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Basic information

Entry
Database: PDB / ID: 3adi
TitleStructure of Arabidopsis HYL1 and its molecular implications for miRNA processing
Components
  • F21M12.9 protein
  • RNA (5'-R(*GP*GP*UP*UP*AP*UP*CP*GP*AP*G)-3')
  • RNA (5'-R(P*CP*UP*CP*GP*AP*UP*AP*AP*CP*C)-3')
KeywordsGENE REGULATION/RNA / HYL1 / miRNA processing mechanism / RNA BINDING PROTEIN / GENE REGULATION-RNA complex
Function / homology
Function and homology information


nuclear dicing body / leaf proximal/distal pattern formation / response to cytokinin / ta-siRNA processing / leaf vascular tissue pattern formation / miRNA-mediated gene silencing by mRNA destabilization / response to auxin / response to abscisic acid / miRNA processing / pre-miRNA processing ...nuclear dicing body / leaf proximal/distal pattern formation / response to cytokinin / ta-siRNA processing / leaf vascular tissue pattern formation / miRNA-mediated gene silencing by mRNA destabilization / response to auxin / response to abscisic acid / miRNA processing / pre-miRNA processing / miRNA binding / double-stranded RNA binding / nuclear speck / identical protein binding / nucleus
Similarity search - Function
AtDRB-like, first double-stranded RNA binding domain, plant / AtDRB-like, second double-stranded RNA binding domain, plant / Double Stranded RNA Binding Domain - #20 / Double-stranded RNA binding motif / Double-stranded RNA binding motif / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain / Double Stranded RNA Binding Domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
RNA / Double-stranded RNA-binding protein 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsYuan, Y.A. / Chen, H.Y.
CitationJournal: Structure / Year: 2010
Title: Structure of arabidopsis HYPONASTIC LEAVES1 and its molecular implications for miRNA processing
Authors: Yang, S.W. / Chen, H.Y. / Yang, J. / Machida, S. / Chua, N.H. / Yuan, Y.A.
History
DepositionJan 22, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: F21M12.9 protein
B: F21M12.9 protein
C: F21M12.9 protein
D: RNA (5'-R(P*CP*UP*CP*GP*AP*UP*AP*AP*CP*C)-3')
E: RNA (5'-R(*GP*GP*UP*UP*AP*UP*CP*GP*AP*G)-3')


Theoretical massNumber of molelcules
Total (without water)31,0545
Polymers31,0545
Non-polymers00
Water00
1
A: F21M12.9 protein
D: RNA (5'-R(P*CP*UP*CP*GP*AP*UP*AP*AP*CP*C)-3')
E: RNA (5'-R(*GP*GP*UP*UP*AP*UP*CP*GP*AP*G)-3')


Theoretical massNumber of molelcules
Total (without water)14,5773
Polymers14,5773
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1700 Å2
ΔGint-10 kcal/mol
Surface area8080 Å2
MethodPISA
2
B: F21M12.9 protein


Theoretical massNumber of molelcules
Total (without water)8,2381
Polymers8,2381
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: F21M12.9 protein


Theoretical massNumber of molelcules
Total (without water)8,2381
Polymers8,2381
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.620, 47.620, 115.377
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein F21M12.9 protein / Hyponastic leave 1 / Putative uncharacterized protein


Mass: 8238.390 Da / Num. of mol.: 3 / Fragment: HYL1 dsRBD1, UNP residues 15-84
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: HYL1 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O04492
#2: RNA chain RNA (5'-R(P*CP*UP*CP*GP*AP*UP*AP*AP*CP*C)-3')


Mass: 3120.925 Da / Num. of mol.: 1 / Fragment: RNA / Source method: obtained synthetically / Details: Synthetic RNA
#3: RNA chain RNA (5'-R(*GP*GP*UP*UP*AP*UP*CP*GP*AP*G)-3')


Mass: 3217.957 Da / Num. of mol.: 1 / Fragment: RNA / Source method: obtained synthetically / Details: Synthetic RNA

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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: 2.11 Å3/Da / Density % sol: 41.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG8000, AS, Cacodylate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE
RadiationMonochromator: 1.54 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3.2→40 Å / Num. obs: 3783 / % possible obs: 97.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.7 % / Rsym value: 0.101 / Net I/σ(I): 19.9
Reflection shellResolution: 3.2→3.3 Å / Redundancy: 3 % / Mean I/σ(I) obs: 4.7 / Rsym value: 0.975

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DI2

1di2


Resolution: 3.2→36.72 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.824 / SU B: 83.395 / SU ML: 0.647 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(I): 2 / ESU R Free: 0.794 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.31724 401 9.6 %RANDOM
Rwork0.2044 ---
obs0.21463 3783 98.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 67.858 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å20 Å20 Å2
2---0.17 Å20 Å2
3---0.35 Å2
Refinement stepCycle: LAST / Resolution: 3.2→36.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1716 422 0 0 2138
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222225
X-RAY DIFFRACTIONr_angle_refined_deg1.6192.2123092
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8755210
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.65723.33381
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.31515315
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5991512
X-RAY DIFFRACTIONr_chiral_restr0.1070.2354
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021525
X-RAY DIFFRACTIONr_nbd_refined0.2640.21076
X-RAY DIFFRACTIONr_nbtor_refined0.3180.21441
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1760.284
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2240.2108
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2360.210
X-RAY DIFFRACTIONr_mcbond_it0.4971.51083
X-RAY DIFFRACTIONr_mcangle_it0.88321713
X-RAY DIFFRACTIONr_scbond_it0.93731401
X-RAY DIFFRACTIONr_scangle_it1.6314.51379
LS refinement shellResolution: 3.201→3.284 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 37 -
Rwork0.266 255 -
obs--97.33 %
Refinement TLS params.Method: refined / Origin x: 19.3489 Å / Origin y: 14.2285 Å / Origin z: -4.5144 Å
111213212223313233
T-0.1729 Å20.0646 Å20.0026 Å2--0.1011 Å20.0585 Å2---0.0806 Å2
L1.7219 °20.3888 °20.4309 °2-1.1726 °2-0.3173 °2--1.8074 °2
S0.1511 Å °-0.3658 Å °0.0035 Å °0.1213 Å °-0.2125 Å °-0.0989 Å °0.141 Å °-0.3722 Å °0.0615 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A14 - 84
2X-RAY DIFFRACTION1B14 - 84
3X-RAY DIFFRACTION1C14 - 84

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