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- PDB-8vjt: Structure of the poly-UG quadruplex (GUGUGU)4 -

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Basic information

Entry
Database: PDB / ID: 8vjt
TitleStructure of the poly-UG quadruplex (GUGUGU)4
ComponentsRNA (5'-R(*GP*UP*GP*UP*GP*U)-3')
KeywordsRNA / RNA quadruplex
Function / homology: / RNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.052 Å
AuthorsBingman, C.A. / Montemayor, E.J. / Roschdi, S. / Nomura, Y. / Butcher, S.E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)2R35GM118131-06 United States
CitationJournal: Nucleic Acids Res. / Year: 2024
Title: Self-assembly and condensation of intermolecular poly(UG) RNA quadruplexes.
Authors: Roschdi, S. / Montemayor, E.J. / Vivek, R. / Bingman, C.A. / Butcher, S.E.
History
DepositionJan 8, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (5'-R(*GP*UP*GP*UP*GP*U)-3')
B: RNA (5'-R(*GP*UP*GP*UP*GP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,13811
Polymers3,8182
Non-polymers3209
Water70339
1
A: RNA (5'-R(*GP*UP*GP*UP*GP*U)-3')
hetero molecules

A: RNA (5'-R(*GP*UP*GP*UP*GP*U)-3')
hetero molecules

A: RNA (5'-R(*GP*UP*GP*UP*GP*U)-3')
hetero molecules

A: RNA (5'-R(*GP*UP*GP*UP*GP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,35424
Polymers7,6374
Non-polymers71820
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_555-y+1/2,x+1/2,z1
crystal symmetry operation4_455y-1/2,-x+1/2,z1
Buried area2870 Å2
ΔGint-83 kcal/mol
Surface area3760 Å2
MethodPISA
2
B: RNA (5'-R(*GP*UP*GP*UP*GP*U)-3')
hetero molecules

B: RNA (5'-R(*GP*UP*GP*UP*GP*U)-3')
hetero molecules

B: RNA (5'-R(*GP*UP*GP*UP*GP*U)-3')
hetero molecules

B: RNA (5'-R(*GP*UP*GP*UP*GP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,19820
Polymers7,6374
Non-polymers56116
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_555-y+1/2,x+1/2,z1
crystal symmetry operation4_455y-1/2,-x+1/2,z1
Buried area2650 Å2
ΔGint-88 kcal/mol
Surface area3960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.821, 32.821, 57.970
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number90
Space group name H-MP4212
Space group name HallP4ab2ab
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z
#3: y+1/2,-x+1/2,z
#4: x+1/2,-y+1/2,-z
#5: -x+1/2,y+1/2,-z
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
Components on special symmetry positions
IDModelComponents
11A-101-

K

21A-102-

K

31A-103-

K

41A-104-

K

51B-101-

K

61B-102-

K

71B-103-

K

81A-207-

HOH

91A-210-

HOH

101A-218-

HOH

111A-220-

HOH

121A-226-

HOH

131B-201-

HOH

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Components

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


Mass: 1909.157 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.04 Å3/Da / Density % sol: 39.83 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Diffraction quality crystals were eventually obtained by sitting drop vapor diffusion by mixing 2 uL of RNA with 2 uL of crystallization reagent containing 200 mM NaCl, 100 mM bis-tris pH 6. ...Details: Diffraction quality crystals were eventually obtained by sitting drop vapor diffusion by mixing 2 uL of RNA with 2 uL of crystallization reagent containing 200 mM NaCl, 100 mM bis-tris pH 6.5 and 50 % PEG 550 MME. Crystals were vitrified by direct immersion into liquid nitrogen

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97619 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 9, 2018
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97619 Å / Relative weight: 1
ReflectionResolution: 1.052→21.726 Å / Num. obs: 14743 / % possible obs: 95.9 % / Redundancy: 12.98 %
Details: Some remarks regarding the mmCIF items written, the PDB Exchange Dictionary (PDBx/mmCIF) Version 5.0 supporting the data files in the current PDB archive (dictionary version 5.325, last ...Details: Some remarks regarding the mmCIF items written, the PDB Exchange Dictionary (PDBx/mmCIF) Version 5.0 supporting the data files in the current PDB archive (dictionary version 5.325, last updated 2020-04-13: http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Index/) and the actual quantities provided by MRFANA (https://github.com/githubgphl/MRFANA) from the autoPROC package (https://www.globalphasing.com/autoproc/). In general, the mmCIF categories here should provide items that are currently used in the PDB archive. If there are alternatives, the one recommended by the PDB developers has been selected. The distinction between *_all and *_obs quantities is not always clear: often only one version is actively used within the PDB archive (or is the one recommended by PDB developers). The intention of distinguishing between classes of reflections before and after some kind of observation criterion was applied, can in principle be useful - but such criteria change in various ways throughout the data processing steps (rejection of overloaded or too partial reflections, outlier/misfit rejections during scaling etc) and there is no retrospect computation of data scaling/merging statistics for the reflections used in the final refinement (where another observation criterion might have been applied). Typical data processing will usually only provide one version of statistics at various stages and these are given in the recommended item here, irrespective of the "_all" and "_obs" connotation, see e.g. the use of _reflns.pdbx_Rmerge_I_obs, _reflns.pdbx_Rrim_I_all and _reflns.pdbx_Rpim_I_all. Please note that all statistics related to "merged intensities" (or "merging") are based on inverse-variance weighting of the individual measurements making up a symmetry-unique reflection. This is standard for several decades now, even if some of the dictionary definitions seem to suggest that a simple "mean" or "average" intensity is being used instead. R-values are always given for all symmetry-equivalent reflections following Friedel's law, i.e. Bijvoet pairs are not treated separately (since we want to describe the overall mean intensity and not the mean I(+) and I(-) here). The Rrim metric is identical to the Rmeas R-value and only differs in name. _reflns.pdbx_number_measured_all is the number of measured intensities just before the final merging step (at which point no additional rejection takes place). _reflns.number_obs is the number of symmetry-unique observations, i.e. the result of merging those measurements via inverse-variance weighting. _reflns.pdbx_netI_over_sigmaI is based on the merged intensities (_reflns.number_obs) as expected. _reflns.pdbx_redundancy is synonymous with "multiplicity". The per-shell item _reflns_shell.number_measured_all corresponds to the overall value _reflns.pdbx_number_measured_all. The per-shell item _reflns_shell.number_unique_all corresponds to the overall value _reflns.number_obs. The per-shell item _reflns_shell.percent_possible_all corresponds to the overall value _reflns.percent_possible_obs. The per-shell item _reflns_shell.meanI_over_sigI_obs corresponds to the overall value given as _reflns.pdbx_netI_over_sigmaI. But be aware of the incorrect definition of the former in the current dictionary!
CC1/2: 0.995 / CC1/2 anomalous: -0.294 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.0221 / Rrim(I) all: 0.0803 / AbsDiff over sigma anomalous: 0.82 / Net I/σ(I): 18.35 / Num. measured all: 191357 / % possible anomalous: 95.5 / Redundancy anomalous: 7.11
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. measured obsNum. unique allNum. unique obsCC1/2CC1/2 anomalousRpim(I) allRrim(I) allAbsDiff over sigma anomalous% possible anomalousRedundancy anomalous% possible all
2.855-21.72613.790.063746.8412276122768908900.993-0.4480.01840.06650.9631008.63100
2.267-2.85512.760.053840.0910339103398108100.9990.2230.01570.05620.95199.57.3499.4
1.98-2.26713.750.059337.5510850108507897890.9980.0330.01670.06170.9511007.71100
1.799-1.9814.390.064634.2511110111107727720.9980.2120.01770.0670.9151008.02100
1.67-1.79914.60.071230.6611346113467777770.999-0.0040.01960.0740.881008.05100
1.572-1.6714.80.078526.77114851148577677610.0550.02180.08160.8551008.09100
1.493-1.57214.820.109621.2811325113257647640.9980.1890.02920.11350.951008.09100
1.428-1.49313.020.145615.64986698667587580.9940.0930.04110.15150.8311007.199.9
1.373-1.42813.350.162813.8310183101837637630.994-0.0510.04560.16920.8131007.2299.5
1.326-1.37313.870.192711.9610586105867637630.9920.050.05360.20020.7891007.53100
1.284-1.32614.070.211111.1910639106397567560.9910.040.05840.21920.7971007.59100
1.248-1.28414.280.233910.410827108277587580.9890.0190.06410.24280.7831007.72100
1.215-1.24814.360.2589.2810610106107397390.9870.0350.07050.26770.7681007.7100
1.185-1.21514.280.27528.610964109647687680.9890.0130.07520.28550.7491007.66100
1.158-1.18514.220.30817.7510722107227547540.9830.0280.08480.320.7911007.66100
1.134-1.15812.80.34666.47941994197367360.990.0610.10060.36150.71899.76.8199.6
1.111-1.13410.020.43924.44667366736666660.955-0.0990.14250.46330.68990.65.3689.9
1.09-1.1118.160.50123.38538053806596590.934-0.0020.18340.53690.73886.64.4286.5
1.071-1.097.090.62622.58415241525865860.8840.0560.24280.67510.73274.63.8777
1.052-1.0715.680.80261.77260526054594590.69-0.0030.35420.88380.68560.43.1462.9

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Processing

Software
NameVersionClassification
autoPROC1.0.5 (20230726)data processing
XDSJun 30, 2023data reduction
Aimless0.7.13data scaling
TRUNCATE8.0.015data processing
PHENIX1.20.1_4487refinement
HKL2Mapphasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.052→21.726 Å / SU ML: 0.0808 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 14.5541
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1606 1471 9.99 %
Rwork0.1483 13255 -
obs0.1496 14726 95.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 13.57 Å2
Refinement stepCycle: LAST / Resolution: 1.052→21.726 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 252 9 39 300
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0069560
X-RAY DIFFRACTIONf_angle_d1.0642868
X-RAY DIFFRACTIONf_chiral_restr0.0495116
X-RAY DIFFRACTIONf_plane_restr0.019424
X-RAY DIFFRACTIONf_dihedral_angle_d14.3081272
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.052-1.090.2318920.2027844X-RAY DIFFRACTION68.98
1.09-1.130.19541170.1531060X-RAY DIFFRACTION86.61
1.13-1.170.15231340.11511206X-RAY DIFFRACTION97.95
1.17-1.220.14481370.10311230X-RAY DIFFRACTION100
1.22-1.290.13191370.10691234X-RAY DIFFRACTION100
1.29-1.370.15531390.11671248X-RAY DIFFRACTION100
1.37-1.470.14271360.12121230X-RAY DIFFRACTION99.56
1.47-1.620.13531400.11181258X-RAY DIFFRACTION99.93
1.62-1.860.12911420.11681268X-RAY DIFFRACTION99.51
1.86-2.340.17081420.15291288X-RAY DIFFRACTION100
2.34-21.7260.17861550.18831389X-RAY DIFFRACTION99.55

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