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- PDB-4jiy: RNA three-way junction stabilized by a supramolecular di-iron(II)... -

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Basic information

Entry
Database: PDB / ID: 4jiy
TitleRNA three-way junction stabilized by a supramolecular di-iron(II) cylinder drug
Components5'-(CGUACG)-3'
KeywordsRNA / THREE-WAY JUNCTION / DRUG-RNA COMPLEX / RNA STRUCTURE RECOGNITION / CYLINDER / SUPRAMOLECULE
Function / homology: / Chem-NPM / RNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.91 Å
AuthorsSigel, R.K.O. / Schnabl, J.A. / Freisinger, E. / Spingler, B. / Hannon, M.J.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2013
Title: Binding of a designed anti-cancer drug to the central cavity of an RNA three-way junction.
Authors: Phongtongpasuk, S. / Paulus, S. / Schnabl, J. / Sigel, R.K. / Spingler, B. / Hannon, M.J. / Freisinger, E.
History
DepositionMar 7, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2013Group: Database references
Revision 1.2Nov 6, 2013Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5'-(CGUACG)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,8677
Polymers1,8911
Non-polymers9766
Water70339
1
A: 5'-(CGUACG)-3'
hetero molecules

A: 5'-(CGUACG)-3'
hetero molecules

A: 5'-(CGUACG)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,60221
Polymers5,6743
Non-polymers2,92918
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area4090 Å2
ΔGint-67 kcal/mol
Surface area3040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.745, 45.745, 45.745
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-102-

FE2

21A-103-

FE2

31A-105-

FE2

41A-106-

FE2

51A-207-

HOH

DetailsBIOMOLECULE: 1, 2 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON BURIED SURFACE AREA. REMARK: THE RNA THREE-WAY JUNCTION IS GENERATED FROM THE ASYMMETRIC UNIT BY THE OPERATIONS. THE TERMINAL 1/3 CYLINDER LIGANDS ARE PART OF THE INFINITE CRYSTAL LATTICE. COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. BIOMOLECULE: 1 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC SOFTWARE USED: PISA TOTAL BURIED SURFACE AREA: 970 ANGSTROM**2 SURFACE AREA OF THE COMPLEX: 3870 ANGSTROM**2 CHANGE IN SOLVENT FREE ENERGY: -5.0 KCAL/MOL APPLY THE FOLLOWING TO CHAINS: A BIOMT1 1 1.000000 0.000000 0.000000 0.00000 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 BIOMT1 2 0.000000 0.000000 1.000000 0.00000 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 BIOMT3 2 0.000000 1.000000 0.000000 0.00000 BIOMT1 3 0.000000 1.000000 0.000000 0.00000 BIOMT2 3 0.000000 0.000000 1.000000 0.00000 BIOMT3 3 1.000000 0.000000 0.000000 0.00000 BIOMOLECULE: 2 AUTHOR DETERMINED BIOLOGICAL UNIT: NONAMERIC APPLY THE FOLLOWING TO CHAINS: A BIOMT1 1 1.000000 0.000000 0.000000 0.00000 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 BIOMT1 2 -1.000000 0.000000 0.000000 68.61750 BIOMT2 2 0.000000 -1.000000 0.000000 91.49000 BIOMT3 2 0.000000 0.000000 1.000000 22.87250 BIOMT1 3 -1.000000 0.000000 0.000000 91.49000 BIOMT2 3 0.000000 1.000000 0.000000 -22.87250 BIOMT3 3 0.000000 0.000000 -1.000000 68.61750 BIOMT1 4 0.000000 0.000000 1.000000 0.00000 BIOMT2 4 1.000000 0.000000 0.000000 0.00000 BIOMT3 4 0.000000 1.000000 0.000000 0.00000 BIOMT1 5 0.000000 0.000000 1.000000 22.87250 BIOMT2 5 -1.000000 0.000000 0.000000 68.61750 BIOMT3 5 0.000000 -1.000000 0.000000 91.49000 BIOMT1 6 0.000000 0.000000 -1.000000 68.61750 BIOMT2 6 -1.000000 0.000000 0.000000 91.49000 BIOMT3 6 0.000000 1.000000 0.000000 -22.87250 BIOMT1 7 0.000000 1.000000 0.000000 0.00000 BIOMT2 7 0.000000 0.000000 1.000000 0.00000 BIOMT3 7 1.000000 0.000000 0.000000 0.00000 BIOMT1 8 0.000000 -1.000000 0.000000 91.49000 BIOMT2 8 0.000000 0.000000 1.000000 22.87250 BIOMT3 8 -1.000000 0.000000 0.000000 68.61750 BIOMT1 9 0.000000 1.000000 0.000000 -22.87250 BIOMT2 9 0.000000 0.000000 -1.000000 68.61750 BIOMT3 9 -1.000000 0.000000 0.000000 91.49000

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Components

#1: RNA chain 5'-(CGUACG)-3'


Mass: 1891.189 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Chemical ChemComp-NPM / N-[(1E)-PYRIDIN-2-YLMETHYLENE]-N-[4-(4-{[(1E)-PYRIDIN-2-YLMETHYLENE]AMINO}BENZYL)PHENYL]AMINE / 1,1-BIS(N-(4-PHENYL)-2-PYRIDYLCARBOXALDIMINE)METHANE


Mass: 376.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H20N4
#3: Chemical
ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)Description
14.2270.84THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS.
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
293.151vapor diffusion, sitting drop8.520% PEG 400, 0.18M MAGNESIUM ACETATE, 0.05M TRIS CHLORIDE, PH 8.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293.15K. 15% PEG 400, 0.165M MAGNESIUM ACETATE, 0.05M TRIS CHLORIDE, PH 8.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293.15K
293.152vapor diffusion, sitting drop8.515% PEG 400, 0.165M MAGNESIUM ACETATE, 0.05M TRIS CHLORIDE, PH 8.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293.15K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
Diffraction source
SourceSiteBeamlineIDWavelengthWavelength (Å)
SYNCHROTRONSLS X06DA10.99990.9999
SYNCHROTRONSLS X06DA20.9999
Detector
TypeIDDetectorDateDetails
MARMOSAIC 225 mm CCD1CCDDec 10, 2009MIRROR, BARTELS MONOCHROMATOR, DUAL CHANNEL CUT CRYSTALS, TOROIDAL MIRROR
MARMOSAIC 225 mm CCD2CCDSep 12, 2009MIRROR, BARTELS MONOCHROMATOR, DUAL CHANNEL CUT CRYSTALS, TOROIDAL MIRROR
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1BARTELS MONOCHROMATORSINGLE WAVELENGTHMx-ray1
2BARTELS MONOCHROMATORMADMx-ray1
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.91→45.745 Å / Num. all: 4826 / Num. obs: 4030 / % possible obs: 99.7 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 2 / Redundancy: 7.5 % / Rmerge(I) obs: 0.0204 / Net I/σ(I): 27.06
Reflection shellResolution: 1.91→2.01 Å / Redundancy: 0.99 % / Rmerge(I) obs: 0.3847 / Mean I/σ(I) obs: 2.67 / Num. unique all: 703 / Rsym value: 0.3847 / % possible all: 98.7

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Processing

Software
NameClassification
RemDAqdata collection
SHELXDphasing
SHELXL-97refinement
XDSdata reduction
XPREPdata reduction
RefinementMethod to determine structure: MAD / Resolution: 1.91→26.41 Å / σ(F): 4 / σ(I): 2 / Stereochemistry target values: KLOSTERMAN & SINE
RfactorNum. reflection% reflectionSelection details
Rfree0.2709 242 5 %RANDOM
Rwork0.224 ---
all-4814 --
obs-4030 83.7 %-
Displacement parametersBiso mean: 51.2 Å2
Refinement stepCycle: LAST / Resolution: 1.91→26.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 125 62 39 226
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.009
X-RAY DIFFRACTIONs_angle_d0.027
X-RAY DIFFRACTIONs_from_restr_planes0.04
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.008
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.004
X-RAY DIFFRACTIONSIMU0.164

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