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- PDB-4g0m: Crystal structure of Arabidopsis thaliana AGO2 MID domain -

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Basic information

Entry
Database: PDB / ID: 4g0m
TitleCrystal structure of Arabidopsis thaliana AGO2 MID domain
ComponentsProtein argonaute 2
KeywordsGENE REGULATION / MID domain / small RNA 5' nucleotide recognition
Function / homology
Function and homology information


modulation by virus of host process / siRNA binding / regulatory ncRNA-mediated gene silencing / regulation of translation / defense response to virus / defense response to bacterium / ribonucleoprotein complex / mRNA binding / nucleus / cytosol
Similarity search - Function
Argonaute linker 2 domain / Protein argonaute, N-terminal / Argonaute-like, PIWI domain / N-terminal domain of argonaute / Argonaute linker 2 domain / DUF1785 / Argonaute, linker 1 domain / Argonaute linker 1 domain / Piwi domain / Piwi domain profile. ...Argonaute linker 2 domain / Protein argonaute, N-terminal / Argonaute-like, PIWI domain / 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 profile. / PAZ domain / Response regulator / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.306 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

Downloads & links

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Assembly

Deposited unit
A: Protein argonaute 2
B: Protein argonaute 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,21511
Polymers33,3512
Non-polymers8659
Water2,414134
1
A: Protein argonaute 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3488
Polymers16,6751
Non-polymers6727
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Protein argonaute 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8673
Polymers16,6751
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.647, 67.647, 223.222
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11B-934-

HOH

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Components

#1: Protein Protein argonaute 2


Mass: 16675.283 Da / Num. of mol.: 2 / Fragment: MID domain, UNP residues 579-727
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: AGO2, At1g31280, T19E23.7T19E23_8 / Plasmid: pSmt3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: Q9SHF3
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 3.83 Å3/Da / Density % sol: 67.87 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.1 M citric acid, 2.0 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: Jan 27, 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: 2.3→32.64 Å / Num. all: 22895 / Num. obs: 21269 / % possible obs: 92.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 2.3→2.38 Å / % possible all: 63.1

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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
DENZOdata reduction
HKL-2000data scaling
PHENIX1.5_2phasing
RefinementMethod to determine structure: SAD / Resolution: 2.306→32.64 Å / SU ML: 0.23 / σ(F): 0.13 / Phase error: 28.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2372 1720 8.09 %random
Rwork0.2058 ---
obs0.2087 21269 89.21 %-
all-24671 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.438 Å2 / ksol: 0.357 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-8.8164 Å20 Å2-0 Å2
2--8.8164 Å20 Å2
3----17.6327 Å2
Refinement stepCycle: LAST / Resolution: 2.306→32.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2101 0 45 134 2280
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072173
X-RAY DIFFRACTIONf_angle_d1.0772931
X-RAY DIFFRACTIONf_dihedral_angle_d16.441801
X-RAY DIFFRACTIONf_chiral_restr0.065321
X-RAY DIFFRACTIONf_plane_restr0.005365
LS refinement shell
Resolution (Å)Num. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.306-2.388400.21651397X-RAY DIFFRACTION60
2.3884-2.484880.22961869X-RAY DIFFRACTION84
2.484-2.5971180.23371992X-RAY DIFFRACTION90
2.597-2.73391810.23751932X-RAY DIFFRACTION91
2.7339-2.90511950.21431951X-RAY DIFFRACTION91
2.9051-3.12922120.21661938X-RAY DIFFRACTION92
3.1292-3.44382230.20461998X-RAY DIFFRACTION93
3.4438-3.94142150.17992053X-RAY DIFFRACTION95
3.9414-4.96292320.16962118X-RAY DIFFRACTION96
4.9629-32.642560.22832301X-RAY DIFFRACTION98

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