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- PDB-6db8: Structural basis for promiscuous binding and activation of fluoro... -

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Basic information

Entry
Database: PDB / ID: 6db8
TitleStructural basis for promiscuous binding and activation of fluorogenic dyes by DIR2s RNA aptamer
Components
  • Fab-Heavy chain
  • Fab-Light chain
  • RNA (60-MER)
KeywordsRNA/IMMUNE SYSTEM / Fluorescent aptamer / Fab / DIR / RNA / RNA-IMMUNE SYSTEM complex
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Chem-G4A / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86541345549 Å
AuthorsShao, Y. / Shelke, S.A. / Laski, A. / Piccirilli, J.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R01AI081987 United States
CitationJournal: Nat Commun / Year: 2018
Title: Structural basis for activation of fluorogenic dyes by an RNA aptamer lacking a G-quadruplex motif.
Authors: Shelke, S.A. / Shao, Y. / Laski, A. / Koirala, D. / Weissman, B.P. / Fuller, J.R. / Tan, X. / Constantin, T.P. / Waggoner, A.S. / Bruchez, M.P. / Armitage, B.A. / Piccirilli, J.A.
History
DepositionMay 2, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Fab-Heavy chain
R: RNA (60-MER)
L: Fab-Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,5254
Polymers67,1223
Non-polymers4031
Water4,540252
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)109.158, 118.442, 119.310
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2

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Components

#1: Antibody Fab-Heavy chain


Mass: 24665.510 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: RNA chain RNA (60-MER)


Mass: 19380.605 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Antibody Fab-Light chain


Mass: 23075.555 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#4: Chemical ChemComp-G4A / 2-[(Z)-(3-methyl-1,3-benzoxazol-2(3H)-ylidene)methyl]-3-(3-sulfopropyl)-1,3-benzothiazol-3-ium


Mass: 403.495 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C19H19N2O4S2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.89 Å3/Da / Density % sol: 57.48 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 50 mM MES, pH 5.6, 10 mM MgCl2, 1.8 M LiSO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.86→80.27 Å / Num. obs: 63989 / % possible obs: 99.15 % / Redundancy: 12.9 % / Biso Wilson estimate: 41.9006599711 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.017 / Rrim(I) all: 0.062 / Net I/σ(I): 21.6
Reflection shellResolution: 1.86→1.91 Å / Redundancy: 11.5 % / Rmerge(I) obs: 2.3 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 3915 / CC1/2: 0.476 / Rpim(I) all: 0.685 / Rrim(I) all: 2.405 / % possible all: 94.9

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
Coot0.8.6.1model building
PHENIX1.11.1_2575phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZKE

4zke


Resolution: 1.86541345549→37.59 Å / SU ML: 0.279977511605 / Cross valid method: FREE R-VALUE / σ(F): 1.33645911288 / Phase error: 28.7196515222
RfactorNum. reflection% reflection
Rfree0.233109193783 3857 3.1252785363 %
Rwork0.219263394781 --
obs0.219691816645 63984 99.1452236156 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 52.6096131687 Å2
Refinement stepCycle: LAST / Resolution: 1.86541345549→37.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3295 1286 27 252 4860
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003797802192674843
X-RAY DIFFRACTIONf_angle_d0.7402181113776872
X-RAY DIFFRACTIONf_chiral_restr0.0419224614266815
X-RAY DIFFRACTIONf_plane_restr0.00486278714805646
X-RAY DIFFRACTIONf_dihedral_angle_d16.72048836171945
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8654-1.88820.3914850478261350.3651658815263612X-RAY DIFFRACTION84.4109033566
1.8882-1.91210.3272019511421510.3448803376394305X-RAY DIFFRACTION99.4864925207
1.9121-1.93720.3611121310731230.3244354622254281X-RAY DIFFRACTION99.6831145315
1.9372-1.96380.3448232605281370.3222334834374330X-RAY DIFFRACTION99.7320830543
1.9638-1.99180.3499763564221170.306256115754277X-RAY DIFFRACTION99.6823956443
1.9918-2.02160.3319554460511270.2941412802854348X-RAY DIFFRACTION99.9553272281
2.0216-2.05310.3119366314751680.2964934326734264X-RAY DIFFRACTION99.8873112463
2.0531-2.08680.3623064386051520.2888104596584300X-RAY DIFFRACTION99.8430141287
2.0868-2.12280.2957212826311230.2773109902444327X-RAY DIFFRACTION99.8205473306
2.1228-2.16140.285790878121290.2652295842664253X-RAY DIFFRACTION99.7723132969
2.1614-2.2030.2587665181771340.2717729274814310X-RAY DIFFRACTION99.8427319703
2.203-2.24790.2955986184821450.2647804401654334X-RAY DIFFRACTION99.7105966162
2.2479-2.29680.2722105283591230.263002553114293X-RAY DIFFRACTION99.7064800181
2.2968-2.35030.3034506540641560.2712999695634251X-RAY DIFFRACTION99.8414136837
2.3503-2.4090.2719611036221360.264096955684297X-RAY DIFFRACTION99.9098489971
2.409-2.47420.3334343872431130.2753220770654339X-RAY DIFFRACTION99.7311827957
2.4742-2.5470.3230144047631500.2707582631814276X-RAY DIFFRACTION99.7296079315
2.547-2.62920.2507820261691420.2704531457174274X-RAY DIFFRACTION99.7966101695
2.6292-2.72320.3417352146671400.2748691991854294X-RAY DIFFRACTION99.6180633565
2.7232-2.83220.2830588458371310.2667227964964280X-RAY DIFFRACTION99.6385814321
2.8322-2.96110.2896589257551600.2560264017564296X-RAY DIFFRACTION99.7314234557
2.9611-3.11720.2502406263391220.2331634972964344X-RAY DIFFRACTION99.888168195
3.1172-3.31260.2098836883691510.2176862342624263X-RAY DIFFRACTION99.773960217
3.3126-3.56830.1905119160191330.2008285479364285X-RAY DIFFRACTION99.5717827361
3.5683-3.92740.1831872007851350.1902360623274273X-RAY DIFFRACTION99.2569241162
3.9274-4.49570.1647067347691380.1700106049284291X-RAY DIFFRACTION98.9499553172
4.4957-5.66390.1860740189851380.1651177086534284X-RAY DIFFRACTION99.9547920434
5.6639-80.34250.2179720422211480.1873187111444275X-RAY DIFFRACTION99.237155037

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