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- PDB-8amm: Crystal structure of AUGUGGCAU duplex with cesium ions -

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Basic information

Entry
Database: PDB / ID: 8amm
TitleCrystal structure of AUGUGGCAU duplex with cesium ions
ComponentsRNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
KeywordsRNA / UG wobble / Ba ions / UGG repeats
Function / homology: / RNA
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.86 Å
AuthorsKiliszek, A. / Rypniewski, W.
Funding support Poland, 1items
OrganizationGrant numberCountry
Other government Poland
CitationJournal: Rna / Year: 2022
Title: Structure and thermodynamics of a UGG motif interacting with Ba2+ and other metal ions: accommodating changes in the RNA structure and the presence of a G(syn)-G(syn) pair.
Authors: Kiliszek, A. / Pluta, M. / Bejger, M. / Rypniewski, W.
History
DepositionAug 3, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 23, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
B: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
C: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
D: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
E: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
F: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
G: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
H: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
I: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
J: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
K: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
L: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
M: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
N: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
O: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
P: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
Q: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
R: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
S: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
T: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
U: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
V: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
Y: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
Z: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
a: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
b: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
c: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
d: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,15856
Polymers80,43728
Non-polymers3,72128
Water00
1
A: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
B: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,0114
Polymers5,7462
Non-polymers2662
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1570 Å2
ΔGint-99 kcal/mol
Surface area3160 Å2
2
C: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
D: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,0114
Polymers5,7462
Non-polymers2662
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1570 Å2
ΔGint-98 kcal/mol
Surface area3150 Å2
3
E: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
F: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,0114
Polymers5,7462
Non-polymers2662
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1590 Å2
ΔGint-99 kcal/mol
Surface area3150 Å2
4
G: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
H: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,0114
Polymers5,7462
Non-polymers2662
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1590 Å2
ΔGint-100 kcal/mol
Surface area3140 Å2
5
I: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
J: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,0114
Polymers5,7462
Non-polymers2662
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1580 Å2
ΔGint-101 kcal/mol
Surface area3180 Å2
6
K: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
L: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,0114
Polymers5,7462
Non-polymers2662
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1570 Å2
ΔGint-99 kcal/mol
Surface area3160 Å2
7
M: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
N: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,0114
Polymers5,7462
Non-polymers2662
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint-99 kcal/mol
Surface area3150 Å2
8
O: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
P: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,0114
Polymers5,7462
Non-polymers2662
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1580 Å2
ΔGint-99 kcal/mol
Surface area3130 Å2
9
Q: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
R: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,0114
Polymers5,7462
Non-polymers2662
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1580 Å2
ΔGint-99 kcal/mol
Surface area3160 Å2
10
S: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
T: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,0114
Polymers5,7462
Non-polymers2662
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1560 Å2
ΔGint-100 kcal/mol
Surface area3160 Å2
11
U: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
V: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,0114
Polymers5,7462
Non-polymers2662
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint-99 kcal/mol
Surface area3170 Å2
12
Y: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
Z: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,0114
Polymers5,7462
Non-polymers2662
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1540 Å2
ΔGint-101 kcal/mol
Surface area3140 Å2
13
a: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
b: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,0114
Polymers5,7462
Non-polymers2662
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint-100 kcal/mol
Surface area3140 Å2
14
c: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
d: RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,0114
Polymers5,7462
Non-polymers2662
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1570 Å2
ΔGint-100 kcal/mol
Surface area3140 Å2
Unit cell
Length a, b, c (Å)28.231, 90.612, 139.933
Angle α, β, γ (deg.)90.000, 91.427, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: RNA chain ...
RNA (5'-R(*AP*UP*GP*UP*GP*GP*CP*AP*U)-3')


Mass: 2872.751 Da / Num. of mol.: 28 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Chemical...
ChemComp-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: Cs / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 2.22 Å3/Da / Density % sol: 44.7 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.08 M NaCl 0.02 M CsCl 0.04 M cacodylate sodium 45% MPD 0.012 M spermine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.917143 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.917143 Å / Relative weight: 1
ReflectionResolution: 2.86→45.31 Å / Num. obs: 30808 / % possible obs: 96 % / Redundancy: 3.5 % / Biso Wilson estimate: 87.12 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.08 / Net I/σ(I): 8.51
Reflection shellResolution: 2.86→3.03 Å / Rmerge(I) obs: 1.586 / Mean I/σ(I) obs: 0.81 / Num. unique obs: 4633 / CC1/2: 0.527

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8AMG

8amg


Resolution: 2.86→45.31 Å / SU ML: 0.5175 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 33.8344
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2688 1828 5.97 %
Rwork0.221 28810 -
obs0.2238 30638 95.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 93.02 Å2
Refinement stepCycle: LAST / Resolution: 2.86→45.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 5320 28 0 5348
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00165963
X-RAY DIFFRACTIONf_angle_d0.46459257
X-RAY DIFFRACTIONf_chiral_restr0.01961237
X-RAY DIFFRACTIONf_plane_restr0.0019253
X-RAY DIFFRACTIONf_dihedral_angle_d10.45332927
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.86-2.940.52871160.48181806X-RAY DIFFRACTION80.55
2.94-3.020.39671470.36992300X-RAY DIFFRACTION98.27
3.02-3.120.36381460.32982334X-RAY DIFFRACTION97.06
3.12-3.230.33721360.30352224X-RAY DIFFRACTION97.76
3.23-3.360.35661410.30612200X-RAY DIFFRACTION96.18
3.36-3.510.35361400.30272258X-RAY DIFFRACTION93.71
3.51-3.70.3391400.29432186X-RAY DIFFRACTION97.36
3.7-3.930.33221480.27112280X-RAY DIFFRACTION97
3.93-4.230.28711460.24772254X-RAY DIFFRACTION98.4
4.23-4.660.27851430.22782230X-RAY DIFFRACTION94.39
4.66-5.330.31691460.21362269X-RAY DIFFRACTION99.26
5.33-6.710.24391410.20942257X-RAY DIFFRACTION96.69
6.71-45.310.14971380.1182212X-RAY DIFFRACTION95.22

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