[English] 日本語
Yorodumi
- PDB-6uor: MicroED structure of OsPYL/RCAR5 (24-29) at 3 e-/A^2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6uor
TitleMicroED structure of OsPYL/RCAR5 (24-29) at 3 e-/A^2
ComponentsAbscisic acid receptor PYL5
KeywordsPROTEIN FIBRIL / protofilament
Function / homology
Function and homology information


negative regulation of protein serine/threonine phosphatase activity / seedling development / seed germination / response to water deprivation / abscisic acid binding / abscisic acid-activated signaling pathway / response to osmotic stress / protein phosphatase inhibitor activity / response to salt stress / signaling receptor activity ...negative regulation of protein serine/threonine phosphatase activity / seedling development / seed germination / response to water deprivation / abscisic acid binding / abscisic acid-activated signaling pathway / response to osmotic stress / protein phosphatase inhibitor activity / response to salt stress / signaling receptor activity / nucleus / cytoplasm / cytosol
Similarity search - Function
Polyketide cyclase/dehydrase / Polyketide cyclase / dehydrase and lipid transport / START-like domain superfamily
Similarity search - Domain/homology
Abscisic acid receptor PYL5
Similarity search - Component
Biological speciesOryza sativa (Asian cultivated rice)
MethodELECTRON CRYSTALLOGRAPHY / electron crystallography / Resolution: 0.9 Å
Model detailsProtofilament structure of OsPYL/RCAR5 peptide determined by nanoEDT
AuthorsGallagher-Jones, M. / Richards, L.S. / Lee, S. / Rodriguez, J.A.
Funding support United States, 3items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)DMR-1548924 United States
Department of Energy (DOE, United States)DE-FC02-02ER63421 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM128867 United States
CitationJournal: IUCrJ / Year: 2020
Title: Atomic structures determined from digitally defined nanocrystalline regions.
Authors: Marcus Gallagher-Jones / Karen C Bustillo / Colin Ophus / Logan S Richards / Jim Ciston / Sangho Lee / Andrew M Minor / Jose A Rodriguez /
Abstract: Nanocrystallography has transformed our ability to interrogate the atomic structures of proteins, peptides, organic molecules and materials. By probing atomic level details in ordered sub-10 nm ...Nanocrystallography has transformed our ability to interrogate the atomic structures of proteins, peptides, organic molecules and materials. By probing atomic level details in ordered sub-10 nm regions of nanocrystals, scanning nanobeam electron diffraction extends the reach of nanocrystallography and in principle obviates the need for diffraction from large portions of one or more crystals. Scanning nanobeam electron diffraction is now applied to determine atomic structures from digitally defined regions of beam-sensitive peptide nanocrystals. Using a direct electron detector, thousands of sparse diffraction patterns over multiple orientations of a given crystal are recorded. Each pattern is assigned to a specific location on a single nanocrystal with axial, lateral and angular coordinates. This approach yields a collection of patterns that represent a tilt series across an angular wedge of reciprocal space: a scanning nanobeam diffraction tomogram. Using this diffraction tomogram, intensities can be digitally extracted from any desired region of a scan in real or diffraction space, exclusive of all other scanned points. Intensities from multiple regions of a crystal or from multiple crystals can be merged to increase data completeness and mitigate missing wedges. It is demonstrated that merged intensities from digitally defined regions of two crystals of a segment from the OsPYL/RCAR5 protein produce fragment-based solutions that can be refined to atomic resolution, analogous to structures determined by selected-area electron diffraction. In allowing atomic structures to now be determined from digitally outlined regions of a nanocrystal, scanning nanobeam diffraction tomography breaks new ground in nanocrystallography.
History
DepositionOct 15, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 30, 2021Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.2Mar 13, 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

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Abscisic acid receptor PYL5


Theoretical massNumber of molelcules
Total (without water)4591
Polymers4591
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)4.730, 11.320, 38.930
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein/peptide Abscisic acid receptor PYL5 / PYR1-like protein 11 / OsPYL11 / PYR1-like protein 5 / OsPYL5 / Regulatory components of ABA receptor 5


Mass: 458.509 Da / Num. of mol.: 1 / Fragment: UNP residues 24-29 / Source method: obtained synthetically / Source: (synth.) Oryza sativa (Asian cultivated rice) / References: UniProt: Q6I5C3

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON CRYSTALLOGRAPHY
EM experimentAggregation state: 3D ARRAY / 3D reconstruction method: electron crystallography

-
Sample preparation

ComponentName: Crystalline assembly of OsPYL/RCAR5 peptide derived from residues 24 - 29
Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Oryza sativa (Asian cultivated rice)
Buffer solutionpH: 7
Buffer componentConc.: 10 % v/v / Name: Ethanol / Formula: C2H6O
SpecimenConc.: 10 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: NO
Specimen supportGrid material: GOLD / Grid mesh size: 400 divisions/in. / Grid type: Homemade
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 10% ethanol

-
Data collection

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F30
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: DIFFRACTION / C2 aperture diameter: 50 µm / Alignment procedure: BASIC
Specimen holderCryogen: NITROGEN
Specimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Temperature (max): 110 K / Temperature (min): 100 K
Image recordingAverage exposure time: 3 sec. / Electron dose: 0.01 e/Å2 / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Num. of diffraction images: 100 / Num. of grids imaged: 1 / Num. of real images: 1
Image scansSampling size: 15.5 µm / Width: 4096 / Height: 4096
EM diffractionCamera length: 1320 mm
EM diffraction shellResolution: 0.9→7.4 Å / Fourier space coverage: 97.7 % / Multiplicity: 8.7 / Num. of structure factors: 1776 / Phase residual: 1 °
EM diffraction statsFourier space coverage: 97.7 % / High resolution: 0.9 Å / Num. of intensities measured: 15449 / Num. of structure factors: 1776 / Phase error: 29.75 ° / Phase residual: 1 ° / Phase error rejection criteria: none / Rmerge: 0.186 / Rsym: 0.198
DiffractionMean temperature: 100 K
Diffraction sourceSource: ELECTRON MICROSCOPE / Type: Technai F30 / Wavelength: 0.0197 Å
DetectorType: TemCam-XF416 / Detector: CMOS / Date: Apr 4, 2019
Radiation wavelengthWavelength: 0.0197 Å / Relative weight: 1
ReflectionResolution: 0.9→7.38 Å / Num. obs: 1776 / % possible obs: 97.7 % / Redundancy: 8.699 % / Biso Wilson estimate: 5.975 Å2 / CC1/2: 0.987 / Rmerge(I) obs: 0.186 / Rrim(I) all: 0.198 / Χ2: 0.849 / Net I/σ(I): 6.76 / Num. measured all: 15449 / Scaling rejects: 9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
0.9-19.2880.4054.0143474714680.9110.4399.4
1-1.18.9510.2485.9927663163090.9740.26597.8
1.1-1.29.6610.2586.2121932312270.9870.27498.3
1.2-1.58.4850.2157.6730633683610.9790.22998.1
1.5-1.87.840.1829.4712701661620.9770.19497.6
1.8-28.0620.15410.1751666640.9770.16697
2-2.38.290.14310.3757271690.9860.15397.2
2.3-36.180.16210.0637764610.9790.17995.3
3-56.5920.11210.9932352490.9910.11894.2
5-83.6670.0998.5822860.9990.10975
8-7.385

-
Processing

Software
NameVersionClassificationNB
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
EM software
IDNameCategory
6Cootmodel fitting
13PHENIXmodel refinement
EM 3D crystal entity∠α: 90 ° / ∠β: 90 ° / ∠γ: 90 ° / A: 4.73 Å / B: 11.32 Å / C: 38.93 Å / Space group name: P212121 / Space group num: 19
CTF correctionType: NONE
3D reconstructionResolution method: DIFFRACTION PATTERN/LAYERLINES / Symmetry type: 3D CRYSTAL
Atomic model buildingB value: 2.2 / Protocol: AB INITIO MODEL / Space: RECIPROCAL
RefinementResolution: 0.9→7.38 Å / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 1.41 / Phase error: 29.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2397 160 9.05 %
Rwork0.2057 1608 -
obs0.2086 1768 97.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 6.34 Å2 / Biso mean: 2.6124 Å2 / Biso min: 0.54 Å2
Refinement stepCycle: final / Resolution: 0.9→7.38 Å /
LigandSolventTotal
Num. atoms0 0 66
Num. residues--6
LS refinement shellResolution: 0.9→7.38 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.2397 160 -
Rwork0.2057 1608 -
obs--97 %

+
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