[English] 日本語
Yorodumi
- PDB-2f8t: Crystal structure of Aa-Ago with externally-bound siRNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2f8t
TitleCrystal structure of Aa-Ago with externally-bound siRNA
Components
  • 26-MER
  • Argonaute proteinArgonaute
KeywordsRNA BINDING PROTEIN/RNA / Argonaute / siRNA / RISC loading complex / RNA BINDING PROTEIN-RNA COMPLEX
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / RNA endonuclease activity / DNA binding / RNA binding / metal ion binding
Similarity search - Function
PAZ domain fold / PAZ domain superfamily / Aquifex aeolicus argonaute, PAZ domain / PAZ domain / Piwi domain / Piwi domain profile. / Piwi domain / Piwi / PAZ domain superfamily / PAZ domain profile. ...PAZ domain fold / PAZ domain superfamily / Aquifex aeolicus argonaute, PAZ domain / PAZ domain / Piwi domain / Piwi domain profile. / Piwi domain / Piwi / PAZ domain superfamily / PAZ domain profile. / Response regulator / Ribonuclease H-like superfamily/Ribonuclease H / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Roll / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / Protein argonaute
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsYuan, Y.R. / Chen, H.Y. / Patel, D.J.
CitationJournal: Structure / Year: 2006
Title: A Potential Protein-RNA Recognition Event along the RISC-Loading Pathway from the Structure of A. aeolicus Argonaute with Externally Bound siRNA.
Authors: Yuan, Y.R. / Pei, Y. / Chen, H.Y. / Tuschl, T. / Patel, D.J.
History
DepositionDec 3, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C: 26-MER
D: 26-MER
A: Argonaute protein
B: Argonaute protein


Theoretical massNumber of molelcules
Total (without water)183,0934
Polymers183,0934
Non-polymers00
Water91951
1
C: 26-MER
D: 26-MER
A: Argonaute protein


Theoretical massNumber of molelcules
Total (without water)99,8283
Polymers99,8283
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Argonaute protein


Theoretical massNumber of molelcules
Total (without water)83,2641
Polymers83,2641
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.200, 118.077, 98.498
Angle α, β, γ (deg.)90.00, 99.57, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: RNA chain 26-MER


Mass: 8281.930 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Protein Argonaute protein / Argonaute


Mass: 83264.367 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Plasmid: pET28b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: O67434
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 2.54 Å3/Da / Density % sol: 51.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEF3350, 25mM NH4F, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEF335011
2NH4F11
3H2O11
4PEF335012
5NH4F12
6H2O12

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 12, 2005
RadiationMonochromator: 206 frames, 1 oscillation / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 3.1→40 Å / Num. obs: 37080 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.3 % / Rmerge(I) obs: 0.085
Reflection shellResolution: 3.11→3.23 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.39 / Num. unique all: 3686 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
MLPHAREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Aa-Ago, pdb entry 1YVU

1yvu


Resolution: 3.1→40 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.838 / SU B: 58.821 / SU ML: 0.478 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.596 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29688 1672 5 %RANDOM
Rwork0.20397 ---
all0.25 31675 --
obs0.20868 31675 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.099 Å2
Baniso -1Baniso -2Baniso -3
1-0.47 Å20 Å2-1.68 Å2
2---0.19 Å20 Å2
3----0.84 Å2
Refinement stepCycle: LAST / Resolution: 3.1→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11728 1062 0 51 12841
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.02213141
X-RAY DIFFRACTIONr_angle_refined_deg1.7222.09217899
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.90751406
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.36923.623552
X-RAY DIFFRACTIONr_dihedral_angle_3_deg24.007152425
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9051590
X-RAY DIFFRACTIONr_chiral_restr0.1050.22024
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.029236
X-RAY DIFFRACTIONr_nbd_refined0.260.25970
X-RAY DIFFRACTIONr_nbtor_refined0.3220.28476
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1870.2412
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2760.2115
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2170.217
X-RAY DIFFRACTIONr_mcbond_it0.7251.57201
X-RAY DIFFRACTIONr_mcangle_it1.327211422
X-RAY DIFFRACTIONr_scbond_it1.45637012
X-RAY DIFFRACTIONr_scangle_it2.4454.56477
LS refinement shellResolution: 3.1→3.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.437 133 -
Rwork0.269 2342 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -21.8896 Å / Origin y: -17.8242 Å / Origin z: 25.9131 Å
111213212223313233
T-0.1607 Å2-0.0219 Å2-0.0193 Å2--0.1322 Å2-0.0223 Å2---0.2912 Å2
L0.9822 °20.1272 °2-0.1137 °2-0.4749 °2-0.0323 °2--0.5537 °2
S-0.0421 Å °-0.0286 Å °-0.0427 Å °-0.1519 Å °0.0674 Å °0.0328 Å °0.0767 Å °-0.0226 Å °-0.0253 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AC3 - 7063 - 706
2X-RAY DIFFRACTION1BD3 - 7063 - 706
3X-RAY DIFFRACTION1CA1 - 261 - 26
4X-RAY DIFFRACTION1DB1 - 241 - 24

+
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