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- PDB-4kxt: Structure of human ARGONAUTE1 in complex with guide RNA -

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Basic information

Entry
Database: PDB / ID: 4kxt
TitleStructure of human ARGONAUTE1 in complex with guide RNA
Components
  • Protein argonaute-1
  • RNA
KeywordsHYDROLASE/RNA / RNase H fold / nuclease / RNA / HYDROLASE-RNA complex
Function / homology
Function and homology information


Regulation of CDH11 mRNA translation by microRNAs / Regulation of NPAS4 mRNA translation / Post-transcriptional silencing by small RNAs / Competing endogenous RNAs (ceRNAs) regulate PTEN translation / Regulation of PTEN mRNA translation / Small interfering RNA (siRNA) biogenesis / Transcriptional Regulation by MECP2 / RNA secondary structure unwinding / RISC-loading complex / RISC complex assembly ...Regulation of CDH11 mRNA translation by microRNAs / Regulation of NPAS4 mRNA translation / Post-transcriptional silencing by small RNAs / Competing endogenous RNAs (ceRNAs) regulate PTEN translation / Regulation of PTEN mRNA translation / Small interfering RNA (siRNA) biogenesis / Transcriptional Regulation by MECP2 / RNA secondary structure unwinding / RISC-loading complex / RISC complex assembly / miRNA-mediated gene silencing by inhibition of translation / miRNA processing / pre-miRNA processing / RISC complex / Regulation of RUNX1 Expression and Activity / miRNA binding / MicroRNA (miRNA) biogenesis / nuclear-transcribed mRNA catabolic process / RNA polymerase II complex binding / Regulation of MECP2 expression and activity / Transcriptional Regulation by VENTX / core promoter sequence-specific DNA binding / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / negative regulation of angiogenesis / TP53 Regulates Metabolic Genes / Transcriptional regulation by small RNAs / MAPK6/MAPK4 signaling / P-body / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Oncogene Induced Senescence / Pre-NOTCH Transcription and Translation / cytoplasmic ribonucleoprotein granule / double-stranded RNA binding / Ca2+ pathway / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / single-stranded RNA binding / positive regulation of transcription by RNA polymerase II / RNA binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
paz domain / Protein argonaute, Mid domain / Argonaute-like, PIWI domain / Mid domain of argonaute / paz domain / Argonaute linker 2 domain / Protein argonaute, N-terminal / N-terminal domain of argonaute / Argonaute linker 2 domain / DUF1785 ...paz domain / Protein argonaute, Mid domain / Argonaute-like, PIWI domain / Mid domain of argonaute / paz domain / 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 / Beta Complex / Ribonuclease H-like superfamily/Ribonuclease H / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / Protein argonaute-1
Similarity search - Component
Biological speciesHomo sapiens (human)
Spodoptera frugiperda (fall armyworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.294 Å
AuthorsNakanishi, K. / Patel, D.J.
CitationJournal: Cell Rep / Year: 2013
Title: Eukaryote-Specific Insertion Elements Control Human ARGONAUTE Slicer Activity.
Authors: Nakanishi, K. / Ascano, M. / Gogakos, T. / Ishibe-Murakami, S. / Serganov, A.A. / Briskin, D. / Morozov, P. / Tuschl, T. / Patel, D.J.
History
DepositionMay 28, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Assembly

Deposited unit
A: Protein argonaute-1
B: RNA


Theoretical massNumber of molelcules
Total (without water)101,6122
Polymers101,6122
Non-polymers00
Water5,188288
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3380 Å2
ΔGint-28 kcal/mol
Surface area37160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.879, 100.249, 136.701
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 / Argonaute1 / hAgo1 / Eukaryotic translation initiation factor 2C 1 / eIF-2C 1 / eIF2C 1 / Putative ...Argonaute1 / hAgo1 / Eukaryotic translation initiation factor 2C 1 / eIF-2C 1 / eIF2C 1 / Putative RNA-binding protein Q99


Mass: 97752.742 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EIF2C1, AGO1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9UL18
#2: RNA chain RNA /


Mass: 3859.432 Da / Num. of mol.: 1 / Fragment: guide RNA / Source method: isolated from a natural source / Source: (natural) Spodoptera frugiperda (fall armyworm)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 288 / 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: 2.36 Å3/Da / Density % sol: 47.79 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 8
Details: 50 mM Tris-HCl pH 8.0, 50 mM sodium chloride, 5 mM magnesium chloride, 1 mM dithiothreitol, 50% glycerol, EVAPORATION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 15, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.294→50 Å / Num. obs: 43638 / % possible obs: 99.9 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3
Reflection shellResolution: 2.294→2.38 Å / % possible all: 99.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.294→48.863 Å / SU ML: 0.28 / σ(F): 1.36 / Phase error: 24.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2282 2000 4.59 %
Rwork0.175 --
obs0.1774 43565 99.53 %
all-43638 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.294→48.863 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6473 222 0 288 6983
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086876
X-RAY DIFFRACTIONf_angle_d1.1659367
X-RAY DIFFRACTIONf_dihedral_angle_d15.5652640
X-RAY DIFFRACTIONf_chiral_restr0.0781037
X-RAY DIFFRACTIONf_plane_restr0.0051171
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.294-2.35120.27951340.21172778X-RAY DIFFRACTION94
2.3512-2.41470.26781420.19192937X-RAY DIFFRACTION100
2.4147-2.48580.25781410.19892929X-RAY DIFFRACTION100
2.4858-2.5660.27091410.18882947X-RAY DIFFRACTION100
2.566-2.65770.25451420.1882949X-RAY DIFFRACTION100
2.6577-2.76410.25751400.19492928X-RAY DIFFRACTION100
2.7641-2.88990.2641430.19392958X-RAY DIFFRACTION100
2.8899-3.04220.30651430.20092984X-RAY DIFFRACTION100
3.0422-3.23280.26421430.19022952X-RAY DIFFRACTION100
3.2328-3.48240.22581430.18832988X-RAY DIFFRACTION100
3.4824-3.83270.23611440.16612994X-RAY DIFFRACTION100
3.8327-4.3870.1951450.14493005X-RAY DIFFRACTION100
4.387-5.52590.18631460.14733039X-RAY DIFFRACTION100
5.5259-48.87360.19991530.18413177X-RAY DIFFRACTION100
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)
11.78670.1232-0.0461.4250.09520.7201-0.0133-0.090.16220.09620.08920.76630.0073-0.4273-0.04090.2813-0.01890.06720.41650.07740.51160.43751.9227-3.2093
20.7768-0.27171.41070.0185-0.01392.70080.0895-0.0294-0.0897-0.0020.06410.07670.0683-0.1256-0.14870.2627-0.01950.00850.21390.03570.22577.09698.4738-36.5713
30.8365-0.2-0.24291.11540.46071.21310.1090.04710.029-0.1614-0.02870.003-0.1576-0.0084-0.06690.18890.0029-0.01280.15740.03350.163631.9536-14.2092-19.3018
40.1216-0.07670.25930.0143-0.11680.3290.0197-0.23450.1064-0.10820.0549-0.0024-0.0989-0.36750.00050.4560.06750.05380.49150.04450.411124.6848-0.8719-26.5557
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 22 through 180 )
2X-RAY DIFFRACTION2chain 'A' and (resid 181 through 355 )
3X-RAY DIFFRACTION3chain 'A' and (resid 356 through 857 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 21 )

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