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- PDB-6n5p: Structure of Human pir-miRNA-340 Apical Loop and One-base-pair Fu... -

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Basic information

Entry
Database: PDB / ID: 6n5p
TitleStructure of Human pir-miRNA-340 Apical Loop and One-base-pair Fused to the YdaO Riboswitch Scaffold
ComponentsRNA (127-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: 2.991 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 (127-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7339
Polymers41,1831
Non-polymers1,5498
Water724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)114.800, 114.800, 115.570
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

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RNA chain , 1 types, 1 molecules A

#1: RNA chain RNA (127-MER)


Mass: 41183.305 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)

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Non-polymers , 5 types, 12 molecules

#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.: 4 / 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.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 5.34 Å3/Da / Density % sol: 76.96 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 1.89 M (NH4)2SO4, 0.214 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: ALS / Beamline: 8.3.1 / Wavelength: 1.116 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 20, 2017
RadiationMonochromator: Water-cooled flat double Si(111) Khozu monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.116 Å / Relative weight: 1
ReflectionResolution: 2.991→75.369 Å / Num. obs: 18192 / % possible obs: 99.9 % / Redundancy: 38.2 % / CC1/2: 1 / Rpim(I) all: 0.016 / Rrim(I) all: 0.101 / Net I/σ(I): 27.1
Reflection shellResolution: 2.991→3.1 Å / Redundancy: 35.7 % / Mean I/σ(I) obs: 2.4 / Num. unique obs: 1819 / CC1/2: 0.848 / Rpim(I) all: 0.324 / Rrim(I) all: 2.02 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4QK8

4qk8


Resolution: 2.991→75.369 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.91
RfactorNum. reflection% reflection
Rfree0.1806 1818 9.99 %
Rwork0.1514 --
obs0.1543 18192 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 401.54 Å2 / Biso mean: 113.5714 Å2 / Biso min: 24.29 Å2
Refinement stepCycle: final / Resolution: 2.991→75.369 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2722 98 4 2824
Biso mean--70.46 54.63 -
Num. residues----127
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053148
X-RAY DIFFRACTIONf_angle_d1.0594905
X-RAY DIFFRACTIONf_chiral_restr0.046650
X-RAY DIFFRACTIONf_plane_restr0.005131
X-RAY DIFFRACTIONf_dihedral_angle_d17.0341565
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.991-3.07190.41121400.384112551395
3.0719-3.16230.27231350.283512191354
3.1623-3.26440.25771400.2212571397
3.2644-3.38110.25051380.187312521390
3.3811-3.51640.21851340.174412041338
3.5164-3.67650.20151400.174612571397
3.6765-3.87030.16691390.155812491388
3.8703-4.11280.1991390.146212561395
4.1128-4.43030.15191400.131412601400
4.4303-4.8760.16011390.129412471386
4.876-5.58140.16251420.128812781420
5.5814-7.03120.17611430.13912841427
7.0312-75.39290.15231490.133513561505
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)
11.99140.51581.29261.57621.23023.81650.2526-0.13310.1377-0.5406-0.11-0.1576-0.1271-0.3346-0.10560.8217-0.02550.04520.62950.03320.7219-59.613713.5613-32.503
25.8249-1.22482.44418.538-3.67466.9119-1.4478-0.55121.96681.07220.96342.9451-2.9511-2.63360.46631.58210.5560.11471.9454-0.11872.3376-76.038619.6658-16.0081
31.82041.2494-0.70723.4544-0.83172.50730.1725-0.05040.17630.1445-0.0639-0.6483-0.08830.7515-0.11080.6615-0.11720.1240.7706-0.08050.8881-39.873717.8003-13.0148
44.4118-0.39870.10113.47220.37221.6668-0.1259-0.34391.6424-0.4284-0.205-1.4725-2.28951.49110.28862.029-0.6697-0.02621.4338-0.0121.7415-33.869434.4344-31.8114
50.7182-0.4177-0.07251.91810.31892.39110.19190.17880.1205-0.3528-0.274-0.165-0.12020.23750.07990.6055-0.00130.10670.60670.02680.7087-48.856314.2289-31.3687
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 11 )A2 - 11
2X-RAY DIFFRACTION2chain 'A' and (resid 12 through 24 )A12 - 24
3X-RAY DIFFRACTION3chain 'A' and (resid 25 through 54 )A25 - 54
4X-RAY DIFFRACTION4chain 'A' and (resid 55 through 74 )A55 - 74
5X-RAY DIFFRACTION5chain 'A' and (resid 75 through 126 )A75 - 126

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