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- PDB-4z4e: Human Argonaute2 Bound to t1-U Target RNA -

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Basic information

Entry
Database: PDB / ID: 4z4e
TitleHuman Argonaute2 Bound to t1-U Target RNA
Components
  • Protein argonaute-2
  • RNA (5'-R(*CP*AP*AP*UP*GP*UP*GP*AP*U)-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')
Keywordsgene regulation/rna / Argonaute2 / gene regulation-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 / 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 ...: / 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 / 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 / negative regulation of amyloid precursor protein biosynthetic process / Small interfering RNA (siRNA) biogenesis / Transcriptional Regulation by MECP2 / positive regulation of trophoblast cell migration / RNA secondary structure unwinding / miRNA metabolic process / RISC-loading complex / mRNA cap binding / regulatory ncRNA-mediated post-transcriptional gene silencing / : / RISC complex assembly / mRNA 3'-UTR AU-rich region binding / miRNA processing / pre-miRNA processing / miRNA-mediated gene silencing by inhibition of translation / siRNA processing / RNA 7-methylguanosine cap binding / siRNA binding / M-decay: degradation of maternal mRNAs by maternally stored factors / regulatory ncRNA-mediated gene silencing / RISC complex / miRNA binding / Regulation of RUNX1 Expression and Activity / MicroRNA (miRNA) biogenesis / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / RNA polymerase II complex binding / Regulation of MECP2 expression and activity / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / negative regulation of translational initiation / core promoter sequence-specific DNA binding / RNA endonuclease activity / translation initiation factor activity / post-embryonic development / positive regulation of translation / P-body / TP53 Regulates Metabolic Genes / Transcriptional regulation by small RNAs / MAPK6/MAPK4 signaling / cytoplasmic ribonucleoprotein granule / Pre-NOTCH Transcription and Translation / positive regulation of angiogenesis / double-stranded RNA binding / Ca2+ pathway / Estrogen-dependent gene expression / single-stranded RNA binding / translation / dendrite / positive regulation of transcription by RNA polymerase II / RNA binding / extracellular exosome / nucleoplasm / membrane / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Protein argonaute-2 / 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 ...Protein argonaute-2 / 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
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 / MOLECULAR REPLACEMENT / Resolution: 1.8 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 1.3Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,10613
Polymers107,4413
Non-polymers66510
Water9,602533
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8490 Å2
ΔGint-65 kcal/mol
Surface area37350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.645, 116.841, 69.744
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 / Cell line (production host): Sf-9 / Production host: Spodoptera frugiperda (fall armyworm)
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*U)-3')


Mass: 3515.162 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 5 types, 543 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 / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#6: Chemical
ChemComp-IPH / PHENOL / Phenol


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


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 533 / 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: 2.11 Å3/Da / Density % sol: 41.66 %
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: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.8→55.6 Å / Num. obs: 82071 / % possible obs: 99.7 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.098 / Rsym value: 0.053 / Net I/σ(I): 10.3
Reflection shellResolution: 1.8→1.9 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4W5O

4w5o


Resolution: 1.8→40.274 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1854 4092 4.99 %
Rwork0.1575 --
obs0.1589 82041 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→40.274 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6429 552 44 533 7558
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077249
X-RAY DIFFRACTIONf_angle_d1.1319945
X-RAY DIFFRACTIONf_dihedral_angle_d13.2942798
X-RAY DIFFRACTIONf_chiral_restr0.0761116
X-RAY DIFFRACTIONf_plane_restr0.0051182
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.82120.28921470.28232697X-RAY DIFFRACTION99
1.8212-1.84340.25121230.25022664X-RAY DIFFRACTION100
1.8434-1.86670.21761330.22412686X-RAY DIFFRACTION100
1.8667-1.89130.24231350.22082689X-RAY DIFFRACTION100
1.8913-1.91720.22641550.20252680X-RAY DIFFRACTION100
1.9172-1.94460.24541380.19452687X-RAY DIFFRACTION100
1.9446-1.97360.23661470.18012661X-RAY DIFFRACTION100
1.9736-2.00450.21111620.17552642X-RAY DIFFRACTION100
2.0045-2.03730.2281480.17042686X-RAY DIFFRACTION100
2.0373-2.07240.18611430.16732696X-RAY DIFFRACTION100
2.0724-2.11010.18431540.16332660X-RAY DIFFRACTION100
2.1101-2.15070.21441530.15982700X-RAY DIFFRACTION100
2.1507-2.19460.19261430.15012690X-RAY DIFFRACTION100
2.1946-2.24230.19831450.15342712X-RAY DIFFRACTION100
2.2423-2.29450.18231450.15332631X-RAY DIFFRACTION100
2.2945-2.35190.18651300.15132716X-RAY DIFFRACTION100
2.3519-2.41540.18791320.15192717X-RAY DIFFRACTION100
2.4154-2.48650.16241460.15182677X-RAY DIFFRACTION100
2.4865-2.56670.22051290.1542699X-RAY DIFFRACTION100
2.5667-2.65850.17851430.15322696X-RAY DIFFRACTION100
2.6585-2.76490.2041290.15172681X-RAY DIFFRACTION100
2.7649-2.89070.1691280.15472704X-RAY DIFFRACTION100
2.8907-3.0430.16921430.15562726X-RAY DIFFRACTION100
3.043-3.23360.21271290.15322704X-RAY DIFFRACTION100
3.2336-3.48320.17331260.15222732X-RAY DIFFRACTION100
3.4832-3.83340.16431400.13922673X-RAY DIFFRACTION100
3.8334-4.38760.15021590.13382690X-RAY DIFFRACTION100
4.3876-5.52560.15581380.13822705X-RAY DIFFRACTION99
5.5256-40.28360.17831490.16412648X-RAY DIFFRACTION96
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)
11.5718-0.58590.71221.3507-0.5842.1082-0.07750.4370.429-0.3575-0.0128-0.1272-0.70230.03710.07730.5355-0.02510.00130.33120.11320.300175.68369.54457.0958
21.5737-0.07650.02141.7679-0.45091.301-0.21460.18510.4446-0.15540.0655-0.0809-0.8186-0.0960.11940.6834-0.0318-0.07060.40380.07480.313573.028610.35494.2934
32.8656-0.00421.23260.90410.14952.3705-0.01680.5374-0.0301-0.2188-0.12090.4485-0.038-0.81720.09290.3571-0.0044-0.03980.969-0.09350.392948.4805-6.373-7.9087
40.8135-0.1180.28650.67150.00471.260.01650.4203-0.0435-0.33760.014-0.0498-0.10950.045-0.00650.2994-0.00180.0390.3778-0.01230.185274.3861-10.84916.325
51.37130.34680.03120.80870.06510.52670.0126-0.0963-0.08740.0642-0.00070.03480.0506-0.0115-0.00150.12870.01940.0020.11620.01220.108761.2245-19.025933.4016
61.62660.1351-0.53090.17250.23940.65320.05320.20060.1038-0.02140.0190.0932-0.0942-0.0717-0.0810.15840.0064-0.00590.16160.00320.17861.8635-22.237519.4229
70.8130.15321.13740.3830.48111.82-0.3430.9630.7134-0.58880.08860.6296-0.4305-0.27840.2850.6005-0.0258-0.15490.71040.24790.575456.78742.72487.7013
82.6725-0.4659-0.53232.65350.13143.2018-0.02470.1867-0.3801-0.1123-0.00530.19330.29880.05040.01150.1637-0.01710.00380.1934-0.04460.200261.4573-26.857815.8901
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 195 )
3X-RAY DIFFRACTION3chain 'A' and (resid 196 through 343 )
4X-RAY DIFFRACTION4chain 'A' and (resid 344 through 419 )
5X-RAY DIFFRACTION5chain 'A' and (resid 420 through 859 )
6X-RAY DIFFRACTION6chain 'B' and (resid 1 through 9 )
7X-RAY DIFFRACTION7chain 'B' and (resid 10 through 21 )
8X-RAY DIFFRACTION8chain 'D' and (resid 1 through 9 )

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