[English] 日本語
Yorodumi
- PDB-4f3t: Human Argonaute-2 - miR-20a complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4f3t
TitleHuman Argonaute-2 - miR-20a complex
Components
  • Protein argonaute-2
  • RNA (5'-R(P*UP*AP*AP*AP*GP*UP*GP*CP*UP*UP*AP*UP*AP*GP*UP*G*CP*AP*GP*G)-3')
KeywordsHydrolase/RNA / HYDROLASE/GENE REGULATION / RNAi / Slicer / RNA / 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 / 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 / RISC complex assembly / regulatory ncRNA-mediated post-transcriptional gene silencing / mRNA 3'-UTR AU-rich region binding / miRNA-mediated gene silencing by inhibition of translation / regulatory ncRNA-mediated gene silencing / M-decay: degradation of maternal mRNAs by maternally stored factors / miRNA processing / RNA 7-methylguanosine cap binding / siRNA binding / pre-miRNA processing / siRNA processing / Regulation of RUNX1 Expression and Activity / RISC complex / MicroRNA (miRNA) biogenesis / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / miRNA binding / RNA polymerase II complex binding / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / Regulation of MECP2 expression and activity / Nuclear events stimulated by ALK signaling in cancer / core promoter sequence-specific DNA binding / negative regulation of translational initiation / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / RNA endonuclease activity / translation initiation factor 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 / translation / dendrite / positive regulation of transcription by RNA polymerase II / RNA binding / extracellular exosome / nucleoplasm / membrane / nucleus / metal ion binding / cytoplasm / cytosol
Similarity search - Function
Protein argonaute-2 / paz domain / paz domain / Protein argonaute, Mid domain / Argonaute-like, PIWI domain / Mid domain of argonaute / Argonaute linker 2 domain / Protein argonaute, N-terminal / N-terminal domain of argonaute / Argonaute linker 2 domain ...Protein argonaute-2 / paz domain / paz domain / Protein argonaute, Mid domain / Argonaute-like, PIWI domain / Mid domain of argonaute / 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 profile. / PAZ domain / 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
PHENOL / : / RNA / RNA (> 10) / Protein argonaute-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.25 Å
AuthorsElkayam, E. / Kuhn, C.-D. / Tocilj, A. / Joshua-Tor, L.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2012
Title: The Structure of Human Argonaute-2 in Complex with miR-20a.
Authors: Elkayam, E. / Kuhn, C.D. / Tocilj, A. / Haase, A.D. / Greene, E.M. / Hannon, G.J. / Joshua-Tor, L.
History
DepositionMay 9, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2012Group: Database references
Revision 1.2Nov 15, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3Feb 28, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein argonaute-2
R: RNA (5'-R(P*UP*AP*AP*AP*GP*UP*GP*CP*UP*UP*AP*UP*AP*GP*UP*G*CP*AP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,1154
Polymers103,9272
Non-polymers1882
Water2,450136
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4360 Å2
ΔGint-29 kcal/mol
Surface area38330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.427, 107.651, 68.718
Angle α, β, γ (deg.)90.000, 106.690, 90.000
Int Tables number4
Space group name H-MP1211
DetailsTHE POLYMERIC CHAIN HAS A BIOLOGICAL UNIT REPRESENTED AS A MONOMER IN SOLUTION

-
Components

#1: Protein Protein argonaute-2 / Argonaute2 / hAgo2 / Eukaryotic translation initiation factor 2C 2 / eIF-2C 2 / eIF2C 2 / PAZ Piwi ...Argonaute2 / hAgo2 / Eukaryotic translation initiation factor 2C 2 / eIF-2C 2 / eIF2C 2 / PAZ Piwi domain protein / PPD / Protein slicer


Mass: 97478.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Cleavable Two-Strepsumo tag (TSS) / Source: (gene. exp.) Homo sapiens (human)
Gene: AGO2, Argonaute2, eIF-2C 2, eIF2C 2, EIF2C2, Eukaryotic translation initiation factor 2C 2, hAgo2, Human Argonaute-2, PAZ Piwi domain protein
Plasmid: pFL, MultiBac / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q9UKV8, Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters
#2: RNA chain RNA (5'-R(P*UP*AP*AP*AP*GP*UP*GP*CP*UP*UP*AP*UP*AP*GP*UP*G*CP*AP*GP*G)-3')


Mass: 6448.871 Da / Num. of mol.: 1 / Fragment: GB bases 8-27 / Source method: obtained synthetically / Details: miR-20a / Source: (synth.) Homo sapiens (human) / References: GenBank: 406982
#3: Chemical ChemComp-IPH / PHENOL


Mass: 94.111 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H6O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 43.12 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 9
Details: microseeding in 100 mM Tris pH=9.0, 10% PEG 3350 (w/v), 8% 2-propanol (v/v), 0.12 M phenol, VAPOR DIFFUSION, HANGING DROP, temperature 290K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationMonochromator: Cryogenically cooled double crystal monochrometer with horizontal focusing sagittal bend second mono crystal with 4:1 magnification ratio and vertically focusing mirror
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionRedundancy: 3.9 % / Av σ(I) over netI: 27.39 / Number: 200364 / Rmerge(I) obs: 0.048 / Χ2: 1.77 / D res high: 2.62 Å / D res low: 50 Å / Num. obs: 51823 / % possible obs: 99.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
7.115099.310.032.1113.8
5.647.1110010.0382.5143.8
4.935.6410010.0412.863.8
4.484.9310010.0382.4213.9
4.164.4810010.0351.9763.9
3.914.1610010.0371.8433.9
3.723.9110010.041.8213.9
3.563.7299.910.0461.7513.9
3.423.5610010.0551.7443.9
3.33.4210010.0651.7463.9
3.23.399.910.0771.6493.9
3.113.210010.0921.6163.9
3.023.1110010.1081.5263.9
2.953.0210010.1331.5043.9
2.882.9510010.161.4573.9
2.822.8810010.1741.4513.9
2.772.8210010.2071.3783.9
2.712.7710010.261.3923.9
2.672.7110010.2961.3563.9
2.622.6710010.3491.3433.8
ReflectionResolution: 2.25→50 Å / Num. all: 42106 / Num. obs: 41096 / % possible obs: 97.6 % / Observed criterion σ(F): -3 / Redundancy: 2.7 % / Rmerge(I) obs: 0.047 / Χ2: 1.426 / Net I/σ(I): 16.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.25-2.292.50.35919450.815192.6
2.29-2.332.70.30820360.826197
2.33-2.382.70.2620600.826198
2.38-2.422.70.2520620.926198.8
2.42-2.482.70.20220770.862199.1
2.48-2.532.70.16420770.911199.2
2.53-2.62.70.14820560.943199.3
2.6-2.672.70.12621040.924199.2
2.67-2.752.70.10520791.005198.9
2.75-2.832.70.08720761.134199.1
2.83-2.942.70.07420731.165198.8
2.94-3.052.70.06120721.141198.4
3.05-3.192.80.05320751.299198.5
3.19-3.362.70.04520831.516198.4
3.36-3.572.70.04120481.655197.8
3.57-3.852.70.0420392.121197.4
3.85-4.232.70.03920702.542197.4
4.23-4.852.70.03920382.98196.3
4.85-6.12.60.03520202.562195.1
6.1-502.80.0320062.314192.7

-
Phasing

PhasingMethod: SAD
Phasing MAD set
IDHighest resolution (Å)Lowest resolution (Å)Power acentricPower centricReflection acentricReflection centric
ISO_12.6341.730025262810
ANO_12.6341.731.3980252500
Phasing MAD set shell
IDResolution (Å)Power acentricPower centricReflection acentricReflection centric
ISO_111.32-41.730025338
ISO_18.16-11.320050345
ISO_16.7-8.160065443
ISO_15.82-6.70078842
ISO_15.22-5.820088340
ISO_14.77-5.2200100342
ISO_14.42-4.7700109140
ISO_14.14-4.4200116137
ISO_13.9-4.1400120935
ISO_13.71-3.900130936
ISO_13.53-3.7100138635
ISO_13.38-3.5300145039
ISO_13.25-3.3800151334
ISO_13.14-3.2500154536
ISO_13.03-3.1400163237
ISO_12.93-3.0300170650
ISO_12.85-2.9300172346
ISO_12.77-2.8500178744
ISO_12.69-2.7700185449
ISO_12.63-2.6900181242
ANO_111.32-41.733.17902530
ANO_18.16-11.323.33705030
ANO_16.7-8.163.84706540
ANO_15.82-6.73.53507880
ANO_15.22-5.823.00908830
ANO_14.77-5.222.598010030
ANO_14.42-4.772.401010900
ANO_14.14-4.422.185011610
ANO_13.9-4.141.924012090
ANO_13.71-3.91.684013080
ANO_13.53-3.711.471013840
ANO_13.38-3.531.236014490
ANO_13.25-3.380.991015130
ANO_13.14-3.250.833015440
ANO_13.03-3.140.689016310
ANO_12.93-3.030.606017040
ANO_12.85-2.930.514017220
ANO_12.77-2.850.449017870
ANO_12.69-2.770.391018530
ANO_12.63-2.690.336018110
Phasing MAD set site
IDCartn x (Å)Cartn y (Å)Cartn z (Å)Atom type symbolB isoOccupancy
143.62327.21441.975SE40.540.6
267.55741.18753.071SE54.740.65
338.58413.33339.132SE52.050.65
470.4327.71357.882SE53.780.64
575.55344.7256.894SE80.020.73
641.3299.73441.938SE63.650.63
785.69655.79455.515SE78.550.6
879.45355.93262.561SE85.690.72
945.71418.74643.864SE71.640.57
1038.204-9.78951.703SE83.660.59
1137.16720.4736.221SE66.820.51
1248.1611.05632.738SE56.380.41
1332.99313.06636.541SE82.340.54
1439.00625.79964.221SE97.810.59
1570.39647.39575.657SE135.010.59
1656.489-5.23650.43SE90.010.34
1743.9881.35253.627SE110.270.45
1877.0149.44982.718SE153.970.56

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
SOLOMONphasing
PHENIX1.7.2_869refinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
RefinementMethod to determine structure: SAD / Resolution: 2.25→47.438 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.79 / σ(F): 1.35 / Phase error: 25.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.254 1295 3.15 %Random
Rwork0.207 ---
obs0.208 41069 97.44 %-
all-41069 --
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.545 Å2 / ksol: 0.346 e/Å3
Displacement parametersBiso max: 177.91 Å2 / Biso mean: 57.952 Å2 / Biso min: 20.78 Å2
Baniso -1Baniso -2Baniso -3
1--0.76 Å2-0 Å21.883 Å2
2---2.289 Å2-0 Å2
3---3.049 Å2
Refinement stepCycle: LAST / Resolution: 2.25→47.438 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6436 298 14 136 6884
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036932
X-RAY DIFFRACTIONf_angle_d0.6749442
X-RAY DIFFRACTIONf_chiral_restr0.0421059
X-RAY DIFFRACTIONf_plane_restr0.0031163
X-RAY DIFFRACTIONf_dihedral_angle_d12.7622654
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.247-2.3360.3541240.2924233435794
2.336-2.4430.3421360.2714476461299
2.443-2.5720.3081420.2434469461199
2.572-2.7330.2951520.2374495464799
2.733-2.9440.3181670.2264430459799
2.944-3.240.2751340.2244486462099
3.24-3.7080.241440.2044442458698
3.708-4.6720.2131500.1754401455197
4.672-47.4490.2311460.194342448894
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)
11.983-0.320.42013.5008-1.38891.68650.03420.3272-0.7607-0.2341-0.0844-0.24710.41440.0224-0.02020.1757-0.05140.06390.2536-0.05870.211235.94874.736745.2862
21.1371-0.2465-0.45521.5847-0.96163.49290.06810.1199-0.3111-0.0050.17960.1131-0.1547-0.0418-0.09530.1089-0.0459-0.00350.2671-0.00620.275536.973310.042558.2023
30.53860.449-0.77051.5806-2.51014.0419-0.1210.0962-0.07070.21010.0585-0.019-0.158-0.19360.03180.2994-0.01860.04230.3014-0.03780.258637.15129.879579.0977
42.5234-0.42590.07151.57850.28261.0327-0.2113-0.49270.8040.20640.12290.0405-0.1619-0.1770.19220.17990.0172-0.08620.3464-0.04660.417920.38244.093161.2143
54.4272-0.0161-0.17021.60620.16731.5141-0.03680.3456-0.1679-0.0680.02970.18880.0692-0.09970.01840.1295-0.0438-0.03130.22040.07730.191618.558529.94945.0498
64.41520.2589-0.87992.1015-0.17124.0756-0.1632-0.51410.23880.3319-0.10760.21650.0467-0.5025-0.02430.1711-0.0103-0.00180.3491-0.03970.342715.617736.705159.0157
70.1587-0.0175-0.19370.181-0.23281.3931-0.1101-0.1916-0.07110.06310.08160.12370.5471-0.00770.09570.38380.0809-0.06030.0624-0.1110.536331.707522.596567.7372
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 23:102 )A23 - 102
2X-RAY DIFFRACTION2( CHAIN A AND RESID 103:269 )A103 - 269
3X-RAY DIFFRACTION3( CHAIN A AND RESID 270:386 )A270 - 386
4X-RAY DIFFRACTION4( CHAIN A AND RESID 387:641 )A387 - 641
5X-RAY DIFFRACTION5( CHAIN A AND RESID 642:775 )A642 - 775
6X-RAY DIFFRACTION6( CHAIN A AND RESID 776:859 )A776 - 859
7X-RAY DIFFRACTION7( CHAIN R AND RESID 1:20 )R1 - 20

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more