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- PDB-5k8h: The X-ray crystal structure of a parallel poly(rA) double helix g... -

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Basic information

Entry
Database: PDB / ID: 5k8h
TitleThe X-ray crystal structure of a parallel poly(rA) double helix generated by rA7 at acidic pH
ComponentsRNA 7-mer
KeywordsRNA / parallel double-helix poly(rA) acidic pH adenine N1 protonation
Function / homologyAMMONIUM ION / RNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.069 Å
AuthorsGleghorn, M.L. / Maquat, L.E.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R37 GM074593 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM22939 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)T32 CA09363 United States
CitationJournal: Nucleic Acids Res. / Year: 2016
Title: Crystal structure of a poly(rA) staggered zipper at acidic pH: evidence that adenine N1 protonation mediates parallel double helix formation.
Authors: Gleghorn, M.L. / Zhao, J. / Turner, D.H. / Maquat, L.E.
History
DepositionMay 30, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2016Group: Database references
Revision 1.2Jul 20, 2016Group: Data collection
Revision 1.3Aug 17, 2016Group: Structure summary
Revision 1.4Oct 12, 2016Group: Database references
Revision 1.5Sep 20, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_struct_oper_list.symmetry_operation
Revision 1.6Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.7Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA 7-mer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,2782
Polymers2,2591
Non-polymers181
Water1448
1
A: RNA 7-mer
hetero molecules

A: RNA 7-mer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,5554
Polymers4,5192
Non-polymers362
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_835-x+3,-y-2,z1
Unit cell
Length a, b, c (Å)21.253, 21.253, 14.946
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
DetailsThe asymmetric unit is rA2, however the input RNA polymer is rA7, and this forms a continual parallel poly(rA) double helix structure. This structure is referred to as a "staggered zipper" since the rA7 strands overlap in a many different registers relative to their opposite, paired strands, to form the helix.

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Components

#1: RNA chain RNA 7-mer


Mass: 2259.483 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4N
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 1.33 Å3/Da / Density % sol: 8 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 3.5
Details: rA7 dissolved in water to 10 mM and was diluted 1/10 v/v in 0.75% PEG 1000. One uL of this was mixed with 1 uL of the following reservoir solution: (0.24 M ammonium sulfate and 0.06 M citric ...Details: rA7 dissolved in water to 10 mM and was diluted 1/10 v/v in 0.75% PEG 1000. One uL of this was mixed with 1 uL of the following reservoir solution: (0.24 M ammonium sulfate and 0.06 M citric acid pH 3.5) to generate a hanging drop over 1 mL of this reservoir solution.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9553 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9553 Å / Relative weight: 1
ReflectionResolution: 1.069→21.25 Å / Num. obs: 1679 / % possible obs: 97.6 % / Redundancy: 19.3 % / CC1/2: 0.994 / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.032 / Net I/σ(I): 15
Reflection shellResolution: 1.069→1.14 Å / Redundancy: 8.9 % / Rmerge(I) obs: 1.059 / Mean I/σ(I) obs: 3.1 / Num. unique all: 247 / CC1/2: 0.987 / Rpim(I) all: 0.333 / % possible all: 87.2

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: rA2 section of the 4JRD

4jrd


Resolution: 1.069→15.028 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.108 146 9.02 %
Rwork0.1061 1473 -
obs0.1063 1619 94.84 %
Refinement stepCycle: LAST / Resolution: 1.069→15.028 Å /
ProteinNucleic acidLigandSolventTotal
Num. atoms0 44 1 8 53
LS refinement shellResolution: 1.069→1.107 Å / Rfactor Rfree: 0.3975 / Rfactor Rwork: 0.318 / Rfactor obs: 0.318

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