[English] 日本語
Yorodumi
- PDB-5uzm: Crystal structure of Glorund qRRM2 domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5uzm
TitleCrystal structure of Glorund qRRM2 domain
ComponentsAT27789p
KeywordsRNA BINDING PROTEIN / quasi-RNA recognition motif / qRRM
Function / homology
Function and homology information


maternal specification of dorsal/ventral axis, oocyte, germ-line encoded / intracellular mRNA localization involved in pattern specification process / Processing of Capped Intron-Containing Pre-mRNA / mRNA Splicing - Major Pathway / pole plasm oskar mRNA localization / regulation of RNA splicing / chromosome organization / wound healing / regulation of translation / ribonucleoprotein complex ...maternal specification of dorsal/ventral axis, oocyte, germ-line encoded / intracellular mRNA localization involved in pattern specification process / Processing of Capped Intron-Containing Pre-mRNA / mRNA Splicing - Major Pathway / pole plasm oskar mRNA localization / regulation of RNA splicing / chromosome organization / wound healing / regulation of translation / ribonucleoprotein complex / mRNA binding / protein-containing complex / RNA binding / nucleoplasm
Similarity search - Function
RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.552 Å
AuthorsTeramoto, T. / Hall, T.M.T.
CitationJournal: Cell Rep / Year: 2017
Title: The Drosophila hnRNP F/H Homolog Glorund Uses Two Distinct RNA-Binding Modes to Diversify Target Recognition.
Authors: Tamayo, J.V. / Teramoto, T. / Chatterjee, S. / Hall, T.M. / Gavis, E.R.
History
DepositionFeb 27, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 22, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2017Group: Database references
Revision 1.2Apr 19, 2017Group: Database references
Revision 1.3Oct 4, 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
A: AT27789p
B: AT27789p


Theoretical massNumber of molelcules
Total (without water)22,0492
Polymers22,0492
Non-polymers00
Water2,288127
1
A: AT27789p


Theoretical massNumber of molelcules
Total (without water)11,0241
Polymers11,0241
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: AT27789p


Theoretical massNumber of molelcules
Total (without water)11,0241
Polymers11,0241
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.770, 28.969, 69.520
Angle α, β, γ (deg.)90.00, 106.77, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein AT27789p / Glorund / isoform A / isoform B


Mass: 11024.400 Da / Num. of mol.: 2 / Fragment: residues 142-234
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: glo, CG6946, Dmel_CG6946 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9VGH5
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 127 / 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: 2.08 Å3/Da / Density % sol: 40.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2 M ammonium acetate, 20% v/v PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 24, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. obs: 23996 / % possible obs: 93.4 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 34.6

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
HKL-2000data collection
HKL-2000data scaling
MOLREPphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2KG0

2kg0


Resolution: 1.552→32.542 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.24 / Phase error: 25.94
RfactorNum. reflection% reflection
Rfree0.239 1214 5.07 %
Rwork0.1934 --
obs0.1957 23924 92.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.552→32.542 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1450 0 0 127 1577
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111523
X-RAY DIFFRACTIONf_angle_d1.072048
X-RAY DIFFRACTIONf_dihedral_angle_d25.327939
X-RAY DIFFRACTIONf_chiral_restr0.065218
X-RAY DIFFRACTIONf_plane_restr0.007274
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5518-1.6140.3053890.24521911X-RAY DIFFRACTION70
1.614-1.68740.30741060.24252279X-RAY DIFFRACTION84
1.6874-1.77640.27221350.24272515X-RAY DIFFRACTION94
1.7764-1.88770.29641410.2222602X-RAY DIFFRACTION97
1.8877-2.03340.24621470.20532634X-RAY DIFFRACTION98
2.0334-2.2380.21851470.18942651X-RAY DIFFRACTION98
2.238-2.56170.22921410.19462682X-RAY DIFFRACTION99
2.5617-3.2270.21851630.19872677X-RAY DIFFRACTION99
3.227-32.54910.23691450.1682759X-RAY DIFFRACTION98

+
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