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- PDB-4kzd: Crystal structure of an RNA aptamer in complex with fluorophore a... -

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Basic information

Entry
Database: PDB / ID: 4kzd
TitleCrystal structure of an RNA aptamer in complex with fluorophore and Fab
Components
  • (BL3-6 Fab antibody, ...) x 2
  • RNA (84-MER)
Keywordsimmune system/rna / G-quadruplex / Fluorescence / Fluorophore binding / In vitro / immune system-rna complex
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / sucrose / Chem-1TU / : / RNA / RNA (> 10)
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.186 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
Revision 1.3May 20, 2015Group: Structure summary
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)76,0877
Polymers75,4273
Non-polymers6604
Water8,395466
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4033
Polymers48,0602
Non-polymers3421
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4920 Å2
ΔGint-59 kcal/mol
Surface area19840 Å2
MethodPISA
3
R: RNA (84-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6844
Polymers27,3661
Non-polymers3183
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,0877
Polymers75,4273
Non-polymers6604
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
Buried area7610 Å2
ΔGint-111 kcal/mol
Surface area33150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.425, 79.602, 95.210
Angle α, β, γ (deg.)90.00, 111.65, 90.00
Int Tables number5
Space group name H-MC121

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Components

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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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RNA chain / Sugars , 2 types, 2 molecules R

#3: RNA chain RNA (84-MER)


Mass: 27366.256 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Spinach RNA aptamer
#4: Polysaccharide beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 4 types, 469 molecules

#5: Chemical ChemComp-K / POTASSIUM ION


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


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-1TU / 4-(3,5-difluoro-4-hydroxybenzyl)-1,2-dimethyl-1H-imidazol-5-ol


Mass: 254.233 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H12F2N2O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 466 / 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: 3.47 Å3/Da / Density % sol: 64.51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 8% Tacsimate, 20% PEG 3,350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 27, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.19→46.69 Å / Num. all: 52772 / Num. obs: 52477 / % possible obs: 98.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 3 % / Rmerge(I) obs: 0.059
Reflection shellResolution: 2.19→2.3 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.615 / Mean I/σ(I) obs: 1.8 / % possible all: 98.3

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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
Starting model: PDB entry 3IVK

3ivk


Resolution: 2.186→46.687 Å / SU ML: 0.29 / σ(F): 1.34 / Phase error: 23.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2108 2000 3.81 %
Rwork0.179 --
obs0.1803 52457 98.01 %
all-52772 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.186→46.687 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3321 1815 43 466 5645
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075483
X-RAY DIFFRACTIONf_angle_d1.1687864
X-RAY DIFFRACTIONf_dihedral_angle_d13.1232236
X-RAY DIFFRACTIONf_chiral_restr0.068946
X-RAY DIFFRACTIONf_plane_restr0.006675
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1857-2.24040.3521420.28343589X-RAY DIFFRACTION99
2.2404-2.3010.29121410.26623573X-RAY DIFFRACTION98
2.301-2.36870.28711440.23993595X-RAY DIFFRACTION98
2.3687-2.44510.2771430.22443614X-RAY DIFFRACTION99
2.4451-2.53250.25021430.21233611X-RAY DIFFRACTION99
2.5325-2.63390.25191440.20433655X-RAY DIFFRACTION99
2.6339-2.75370.24091440.20453614X-RAY DIFFRACTION98
2.7537-2.89890.24131420.20353594X-RAY DIFFRACTION98
2.8989-3.08050.23461430.19313601X-RAY DIFFRACTION99
3.0805-3.31830.22841430.18173584X-RAY DIFFRACTION98
3.3183-3.65210.23091410.16543566X-RAY DIFFRACTION96
3.6521-4.18030.17341420.15213597X-RAY DIFFRACTION98
4.1803-5.26560.15181430.13733608X-RAY DIFFRACTION97
5.2656-46.69780.18061450.16963656X-RAY DIFFRACTION97

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