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- PDB-7u0y: Crystal structure of Pepper RNA aptamer in complex with HBC599 li... -

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Basic information

Entry
Database: PDB / ID: 7u0y
TitleCrystal structure of Pepper RNA aptamer in complex with HBC599 ligand and Fab BL3-6
Components
  • Fab BL3-6 heavy chain
  • Fab BL3-6 light chain
  • RNA aptamer
KeywordsIMMUNE SYSTEM/RNA / fluorogenic RNA / antibody / RNA / IMMUNE SYSTEM-RNA complex
Function / homologyChem-KY6 / RNA / RNA (> 10)
Function and homology information
Biological speciesMus musculus (house mouse)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.66 Å
AuthorsRees, H.C. / Piccirilli, J.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM102489 United States
CitationJournal: Acs Chem.Biol. / Year: 2022
Title: Structural Basis for Fluorescence Activation by Pepper RNA.
Authors: Rees, H.C. / Gogacz, W. / Li, N.S. / Koirala, D. / Piccirilli, J.A.
History
DepositionFeb 19, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Fab BL3-6 heavy chain
L: Fab BL3-6 light chain
R: RNA aptamer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,9116
Polymers68,5033
Non-polymers4083
Water2,828157
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis, The mobility of the RNA was decreased significantly after incubation with Fab BL3-6, suggesting successful binding.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.247, 96.071, 148.165
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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RNA chain , 1 types, 1 molecules R

#3: RNA chain RNA aptamer


Mass: 21734.830 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Antibody , 2 types, 2 molecules HL

#1: Antibody Fab BL3-6 heavy chain


Mass: 23662.418 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 Fab BL3-6 light chain


Mass: 23105.582 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, 160 molecules

#4: Chemical ChemComp-KY6 / 4-[(Z)-1-cyano-2-{6-[(2-hydroxyethyl)(methyl)amino]-1-benzothiophen-2-yl}ethenyl]benzonitrile


Mass: 359.444 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H17N3OS / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 3.12 Å3/Da / Density % sol: 63.75 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M Ammonium Acetate, 0.1 M BIS-TRIS pH 6.5, 45% v/v (+/-)-2-Methyl-2,4-pentanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 22, 2021
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.66→80.61 Å / Num. obs: 25179 / % possible obs: 96.79 % / Observed criterion σ(I): 3.3 / Redundancy: 3.3 % / Biso Wilson estimate: 84.72 Å2 / CC1/2: 0.997 / Net I/σ(I): 15.61
Reflection shellResolution: 2.66→2.79 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.461 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2793 / CC1/2: 0.75 / Rpim(I) all: 0.447 / Rrim(I) all: 0.643 / % possible all: 82.2

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
Cootmodel building
MOSFLMdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KZD

4kzd


Resolution: 2.66→58.67 Å / SU ML: 0.4449 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 29.8664
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2548 1999 7.99 %
Rwork0.2186 23029 -
obs0.2215 25028 96.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 81.8 Å2
Refinement stepCycle: LAST / Resolution: 2.66→58.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3290 1439 28 157 4914
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054998
X-RAY DIFFRACTIONf_angle_d0.80127107
X-RAY DIFFRACTIONf_chiral_restr0.0431848
X-RAY DIFFRACTIONf_plane_restr0.0051655
X-RAY DIFFRACTIONf_dihedral_angle_d14.99261994
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.66-2.720.43151100.43461268X-RAY DIFFRACTION75.8
2.72-2.80.42861300.33471495X-RAY DIFFRACTION89.38
2.8-2.880.32071410.30631628X-RAY DIFFRACTION97.68
2.88-2.970.36161440.28471665X-RAY DIFFRACTION99.12
2.97-3.080.34491470.28491689X-RAY DIFFRACTION99.4
3.08-3.20.35131450.29991667X-RAY DIFFRACTION99.18
3.2-3.350.33241460.27911675X-RAY DIFFRACTION99.4
3.35-3.520.29371450.24561678X-RAY DIFFRACTION98.97
3.52-3.740.27471440.21471664X-RAY DIFFRACTION98.53
3.74-4.030.27181490.23491712X-RAY DIFFRACTION99.73
4.03-4.440.24761440.19411670X-RAY DIFFRACTION98.11
4.44-5.080.20061490.16721705X-RAY DIFFRACTION98.41
5.08-6.40.18831490.19871710X-RAY DIFFRACTION97.79
6.4-58.670.23421560.19621803X-RAY DIFFRACTION97.51

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