[English] 日本語
Yorodumi
- PDB-1mij: Crystal Structure of the Homeo-prospero Domain of D. melanogaster... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1mij
TitleCrystal Structure of the Homeo-prospero Domain of D. melanogaster Prospero
ComponentsProtein prospero
KeywordsTRANSCRIPTION / homeodomain / DNA-binding domain / prospero domain / 4-helix bundle
Function / homology
Function and homology information


regulation of R7 cell differentiation / asymmetric neuroblast division resulting in ganglion mother cell formation / dendrite guidance / ganglion mother cell fate determination / R7 cell fate commitment / cell dedifferentiation / male courtship behavior / basal cortex / regulation of neuroblast proliferation / negative regulation of axonogenesis ...regulation of R7 cell differentiation / asymmetric neuroblast division resulting in ganglion mother cell formation / dendrite guidance / ganglion mother cell fate determination / R7 cell fate commitment / cell dedifferentiation / male courtship behavior / basal cortex / regulation of neuroblast proliferation / negative regulation of axonogenesis / asymmetric neuroblast division / neuroblast differentiation / axonogenesis involved in innervation / glial cell differentiation / apical cortex / peripheral nervous system development / regulation of protein localization to nucleus / G1 to G0 transition / dendrite morphogenesis / regulation of DNA-binding transcription factor activity / negative regulation of neuroblast proliferation / regulation of neuron differentiation / positive regulation of neuroblast proliferation / axon development / neuroblast proliferation / cell fate commitment / synapse assembly / axonogenesis / central nervous system development / axon guidance / brain development / protein localization / DNA-binding transcription repressor activity, RNA polymerase II-specific / sensory perception of taste / nervous system development / cell cortex / regulation of gene expression / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of cell population proliferation / negative regulation of gene expression / positive regulation of gene expression / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleus / plasma membrane
Similarity search - Function
Homeo-prospero domain / Homeo-prospero domain / Homeo-prospero domain superfamily / Prospero homeodomain family / Homeo-prospero domain / Homeo-Prospero domain profile. / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Homeobox protein prospero
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.05 Å
AuthorsRyter, J.M. / Doe, C.Q. / Matthews, B.W.
CitationJournal: Structure / Year: 2002
Title: Structure of the DNA Binding Region of Prospero Reveals a Novel Homeo-Prospero Domain
Authors: Ryter, J.M. / Doe, C.Q. / Matthews, B.W.
History
DepositionAug 23, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein prospero


Theoretical massNumber of molelcules
Total (without water)18,4541
Polymers18,4541
Non-polymers00
Water1,49583
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.300, 49.900, 51.500
Angle α, β, γ (deg.)90.00, 97.40, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Protein prospero


Mass: 18454.402 Da / Num. of mol.: 1 / Fragment: Homeo-prospero Domain (residues 1245-1396)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: PROS / Plasmid: PET28B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P29617
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 2.44 Å3/Da / Density % sol: 49.51 %
Crystal growTemperature: 323 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 4000, Tris, n-tetradecyl beta-D-maltoside, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 323K
Crystal grow
*PLUS
pH: 7.9
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
15.8 mg/mlprotein1drop
215 mMHEPES1droppH7.9
3150 mM1dropNaCl
410 %glycerol1drop
521 %PEG40001reservoir
6100 mMTris1reservoirpH8.5
70.01 mMn-tetradecyl-beta-D-maltoside1reservoir

-
Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9790, 0.9793, 0.9611
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 28, 2001
RadiationMonochromator: double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.97931
30.96111
ReflectionResolution: 2.05→500 Å / Num. all: 11045 / Num. obs: 11045 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection
*PLUS
Rmerge(I) obs: 0.06

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
CNS1refinement
RefinementMethod to determine structure: MAD / Resolution: 2.05→500 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.256 1081 -RANDOM
Rwork0.216 ---
all-11045 --
obs-11045 98 %-
Refinement stepCycle: LAST / Resolution: 2.05→500 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1351 0 0 83 1434
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005949
X-RAY DIFFRACTIONc_angle_deg0.99462
X-RAY DIFFRACTIONc_mcbond_it1.3631.5
X-RAY DIFFRACTIONc_scbond_it2.2612
X-RAY DIFFRACTIONc_mcangle_it2.1852
X-RAY DIFFRACTIONc_scangle_it3.2992.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
Refinement
*PLUS
Lowest resolution: 500 Å / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg0.99

+
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