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- PDB-6n5n: Structure of Human pir-miRNA-208a Apical Loop and One-base-pair F... -

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Basic information

Entry
Database: PDB / ID: 6n5n
TitleStructure of Human pir-miRNA-208a Apical Loop and One-base-pair Fused to the YdaO Riboswitch Scaffold
ComponentsRNA (125-MER)
KeywordsRNA / microRNA / RNA processing / Protein-RNA interaction
Function / homologyChem-2BA / : / RNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.951 Å
AuthorsShoffner, G.M. / Peng, Z. / Guo, F.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1616265 United States
CitationJournal: To Be Published
Title: Three-dimensional structures of pri-miRNA apical junctions and loops revealed by scaffold-directed crystallography
Authors: Shoffner, G.M. / Peng, Z. / Guo, F.
History
DepositionNov 22, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (125-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,1919
Polymers40,5701
Non-polymers1,6218
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)114.680, 114.680, 114.810
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: RNA chain RNA (125-MER)


Mass: 40569.992 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Production host: in vitro transcription vector pT7-Fluc(deltai) (others)
#2: Chemical ChemComp-2BA / (2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-2,9-bis(6-amino-9H-purin-9-yl)octahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8 ]tetraoxadiphosphacyclododecine-3,5,10,12-tetrol 5,12-dioxide / bis-(3',5')-cyclic-dimeric-Adenosine-monophosphate


Mass: 658.412 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H24N10O12P2
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4

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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: 5.37 Å3/Da / Density % sol: 77.1 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 1.9 M (NH4)2SO4, 0.2 M Li2SO4, and 0.1 M HEPES pH 7.4
Temp details: Room Temperature

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.95→75.112 Å / Num. obs: 18748 / % possible obs: 99.9 % / Redundancy: 19.9 % / CC1/2: 0.999 / Rpim(I) all: 0.02 / Rrim(I) all: 0.09 / Net I/σ(I): 24.9
Reflection shellResolution: 2.95→3.03 Å / Redundancy: 20.7 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1875 / CC1/2: 0.83 / Rpim(I) all: 0.476 / Rrim(I) all: 2.45 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4QK8

4qk8


Resolution: 2.951→75.112 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 22.24
RfactorNum. reflection% reflection
Rfree0.1855 1873 10 %
Rwork0.1683 --
obs0.17 18726 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 555.18 Å2 / Biso mean: 122.2787 Å2 / Biso min: 48.22 Å2
Refinement stepCycle: final / Resolution: 2.951→75.112 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2682 102 0 2784
Biso mean--75.77 --
Num. residues----125
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9511-3.03090.41231380.39551239137799
3.0309-3.12010.32071430.290612831426100
3.1201-3.22080.32321400.258512661406100
3.2208-3.33590.32981450.231412961441100
3.3359-3.46950.26711400.213612801420100
3.4695-3.62740.21851430.21812821425100
3.6274-3.81870.19561440.177112941438100
3.8187-4.05790.19221430.171612871430100
4.0579-4.37120.20271440.158312991443100
4.3712-4.8110.1581450.144413001445100
4.811-5.5070.14771460.142613121458100
5.507-6.93740.14371460.14413211467100
6.9374-75.13640.15241560.144313941550100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.023-0.01480.0290.20970.01850.1377-0.5821-0.09450.11380.52110.24510.8211-0.4464-1.9998-00.97980.19610.15761.4255-0.1271.1336-72.78716.156-16.38
2-0.077-0.112-0.40372.4098-0.76390.83530.1399-0.11970.05920.2361-0.2412-0.2476-0.05140.0575-00.7365-0.13260.04560.6097-0.0230.6952-45.79511.159-8.27
30.59680.59790.06490.52760.64470.65240.05220.0350.0171-0.01970.124-0.445-0.22340.596400.7921-0.17160.09710.7772-0.05290.8261-41.23825.767-14.57
41.935-0.4709-0.69440.8075-1.36041.82870.233-0.2170.4097-0.458-0.2619-0.2714-1.21350.5075-0.01620.9988-0.25540.27140.85030.08940.7846-36.69129.446-34.294
50.3006-0.82410.34480.838-0.78380.20670.22050.71020.2284-0.9623-0.29770.19870.26710.1909-00.94420.23560.11370.8603-0.00980.701-46.582-0.172-45.955
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 11:24 )A11 - 24
2X-RAY DIFFRACTION2( CHAIN A AND ( RESID 25:37 OR RESID 98:108 ) )A25 - 37
3X-RAY DIFFRACTION2( CHAIN A AND ( RESID 25:37 OR RESID 98:108 ) )A98 - 108
4X-RAY DIFFRACTION3( CHAIN A AND ( RESID 41:50 OR RESID 89:97 ) )A41 - 50
5X-RAY DIFFRACTION3( CHAIN A AND ( RESID 41:50 OR RESID 89:97 ) )A89 - 97
6X-RAY DIFFRACTION4( CHAIN A AND ( RESID 51:75 OR RESID 83:88 ) )A51 - 75
7X-RAY DIFFRACTION4( CHAIN A AND ( RESID 51:75 OR RESID 83:88 ) )A83 - 88
8X-RAY DIFFRACTION5( CHAIN A AND ( RESID 77:82 OR RESID 119:125 ) )A77 - 82
9X-RAY DIFFRACTION5( CHAIN A AND ( RESID 77:82 OR RESID 119:125 ) )A119 - 125

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