[English] 日本語
Yorodumi
- PDB-4g0x: Crystal Structure of Arabidopsis thaliana AGO1 MID domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4g0x
TitleCrystal Structure of Arabidopsis thaliana AGO1 MID domain
ComponentsProtein argonaute 1
KeywordsGENE REGULATION / MID domain / small RNA 5' nucleotide recognition
Function / homology
Function and homology information


adaxial/abaxial pattern specification / adventitious root development / auxin metabolic process / leaf morphogenesis / leaf proximal/distal pattern formation / RNAi-mediated antiviral immune response / leaf vascular tissue pattern formation / response to far red light / post-transcriptional gene silencing / response to auxin ...adaxial/abaxial pattern specification / adventitious root development / auxin metabolic process / leaf morphogenesis / leaf proximal/distal pattern formation / RNAi-mediated antiviral immune response / leaf vascular tissue pattern formation / response to far red light / post-transcriptional gene silencing / response to auxin / miRNA-mediated post-transcriptional gene silencing / siRNA binding / miRNA binding / RNA endonuclease activity / regulation of translation / defense response to virus / cell differentiation / ribonucleoprotein complex / mRNA binding / innate immune response / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Argonaut, glycine-rich domain / Glycine-rich region of argonaut / 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 ...Argonaut, glycine-rich domain / Glycine-rich region of argonaut / 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 / PAZ domain profile. / Response regulator / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.35 Å
AuthorsFrank, F. / Hauver, J. / Sonenberg, N. / Nagar, B.
CitationJournal: Embo J. / Year: 2012
Title: Arabidopsis Argonaute MID domains use their nucleotide specificity loop to sort small RNAs.
Authors: Frank, F. / Hauver, J. / Sonenberg, N. / Nagar, B.
History
DepositionJul 10, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2012Group: Database references
Revision 1.2Sep 12, 2012Group: Database references

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein argonaute 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1546
Polymers16,6741
Non-polymers4805
Water3,117173
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.250, 60.973, 67.809
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Protein argonaute 1


Mass: 16673.633 Da / Num. of mol.: 1 / Fragment: MID domain, UNP residues 593-738
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: AGO1, At1g48410, F11A17.3, T1N15.2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: O04379
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 173 / 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: 2.31 Å3/Da / Density % sol: 46.73 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.1 M citric acid, 2 M ammonium sulfate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.9792 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Feb 27, 2010
RadiationMonochromator: KOHZU double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.35→30 Å / Num. all: 36996 / Num. obs: 35331 / % possible obs: 95.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 1.35→1.4 Å / % possible all: 71.9

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX(phenix.refine: 1.5_2)model building
PHENIX(phenix.refine: 1.5_2)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.5_2phasing
RefinementMethod to determine structure: SAD / Resolution: 1.35→22.67 Å / SU ML: 0.25 / σ(F): 1.34 / Phase error: 16.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1788 3527 5.63 %
Rwork0.1623 --
obs0.1632 62602 95.5 %
all-38732 -
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.2111 Å2-0 Å20 Å2
2---4.9042 Å2-0 Å2
3---6.4266 Å2
Refinement stepCycle: LAST / Resolution: 1.35→22.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1146 0 25 173 1344
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111241
X-RAY DIFFRACTIONf_angle_d1.3521695
X-RAY DIFFRACTIONf_dihedral_angle_d15.489485
X-RAY DIFFRACTIONf_chiral_restr0.074196
X-RAY DIFFRACTIONf_plane_restr0.006215
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.36850.19721030.19131656X-RAY DIFFRACTION67
1.3685-1.3880.20691100.18521857X-RAY DIFFRACTION73
1.388-1.40880.20651170.18591938X-RAY DIFFRACTION80
1.4088-1.43080.19051290.17382180X-RAY DIFFRACTION87
1.4308-1.45420.21461350.16472256X-RAY DIFFRACTION91
1.4542-1.47930.19841390.15812311X-RAY DIFFRACTION94
1.4793-1.50620.16681420.15842377X-RAY DIFFRACTION96
1.5062-1.53520.16141530.15442449X-RAY DIFFRACTION99
1.5352-1.56650.17851470.15382461X-RAY DIFFRACTION100
1.5665-1.60050.16241470.1552459X-RAY DIFFRACTION100
1.6005-1.63780.17861470.14672485X-RAY DIFFRACTION100
1.6378-1.67870.17181430.1532498X-RAY DIFFRACTION100
1.6787-1.72410.18861470.15142464X-RAY DIFFRACTION100
1.7241-1.77480.16541440.15072469X-RAY DIFFRACTION100
1.7748-1.83210.17081500.14862478X-RAY DIFFRACTION100
1.8321-1.89750.19981510.14782473X-RAY DIFFRACTION100
1.8975-1.97340.17881490.15322477X-RAY DIFFRACTION100
1.9734-2.06320.17071480.14692468X-RAY DIFFRACTION100
2.0632-2.17190.16921490.14742458X-RAY DIFFRACTION100
2.1719-2.30780.19571470.14972477X-RAY DIFFRACTION100
2.3078-2.48580.15731460.15862489X-RAY DIFFRACTION100
2.4858-2.73560.1951460.16652476X-RAY DIFFRACTION100
2.7356-3.13060.15511450.17262471X-RAY DIFFRACTION100
3.1306-3.94080.19611480.16132473X-RAY DIFFRACTION100
3.9408-22.67280.17261450.192475X-RAY DIFFRACTION100

+
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