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- PDB-7szu: Crystal structure of Pepper RNA aptamer in complex with HBC ligan... -

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Basic information

Entry
Database: PDB / ID: 7szu
TitleCrystal structure of Pepper RNA aptamer in complex with HBC ligand and Fab BL3-6
Components
  • BL3-6 Fab heavy chain
  • BL3-6 Fab light chain
  • RNA aptamer
KeywordsIMMUNE SYSTEM/RNA / fluorogenic / IMMUNE SYSTEM-RNA complex
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Chem-J8F / RNA / RNA (> 10)
Function and homology information
Biological speciesMus musculus (house mouse)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 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
DepositionNov 29, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 27, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 20, 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
R: RNA aptamer
H: BL3-6 Fab heavy chain
L: BL3-6 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,0647
Polymers68,6893
Non-polymers3754
Water9,836546
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis, EMSA
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.609, 96.992, 148.255
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

#1: 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

#2: Antibody BL3-6 Fab heavy chain


Mass: 23749.498 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)
#3: Antibody BL3-6 Fab light chain


Mass: 23204.668 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 , 4 types, 550 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Mg
#5: Chemical ChemComp-J8F / 4-[(~{Z})-1-cyano-2-[4-[2-hydroxyethyl(methyl)amino]phenyl]ethenyl]benzenecarbonitrile


Mass: 303.358 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C19H17N3O / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 546 / 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: 3.16 Å3/Da / Density % sol: 61.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.02 M Magnesium sulfate hydrate 0.002 M Cobalt(II) chloride hexahydrate 0.05 M Sodium cacodylate trihydrate pH 6.0 25% v/v (+/-)-2-Methyl-2,4-pentanediol, 0.0005 M Spermine

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 10, 2021
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.239→148.255 Å / Num. obs: 43646 / % possible obs: 99.9 % / Redundancy: 6.8 % / Biso Wilson estimate: 62.32 Å2 / CC1/2: 0.999 / Net I/σ(I): 17.9
Reflection shellResolution: 2.24→2.31 Å / Redundancy: 6.9 % / Rmerge(I) obs: 1.449 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 3937 / CC1/2: 0.605 / Rpim(I) all: 0.593 / % possible all: 99.2

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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: 2.24→58.9 Å / SU ML: 0.3874 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.6424
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2626 1999 4.59 %
Rwork0.2194 41547 -
obs0.2213 43546 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 69.89 Å2
Refinement stepCycle: LAST / Resolution: 2.24→58.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3303 1407 58 546 5314
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00255009
X-RAY DIFFRACTIONf_angle_d0.58157125
X-RAY DIFFRACTIONf_chiral_restr0.0375849
X-RAY DIFFRACTIONf_plane_restr0.0034658
X-RAY DIFFRACTIONf_dihedral_angle_d14.36692005
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.24-2.290.41111390.35082903X-RAY DIFFRACTION98.51
2.29-2.360.40171420.33412918X-RAY DIFFRACTION99.9
2.36-2.430.37881400.31032924X-RAY DIFFRACTION99.93
2.43-2.50.35441410.30662923X-RAY DIFFRACTION99.8
2.5-2.590.33451410.28412928X-RAY DIFFRACTION100
2.59-2.70.371420.29572942X-RAY DIFFRACTION99.97
2.7-2.820.39541410.2982949X-RAY DIFFRACTION99.97
2.82-2.970.36391430.27362960X-RAY DIFFRACTION100
2.97-3.150.26191420.24012951X-RAY DIFFRACTION99.94
3.16-3.40.28871410.24012956X-RAY DIFFRACTION99.81
3.4-3.740.26771430.20862983X-RAY DIFFRACTION99.9
3.74-4.280.23811460.1933001X-RAY DIFFRACTION99.94
4.28-5.390.18971450.16753044X-RAY DIFFRACTION99.94
5.4-58.90.23261530.20363165X-RAY DIFFRACTION99.55

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