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- PDB-4kze: Crystal structure of an RNA aptamer in complex with Fab -

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Basic information

Entry
Database: PDB / ID: 4kze
TitleCrystal structure of an RNA aptamer in complex with Fab
Components
  • (BL3-6 Fab antibody, ...) x 2
  • RNA (84-MER)
Keywordsimmune system/rna / G-quadruplex / Fluorescence / Fluorophore binding / immune system-rna complex
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / : / RNA / RNA (> 10)
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.404 Å
AuthorsHuang, H. / Suslov, N.B. / Li, N. / Koldobskaya, Y. / Rice, P.A. / Piccirilli, J.A.
CitationJournal: Nat.Chem.Biol. / Year: 2014
Title: A G-quadruplex-containing RNA activates fluorescence in a GFP-like fluorophore.
Authors: Huang, H. / Suslov, N.B. / Li, N.S. / Shelke, S.A. / Evans, M.E. / Koldobskaya, Y. / Rice, P.A. / Piccirilli, J.A.
History
DepositionMay 29, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 18, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 9, 2014Group: Database references
Revision 1.2Jul 30, 2014Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: BL3-6 Fab antibody, heavy chain
L: BL3-6 Fab antibody, light chain
R: RNA (84-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,5705
Polymers75,5073
Non-polymers632
Water4,954275
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
H: BL3-6 Fab antibody, heavy chain
L: BL3-6 Fab antibody, light chain


Theoretical massNumber of molelcules
Total (without water)48,0602
Polymers48,0602
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3800 Å2
ΔGint-28 kcal/mol
Surface area20080 Å2
MethodPISA
3
R: RNA (84-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5103
Polymers27,4461
Non-polymers632
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
R: RNA (84-MER)
hetero molecules

H: BL3-6 Fab antibody, heavy chain
L: BL3-6 Fab antibody, light chain


Theoretical massNumber of molelcules
Total (without water)75,5705
Polymers75,5073
Non-polymers632
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
Buried area6590 Å2
ΔGint-78 kcal/mol
Surface area33550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.941, 80.104, 94.519
Angle α, β, γ (deg.)90.00, 111.86, 90.00
Int Tables number5
Space group name H-MC121

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Components

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RNA chain , 1 types, 1 molecules R

#3: RNA chain RNA (84-MER)


Mass: 27446.234 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Spinach RNA aptamer

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Antibody , 2 types, 2 molecules HL

#1: Antibody BL3-6 Fab antibody, heavy chain


Mass: 24665.510 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#2: Antibody BL3-6 Fab antibody, light chain


Mass: 23394.891 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)

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Non-polymers , 3 types, 277 molecules

#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 275 / 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: 3.42 Å3/Da / Density % sol: 64.02 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 8% Tacsimate, 20% PEG 3,350, 0.1 M HEPES, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 7.2

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 7, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.4→45.37 Å / Num. all: 38347 / Num. obs: 38273 / % possible obs: 96.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 2.9 % / Rmerge(I) obs: 0.066
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.536 / Mean I/σ(I) obs: 1.9 / % possible all: 95.3

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
RAPDmodel building
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
RAPDdata scaling
RAPDphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.404→45.366 Å / SU ML: 0.28 / σ(F): 1.35 / Phase error: 25.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2239 1998 5.22 %
Rwork0.1864 --
obs0.1884 38250 96.08 %
all-38347 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.404→45.366 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3321 1819 2 275 5417
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085438
X-RAY DIFFRACTIONf_angle_d1.117792
X-RAY DIFFRACTIONf_dihedral_angle_d14.442221
X-RAY DIFFRACTIONf_chiral_restr0.063937
X-RAY DIFFRACTIONf_plane_restr0.006674
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.404-2.46410.33541390.272530X-RAY DIFFRACTION93
2.4641-2.53080.29071410.24922564X-RAY DIFFRACTION96
2.5308-2.60520.2831430.23592593X-RAY DIFFRACTION97
2.6052-2.68930.31281440.23362590X-RAY DIFFRACTION97
2.6893-2.78540.34561410.242571X-RAY DIFFRACTION96
2.7854-2.89690.28591400.22742541X-RAY DIFFRACTION95
2.8969-3.02870.24181440.21952607X-RAY DIFFRACTION98
3.0287-3.18840.23271440.20252620X-RAY DIFFRACTION98
3.1884-3.38810.2191440.18922609X-RAY DIFFRACTION97
3.3881-3.64960.20651410.17722560X-RAY DIFFRACTION95
3.6496-4.01660.21671470.16342648X-RAY DIFFRACTION98
4.0166-4.59730.17451400.14722543X-RAY DIFFRACTION95
4.5973-5.79030.18291470.15382679X-RAY DIFFRACTION98
5.7903-45.37420.20191430.18012597X-RAY DIFFRACTION94

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