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- PDB-6hu6: Structure of ARF1 RNA -

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Basic information

Entry
Database: PDB / ID: 6hu6
TitleStructure of ARF1 RNA
Components
  • (RNA (19-MER)) x 2
  • RNA (5'-R(*CP*UP*GP*GP*UP*AP*CP*UP*C)-3')
  • RNA (5'-R(*GP*AP*GP*UP*GP*CP*CP*AP*GP*A)-3')
KeywordsRNA / dsRBD / RNA localization / SMD / Staufen
Function / homologyAMMONIUM ION / RNA / RNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.904 Å
AuthorsEmmerich, C. / Lazzaretti, D. / Bandholz-Cajamarca, L. / Bono, F.
Funding support Germany, 2items
OrganizationGrant numberCountry
European Research Council310957 Germany
German Research FoundationBO3588/2-1 Germany
CitationJournal: Life Sci Alliance / Year: 2018
Title: The crystal structure of Staufen1 in complex with a physiological RNA sheds light on substrate selectivity.
Authors: Lazzaretti, D. / Bandholz-Cajamarca, L. / Emmerich, C. / Schaaf, K. / Basquin, C. / Irion, U. / Bono, F.
History
DepositionOct 5, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 21, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 28, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2May 15, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2
Item: _citation.country / _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
A: RNA (19-MER)
E: RNA (19-MER)
B: RNA (5'-R(*GP*AP*GP*UP*GP*CP*CP*AP*GP*A)-3')
F: RNA (5'-R(*CP*UP*GP*GP*UP*AP*CP*UP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2677
Polymers18,2134
Non-polymers543
Water72140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3390 Å2
ΔGint-9 kcal/mol
Surface area10270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.803, 43.803, 452.087
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-101-

NH4

21A-102-

NH4

31A-102-

NH4

41A-202-

HOH

51E-301-

HOH

61B-210-

HOH

71B-211-

HOH

81B-216-

HOH

91B-222-

HOH

101F-303-

HOH

111F-304-

HOH

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Components

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RNA chain , 4 types, 4 molecules AEBF

#1: RNA chain RNA (19-MER)


Mass: 6092.688 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: RNA chain RNA (19-MER)


Mass: 6071.617 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: RNA chain RNA (5'-R(*GP*AP*GP*UP*GP*CP*CP*AP*GP*A)-3')


Mass: 3240.012 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: RNA chain RNA (5'-R(*CP*UP*GP*GP*UP*AP*CP*UP*C)-3')


Mass: 2808.703 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 2 types, 43 molecules

#5: Chemical ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: H4N
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 2.29 Å3/Da / Density % sol: 46.32 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 1.7 M (NH4)2SO4, 100 mM Tri-sodium citrate pH 6.2

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→38 Å / Num. obs: 25323 / % possible obs: 99.9 % / Redundancy: 10.3 % / Net I/σ(I): 13.52
Reflection shellResolution: 1.9→2.02 Å

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementResolution: 1.904→37.802 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.17
RfactorNum. reflection% reflection
Rfree0.2488 693 5.01 %
Rwork0.2262 --
obs0.2274 13826 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.904→37.802 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1207 3 40 1250
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0191346
X-RAY DIFFRACTIONf_angle_d2.4072091
X-RAY DIFFRACTIONf_dihedral_angle_d6.348669
X-RAY DIFFRACTIONf_chiral_restr0.099282
X-RAY DIFFRACTIONf_plane_restr0.01457
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9043-2.05130.32031340.30262540X-RAY DIFFRACTION100
2.0513-2.25770.36411360.2752578X-RAY DIFFRACTION100
2.2577-2.58440.37031380.29952609X-RAY DIFFRACTION100
2.5844-3.25580.28531370.26962602X-RAY DIFFRACTION99
3.2558-37.80910.18441480.17732804X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -9.0468 Å / Origin y: 12.2677 Å / Origin z: -37.7518 Å
111213212223313233
T0.3467 Å20.0136 Å2-0.0106 Å2-0.4168 Å2-0.0201 Å2--0.3413 Å2
L-0.3563 °2-0.1005 °20.018 °2-0.0697 °20.0288 °2---0.0709 °2
S0.1675 Å °0.0559 Å °0.1267 Å °-0.0845 Å °0.1277 Å °-0.077 Å °0.0195 Å °0.0049 Å °0.0009 Å °
Refinement TLS groupSelection details: all

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