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- PDB-6n5k: Structure of Human pir-miRNA-449c Apical Loop and One-base-pair F... -

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Basic information

Entry
Database: PDB / ID: 6n5k
TitleStructure of Human pir-miRNA-449c 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: 3.098 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)42,0577
Polymers40,5561
Non-polymers1,5016
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)113.960, 113.960, 114.830
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 (125-MER)


Mass: 40555.961 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.: 2 / 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.: 6 / 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: 5.31 Å3/Da / Density % sol: 76.82 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: Magnesium chloride, Cyclic di-AMP, Potassium Chloride, HEPEs
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: Nov 12, 2017
RadiationMonochromator: 0.9791 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 3.098→74.847 Å / Num. obs: 16089 / % possible obs: 100 % / Redundancy: 39.8 % / CC1/2: 1 / Rpim(I) all: 0.019 / Rrim(I) all: 0.112 / Net I/σ(I): 26.6
Reflection shellResolution: 3.098→3.18 Å / Redundancy: 39.2 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 16089 / CC1/2: 0.866 / Rpim(I) all: 0.444 / Rrim(I) all: 2.33 / % possible all: 100

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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: 3.098→74.847 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 22.54
RfactorNum. reflection% reflection
Rfree0.1864 1607 10.01 %
Rwork0.1769 --
obs0.1778 16046 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 312.56 Å2 / Biso mean: 123.8776 Å2 / Biso min: 69.14 Å2
Refinement stepCycle: final / Resolution: 3.098→74.847 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2681 96 6 2783
Biso mean--86.96 85.71 -
Num. residues----125
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.0981-3.19810.421430.385612851428100
3.1981-3.31240.27311460.271313081454100
3.3124-3.44510.26641430.23581280142399
3.4451-3.60190.2591420.238112841426100
3.6019-3.79170.20791450.21771305145099
3.7917-4.02930.20681450.201712981443100
4.0293-4.34040.21341440.176712971441100
4.3404-4.77710.19021470.159513191466100
4.7771-5.46820.14911470.15913281475100
5.4682-6.88860.16281480.153513301478100
6.8886-74.86860.15061570.148214051562100
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)
10.46190.65690.30970.4542-0.06050.55780.08790.01670.92510.1641-0.01421.1536-0.9265-1.1447-01.13210.1010.11421.3642-0.12361.5554-73.074516.3911-16.978
2-0.378-0.148-0.05721.9749-0.84030.91930.0971-0.01590.05840.2458-0.1315-0.1398-0.04720.0289-00.8596-0.12310.01740.7815-0.04120.8637-45.759910.4962-8.3192
3-0.0020.1927-0.07850.09061.286-0.38370.02660.00250.03930.01080.2425-0.2731-0.3660.567600.9637-0.18370.07330.9983-0.05711.0168-40.969326.9852-14.8767
43.2993-1.7648-1.77230.2699-0.95982.7590.5665-0.19060.7066-0.2743-0.2656-0.545-1.05590.8921-01.1327-0.33410.29341.06580.09961.0437-35.556229.2043-34.4029
50.1704-1.4695-0.05651.231-0.98550.40710.38370.3840.0278-0.6838-0.3187-0.0557-0.0653-0.24401.10560.21250.10871.0049-0.03940.8817-47.3336-0.298-46.3659
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth seq-ID
1X-RAY DIFFRACTION1resid 11:230
2X-RAY DIFFRACTION2resid 24:36 or resid 97:1070
3X-RAY DIFFRACTION3resid 40:49 or resid 88:960
4X-RAY DIFFRACTION4resid 50:74 or resid 82:870
5X-RAY DIFFRACTION5resid 76:81 or resid 118:1250

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