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- PDB-4g0q: Crystal structure of Arabidopsis thaliana AGO1 MID domain in comp... -

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Basic information

Entry
Database: PDB / ID: 4g0q
TitleCrystal structure of Arabidopsis thaliana AGO1 MID domain in complex with CMP
ComponentsProtein argonaute 1
KeywordsGENE REGULATION / MID domain / small RNA 5' nucleotide recognition
Function / homology
Function and homology information


adaxial/abaxial pattern specification / adventitious root development / leaf morphogenesis / auxin metabolic process / leaf proximal/distal pattern formation / RNAi-mediated antiviral immune response / leaf vascular tissue pattern formation / response to far red light / post-transcriptional gene silencing / response to auxin ...adaxial/abaxial pattern specification / adventitious root development / leaf morphogenesis / auxin metabolic process / leaf proximal/distal pattern formation / RNAi-mediated antiviral immune response / leaf vascular tissue pattern formation / response to far red light / post-transcriptional gene silencing / response to auxin / miRNA-mediated post-transcriptional gene silencing / siRNA binding / miRNA binding / RNA endonuclease activity / regulation of translation / defense response to virus / cell differentiation / ribonucleoprotein complex / mRNA binding / innate immune response / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Argonaut, glycine-rich domain / Glycine-rich region of argonaut / Protein argonaute, Mid domain / Argonaute-like, PIWI domain / Mid domain of argonaute / Argonaute linker 2 domain / Protein argonaute, N-terminal / N-terminal domain of argonaute / Argonaute linker 2 domain / DUF1785 ...Argonaut, glycine-rich domain / Glycine-rich region of argonaut / Protein argonaute, Mid domain / Argonaute-like, PIWI domain / Mid domain of argonaute / Argonaute linker 2 domain / Protein argonaute, N-terminal / N-terminal domain of argonaute / Argonaute linker 2 domain / DUF1785 / Argonaute, linker 1 domain / Argonaute linker 1 domain / Piwi domain / Piwi domain profile. / Piwi domain / Piwi / PAZ domain superfamily / PAZ / PAZ domain / PAZ domain / PAZ domain profile. / Response regulator / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CYTIDINE-5'-MONOPHOSPHATE / Protein argonaute 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.8 Å
AuthorsFrank, F. / Hauver, J. / Sonenberg, N. / Nagar, B.
CitationJournal: Embo J. / Year: 2012
Title: Arabidopsis Argonaute MID domains use their nucleotide specificity loop to sort small RNAs.
Authors: Frank, F. / Hauver, J. / Sonenberg, N. / Nagar, B.
History
DepositionJul 9, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2012Group: Database references
Revision 1.2Sep 12, 2012Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein argonaute 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7622
Polymers16,4391
Non-polymers3231
Water2,360131
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.103, 60.861, 69.120
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Protein argonaute 1


Mass: 16439.156 Da / Num. of mol.: 1 / Fragment: MID domain, UNP residues 593-738
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: AGO1, At1g48410, F11A17.3, T1N15.2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: O04379
#2: Chemical ChemComp-C5P / CYTIDINE-5'-MONOPHOSPHATE / Cytidine monophosphate


Mass: 323.197 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N3O8P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 2.37 Å3/Da / Density % sol: 48.18 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.1 M citric acid, 2 M ammonium sulfate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Mar 4, 2010
RadiationMonochromator: Varimax HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→30.431 Å / Num. all: 25330 / Num. obs: 25305 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 1.8→1.86 Å / % possible all: 99.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX(phenix.refine: 1.5_2)model building
PHENIX(phenix.refine: 1.5_2)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.5_2phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.8→30.431 Å / SU ML: 0.18 / σ(F): 0.12 / Phase error: 20.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2124 647 4.42 %random
Rwork0.1842 ---
obs0.1855 14651 96.48 %-
all-15186 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.735 Å2 / ksol: 0.344 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-9.2187 Å2-0 Å2-0 Å2
2---8.9119 Å20 Å2
3----0.3068 Å2
Refinement stepCycle: LAST / Resolution: 1.8→30.431 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1146 0 21 131 1298
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061197
X-RAY DIFFRACTIONf_angle_d0.961623
X-RAY DIFFRACTIONf_dihedral_angle_d21.208488
X-RAY DIFFRACTIONf_chiral_restr0.066189
X-RAY DIFFRACTIONf_plane_restr0.004206
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.93490.2671250.2182599X-RAY DIFFRACTION91
1.9349-2.12950.25311190.18412751X-RAY DIFFRACTION97
2.1295-2.43760.22481280.172796X-RAY DIFFRACTION97
2.4376-3.07060.22241360.1762833X-RAY DIFFRACTION98
3.0706-30.4310.18781390.18463025X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 19.4553 Å / Origin y: 35.1399 Å / Origin z: 44.4934 Å
111213212223313233
T0.1429 Å20.0062 Å20.017 Å2-0.1564 Å20.0007 Å2--0.1328 Å2
L0.2982 °2-0.0858 °2-0.2428 °2-1.7972 °2-0.3909 °2--0.4852 °2
S0.0297 Å °0.0345 Å °-0.0002 Å °0.0294 Å °-0.0224 Å °0.0861 Å °0.0276 Å °0.0526 Å °0 Å °
Refinement TLS groupSelection details: all

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