0.0343 Å2-0.033 Å2--0.053 Å2
L9.1186 °20.7941 °20.53 °2-4.8418 °20.5381 °2--2.8822 °2
S-0.0957 Å °0.3283 Å °-0.0217 Å °-0.1911 Å °0.0011 Å °-0.1268 Å °-0.0154 Å °-0.02 Å °0.0946 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 20
2X-RAY DIFFRACTION1B1 - 20
3X-RAY DIFFRACTION1A101 - 103
4X-RAY DIFFRACTION1B101 - 102
5X-RAY DIFFRACTION1A201 - 253
6X-RAY DIFFRACTION1B201 - 225

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