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- PDB-4z4c: Human Argonaute2 Bound to t1-C Target RNA -

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Basic information

Entry
Database: PDB / ID: 4z4c
TitleHuman Argonaute2 Bound to t1-C Target RNA
Components
  • Protein argonaute-2
  • RNA (5'-R(*CP*AP*AP*UP*GP*UP*GP*AP*C)-3')
  • RNA (5'-R(P*UP*UP*CP*AP*CP*AP*UP*UP*GP*CP*CP*CP*AP*AP*GP*UP*CP*UP*U)-3')
Keywordshydrolase/rna / Argonaute2 / miRNA / hydrolase-rna complex
Function / homology
Function and homology information


: / endoribonuclease activity, cleaving miRNA-paired mRNA / endoribonuclease activity, cleaving siRNA-paired mRNA / siRNA-mediated gene silencing by mRNA destabilization / miRNA-mediated gene silencing by mRNA destabilization / Post-transcriptional silencing by small RNAs / Competing endogenous RNAs (ceRNAs) regulate PTEN translation / Regulation of CDH11 mRNA translation by microRNAs / Regulation of NPAS4 mRNA translation / Regulation of PTEN mRNA translation ...: / endoribonuclease activity, cleaving miRNA-paired mRNA / endoribonuclease activity, cleaving siRNA-paired mRNA / siRNA-mediated gene silencing by mRNA destabilization / miRNA-mediated gene silencing by mRNA destabilization / Post-transcriptional silencing by small RNAs / Competing endogenous RNAs (ceRNAs) regulate PTEN translation / Regulation of CDH11 mRNA translation by microRNAs / Regulation of NPAS4 mRNA translation / Regulation of PTEN mRNA translation / negative regulation of amyloid precursor protein biosynthetic process / Small interfering RNA (siRNA) biogenesis / positive regulation of trophoblast cell migration / Transcriptional Regulation by MECP2 / miRNA metabolic process / RISC-loading complex / mRNA cap binding / regulatory ncRNA-mediated post-transcriptional gene silencing / RISC complex assembly / miRNA processing / miRNA-mediated gene silencing by inhibition of translation / pre-miRNA processing / RNA 7-methylguanosine cap binding / siRNA processing / regulation of synapse maturation / siRNA binding / Regulation of MITF-M-dependent genes involved in apoptosis / mRNA 3'-UTR AU-rich region binding / M-decay: degradation of maternal mRNAs by maternally stored factors / RISC complex / regulatory ncRNA-mediated gene silencing / TGFBR3 expression / Regulation of RUNX1 Expression and Activity / P-body assembly / miRNA binding / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / MicroRNA (miRNA) biogenesis / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / RNA polymerase II complex binding / Regulation of MECP2 expression and activity / core promoter sequence-specific DNA binding / Nuclear events stimulated by ALK signaling in cancer / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / negative regulation of translational initiation / translation initiation factor activity / RNA endonuclease activity / post-embryonic development / positive regulation of translation / TP53 Regulates Metabolic Genes / Transcriptional regulation by small RNAs / P-body / MAPK6/MAPK4 signaling / Pre-NOTCH Transcription and Translation / cytoplasmic ribonucleoprotein granule / positive regulation of angiogenesis / double-stranded RNA binding / Ca2+ pathway / Estrogen-dependent gene expression / single-stranded RNA binding / postsynapse / translation / dendrite / glutamatergic synapse / positive regulation of transcription by RNA polymerase II / RNA binding / extracellular exosome / nucleoplasm / metal ion binding / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
Protein argonaute-2 / paz domain / Protein argonaute, Mid domain / Mid domain of argonaute / Argonaute linker 2 domain / Protein argonaute, N-terminal / Argonaute-like, PIWI domain / N-terminal domain of argonaute / Argonaute linker 2 domain / paz domain ...Protein argonaute-2 / paz domain / Protein argonaute, Mid domain / Mid domain of argonaute / Argonaute linker 2 domain / Protein argonaute, N-terminal / Argonaute-like, PIWI domain / N-terminal domain of argonaute / Argonaute linker 2 domain / paz domain / DUF1785 / Argonaute, linker 1 domain / Argonaute linker 1 domain / Piwi domain profile. / Piwi domain / Piwi domain / Piwi / PAZ domain superfamily / PAZ / PAZ domain / PAZ domain profile. / PAZ domain / Response regulator / Ribonuclease H-like superfamily/Ribonuclease H / Beta Complex / 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
ISOPROPYL ALCOHOL / PHENOL / PHOSPHATE ION / RNA / RNA (> 10) / Protein argonaute-2
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.303 Å
AuthorsSchirle, N.T. / MacRae, I.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM104475 United States
CitationJournal: Elife / Year: 2015
Title: Water-mediated recognition of t1-adenosine anchors Argonaute2 to microRNA targets.
Authors: Schirle, N.T. / Sheu-Gruttadauria, J. / Chandradoss, S.D. / Joo, C. / MacRae, I.J.
History
DepositionApr 2, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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: RNA (5'-R(P*UP*UP*CP*AP*CP*AP*UP*UP*GP*CP*CP*CP*AP*AP*GP*UP*CP*UP*U)-3')
D: RNA (5'-R(*CP*AP*AP*UP*GP*UP*GP*AP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,14013
Polymers107,4403
Non-polymers69910
Water5,026279
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8600 Å2
ΔGint-68 kcal/mol
Surface area37400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.692, 116.561, 69.606
Angle α, β, γ (deg.)90.00, 92.43, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Protein argonaute-2 / hAgo2 / Argonaute RISC catalytic component 2 / Eukaryotic translation initiation factor 2C 2 / ...hAgo2 / Argonaute RISC catalytic component 2 / Eukaryotic translation initiation factor 2C 2 / eIF2C 2 / PAZ Piwi domain protein / PPD / Protein slicer


Mass: 97378.180 Da / Num. of mol.: 1 / Mutation: S387D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AGO2, EIF2C2 / Plasmid: pFastBac / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf-9
References: UniProt: Q9UKV8, Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters

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RNA chain , 2 types, 2 molecules BD

#2: RNA chain RNA (5'-R(P*UP*UP*CP*AP*CP*AP*UP*UP*GP*CP*CP*CP*AP*AP*GP*UP*CP*UP*U)-3')


Mass: 6547.876 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: RNA chain RNA (5'-R(*CP*AP*AP*UP*GP*UP*GP*AP*C)-3')


Mass: 3514.178 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 5 types, 289 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#6: Chemical
ChemComp-IPH / PHENOL


Mass: 94.111 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H6O
#7: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 279 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 41.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, Tris, Isopropanol, Phenol, Magnesium

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 11, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 2.3→38.85 Å / Num. obs: 38614 / % possible obs: 98.4 % / Redundancy: 3.5 % / Net I/σ(I): 13.1
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 2.2 / % possible all: 96.3

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementResolution: 2.303→35.305 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2186 1880 4.87 %
Rwork0.1693 --
obs0.1717 38580 98.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.303→35.305 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6429 568 45 279 7321
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0147268
X-RAY DIFFRACTIONf_angle_d1.4549975
X-RAY DIFFRACTIONf_dihedral_angle_d13.8312806
X-RAY DIFFRACTIONf_chiral_restr0.0631121
X-RAY DIFFRACTIONf_plane_restr0.0081182
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3031-2.36530.28821390.23752691X-RAY DIFFRACTION95
2.3653-2.43490.27291410.21372857X-RAY DIFFRACTION99
2.4349-2.51350.26911370.20692819X-RAY DIFFRACTION98
2.5135-2.60330.28041450.20322770X-RAY DIFFRACTION98
2.6033-2.70750.27321450.20142834X-RAY DIFFRACTION99
2.7075-2.83070.24471420.18632861X-RAY DIFFRACTION99
2.8307-2.97980.26421390.19242813X-RAY DIFFRACTION99
2.9798-3.16640.24661380.18752825X-RAY DIFFRACTION97
3.1664-3.41070.22731310.17542853X-RAY DIFFRACTION99
3.4107-3.75360.23761570.16782841X-RAY DIFFRACTION99
3.7536-4.2960.19461570.1392814X-RAY DIFFRACTION98
4.296-5.40930.15291540.13522861X-RAY DIFFRACTION99
5.4093-35.30940.18081550.15022861X-RAY DIFFRACTION98
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)
11.4738-0.68930.79731.5434-0.60652.0743-0.11180.35490.381-0.309-0.007-0.1388-0.6254-0.04190.08660.5374-0.0267-0.00280.39210.05950.400175.55639.36427.3847
21.5719-0.37430.0091.7887-0.74841.234-0.30990.10520.3859-0.14050.1617-0.1574-0.8041-0.07110.12160.576-0.0404-0.01420.35050.02420.313173.60167.34375.148
31.4017-0.17290.46550.4232-0.13271.846-0.01990.6024-0.0713-0.2111-0.01360.1827-0.0208-0.45650.03380.3516-0.0420.00650.6969-0.08240.363156.0263-7.9893-3.9453
41.62890.5036-0.06510.62570.00710.5645-0.0017-0.107-0.05080.0231-0.00260.05420.0327-0.00170.00530.17540.02550.00340.145-0.0020.163561.2642-19.162933.3739
51.52590.4273-0.59570.4373-0.07880.94590.0360.11390.16370.00630.15460.1556-0.1436-0.1499-0.19470.18840.0229-0.00330.1860.00750.253961.8686-22.283319.4061
60.35280.28310.39680.22090.34060.5063-0.43520.80930.565-0.18410.05710.118-0.4642-0.29870.40480.62680.0058-0.07330.77430.21970.665856.82372.74477.7527
74.7257-0.3564-1.2223.93241.06794.4813-0.0552-0.1444-0.56580.0275-0.01890.44720.28160.13910.05440.2194-0.0260.01650.22250.02260.260661.927-27.95516.5231
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 22 through 102 )
2X-RAY DIFFRACTION2chain 'A' and (resid 103 through 212 )
3X-RAY DIFFRACTION3chain 'A' and (resid 213 through 419 )
4X-RAY DIFFRACTION4chain 'A' and (resid 420 through 859 )
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 9 )
6X-RAY DIFFRACTION6chain 'B' and (resid 10 through 21 )
7X-RAY DIFFRACTION7chain 'D' and (resid 1 through 9 )

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