[English] 日本語
Yorodumi
- PDB-6ra4: Human ARGONAUTE-2 PAZ DOMAIN (214-347) IN COMPLEX WITH CGUGACUCU -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ra4
TitleHuman ARGONAUTE-2 PAZ DOMAIN (214-347) IN COMPLEX WITH CGUGACUCU
Components
  • Protein argonaute-2
  • RNA (5'-R(*CP*GP*UP*GP*AP*CP*UP*CP*U)-3')
KeywordsRNA BINDING PROTEIN / SIRNA / PAZ DOMAIN
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 / Regulation of RUNX1 Expression and Activity / MicroRNA (miRNA) biogenesis / miRNA binding / 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 / negative regulation of translational initiation / RNA endonuclease activity / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / 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. / Beta Complex / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Mainly Beta
Similarity search - Domain/homology
RNA / Protein argonaute-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsRondeau, J.-M. / Bourgier, E.
CitationJournal: J.Chem.Inf.Model. / Year: 2019
Title: How to Computationally Stack the Deck for Hit-to-Lead Generation: In Silico Molecular Interaction Energy Profiling for de Novo siRNA Guide Strand Surrogate Selection.
Authors: Greenidge, P.A. / Blommers, M.J.J. / Priestle, J.P. / Hunziker, J.
History
DepositionApr 5, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 8, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein argonaute-2
B: Protein argonaute-2
L: RNA (5'-R(*CP*GP*UP*GP*AP*CP*UP*CP*U)-3')
M: RNA (5'-R(*CP*GP*UP*GP*AP*CP*UP*CP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4366
Polymers37,2524
Non-polymers1842
Water1,946108
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4570 Å2
ΔGint-36 kcal/mol
Surface area16480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.617, 87.672, 56.832
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11M-615-

HOH

-
Components

#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: 15817.429 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AGO2, EIF2C2 / Cell line (production host): BL21(DE3)* / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9UKV8, Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters
#2: RNA chain RNA (5'-R(*CP*GP*UP*GP*AP*CP*UP*CP*U)-3')


Mass: 2808.703 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 2.43 Å3/Da / Density % sol: 49.34 % / Description: rods
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: Drop was a 1:1 mix of protein stock (9.4MG/ML HAGO2 PAZ [214 TO 347] IN 100MM POTASSIUM CHLORIDE, 10MM DTT, 5MM HEPES/KOH PH 7.6, WITH A 1.1-FOLD EXCESS OF OLIGONUCLEOTIDE ADDED FROM A 1. ...Details: Drop was a 1:1 mix of protein stock (9.4MG/ML HAGO2 PAZ [214 TO 347] IN 100MM POTASSIUM CHLORIDE, 10MM DTT, 5MM HEPES/KOH PH 7.6, WITH A 1.1-FOLD EXCESS OF OLIGONUCLEOTIDE ADDED FROM A 1.75MM STOCK SOLUTION IN 100MM POTASSIUM CHLORIDE, 10MM DTT, 5MM HEPES) and reservoir solution (0.2M sodium CHLORIDE 20% PEG 3,350)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9999 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 30, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.9→100 Å / Num. obs: 29356 / % possible obs: 99.1 % / Redundancy: 7.3 % / Biso Wilson estimate: 31.4 Å2 / Rmerge(I) obs: 0.042 / Χ2: 1.017 / Net I/σ(I): 48 / Num. measured all: 213970
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.504 / Mean I/σ(I) obs: 3.29 / Num. unique obs: 3009 / Χ2: 1.546 / % possible all: 99

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
HKL-20001.98.7data reduction
SCALEPACK1.98.7data scaling
PHASERphasing
CNS2002refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→28.89 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 18239992 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.268 1425 4.9 %RANDOM
Rwork0.239 ---
obs-29003 99 %-
Solvent computationBsol: 43.0227 Å2 / ksol: 0.3696 e/Å3
Displacement parametersBiso max: 99.11 Å2 / Biso mean: 45.1 Å2 / Biso min: 24.4 Å2
Baniso -1Baniso -2Baniso -3
1--6.67 Å20 Å20 Å2
2--3.05 Å20 Å2
3---3.62 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.24 Å
Refinement stepCycle: final / Resolution: 1.9→28.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2102 370 12 108 2592
Biso mean--55.38 42.19 -
Num. residues----275
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d21.2
X-RAY DIFFRACTIONc_improper_angle_d1.24
X-RAY DIFFRACTIONc_mcbond_it1.651.5
X-RAY DIFFRACTIONc_mcangle_it2.62
X-RAY DIFFRACTIONc_scbond_it2.212
X-RAY DIFFRACTIONc_scangle_it3.392.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.371 256 5.4 %
Rwork0.306 4497 -
all-4753 -
obs--99.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3dna-rna.paramdna-rna.top
X-RAY DIFFRACTION4glycerol.paramglycerol.top

+
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://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