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- PDB-4z4f: Human Argonaute2 Bound to t1-DAP Target RNA -

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Basic information

Entry
Database: PDB / ID: 4z4f
TitleHuman Argonaute2 Bound to t1-DAP Target RNA
Components
  • Protein argonaute-2
  • RNA (5'-R(*CP*AP*AP*UP*GP*UP*GP*AP*(N6G)P*A)-3')
  • RNA (5'-R(P*UP*UP*CP*AP*CP*AP*UP*UP*GP*CP*CP*CP*AP*AP*GP*UP*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 / 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 / RISC-loading complex / miRNA metabolic process / mRNA cap binding / RISC complex assembly / regulatory ncRNA-mediated post-transcriptional gene silencing / miRNA processing / miRNA-mediated gene silencing by inhibition of translation / pre-miRNA processing / RNA 7-methylguanosine cap binding / siRNA processing / siRNA binding / regulation of synapse maturation / mRNA 3'-UTR AU-rich region binding / M-decay: degradation of maternal mRNAs by maternally stored factors / Regulation of MITF-M-dependent genes involved in apoptosis / RISC complex / regulatory ncRNA-mediated gene silencing / TGFBR3 expression / Regulation of RUNX1 Expression and Activity / miRNA binding / P-body assembly / 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 / 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 / translation initiation factor activity / negative regulation of translational initiation / RNA endonuclease activity / positive regulation of translation / post-embryonic development / TP53 Regulates Metabolic Genes / P-body / Transcriptional regulation by small RNAs / 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 / cytoplasm / cytosol
Similarity search - Function
Protein argonaute-2 / paz domain / 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 ...Protein argonaute-2 / paz domain / 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 / 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
PHENOL / RNA / RNA (> 10) / Protein argonaute-2
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsSchirle, N.T. / MacRae, I.J.
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 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 / pdbx_struct_oper_list / struct_conn / struct_conn_type
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 / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.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*UP*U)-3')
D: RNA (5'-R(*CP*AP*AP*UP*GP*UP*GP*AP*(N6G)P*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,8359
Polymers107,4793
Non-polymers3556
Water28816
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8460 Å2
ΔGint-66 kcal/mol
Surface area38160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.859, 116.591, 70.375
Angle α, β, γ (deg.)90.00, 92.52, 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*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*(N6G)P*A)-3')


Mass: 3553.217 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 22 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-IPH / PHENOL


Mass: 94.111 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H6O
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 2.13 Å3/Da / Density % sol: 42.26 %
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: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 3, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.8→38.86 Å / Num. obs: 21078 / % possible obs: 95 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.098 / Rsym value: 0.097 / Net I/σ(I): 9.9
Reflection shellResolution: 2.8→2.95 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: 2.8→35.46 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.233 1049 4.99 %
Rwork0.1839 --
obs0.1863 21036 94.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→35.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6421 571 24 16 7032
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067227
X-RAY DIFFRACTIONf_angle_d0.9039900
X-RAY DIFFRACTIONf_dihedral_angle_d13.6452797
X-RAY DIFFRACTIONf_chiral_restr0.0431117
X-RAY DIFFRACTIONf_plane_restr0.0041180
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8002-2.94780.35511390.2822756X-RAY DIFFRACTION92
2.9478-3.13240.28511500.23882882X-RAY DIFFRACTION96
3.1324-3.3740.27961400.20152955X-RAY DIFFRACTION97
3.374-3.71330.26771450.19342750X-RAY DIFFRACTION92
3.7133-4.24980.20531580.1652926X-RAY DIFFRACTION98
4.2498-5.35130.22031610.15652853X-RAY DIFFRACTION95
5.3513-35.46280.18861560.16822865X-RAY DIFFRACTION93
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)
12.0494-0.74230.50721.8584-0.57532.4247-0.00450.49120.7922-0.4611-0.1156-0.2572-0.9202-0.06470.10870.74150.0220.01740.48590.14530.549975.028912.31285.4318
24.15410.14091.40351.1098-0.02433.1037-0.26340.43130.3282-0.1550.09350.092-0.6050.06380.18930.4648-0.01310.03220.40410.0760.276871.4458-3.30244.6612
31.5315-0.19550.72510.5463-0.32232.11690.00170.70420.0711-0.30240.02680.1662-0.0982-0.3904-0.02170.51640.01250.01720.7636-0.03920.468655.522-8.7683-4.4463
42.52030.3743-0.20551.33280.11131.33750.0058-0.1298-0.15180.0809-0.00710.16720.1016-0.07410.00340.20960.0386-0.00960.19580.02960.20661.3874-20.106333.5092
50.86980.19340.27430.60350.90591.39490.06520.35620.64510.08720.10110.2557-0.8466-0.1842-0.1180.60910.07950.01950.38020.14080.587761.7666-14.120817.169
61.9999-0.58912.15531.06420.26553.26980.11051.36410.6095-0.9481-0.25051.7407-0.4487-0.65950.13731.71240.1164-0.42492.03690.16132.038645.76257.0921-8.4304
73.8132-1.36141.86533.3257-2.53414.5640.2985-0.0145-0.5361-0.29540.02360.21350.9187-0.0063-0.37680.5389-0.0046-0.03130.29710.02060.393262.5838-29.441117.2138
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 22 through 138 )
2X-RAY DIFFRACTION2chain 'A' and (resid 139 through 238 )
3X-RAY DIFFRACTION3chain 'A' and (resid 239 through 419 )
4X-RAY DIFFRACTION4chain 'A' and (resid 420 through 859 )
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 15 )
6X-RAY DIFFRACTION6chain 'B' and (resid 16 through 21 )
7X-RAY DIFFRACTION7chain 'D' and (resid 1 through 10 )

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