[English] 日本語
Yorodumi
- PDB-6lp3: Structural basis and functional analysis epo1-bem3p complex for b... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6lp3
TitleStructural basis and functional analysis epo1-bem3p complex for bud growth
Components
  • GTPase-activating protein BEM3
  • Uncharacterized protein YMR124W
KeywordsCELL ADHESION / Budding yeast / Organelle inheritance / Endoplasmic reticulum inheritance / Polarisome / Epo1p / Bem3p.
Function / homology
Function and homology information


endoplasmic reticulum polarization / RHOF GTPase cycle / CDC42 GTPase cycle / septin ring organization / RHOD GTPase cycle / RHOV GTPase cycle / site of polarized growth / RHOA GTPase cycle / incipient cellular bud site / cellular bud tip ...endoplasmic reticulum polarization / RHOF GTPase cycle / CDC42 GTPase cycle / septin ring organization / RHOD GTPase cycle / RHOV GTPase cycle / site of polarized growth / RHOA GTPase cycle / incipient cellular bud site / cellular bud tip / cell tip / cellular bud neck / phosphatidylinositol-3-phosphate binding / mating projection tip / small GTPase-mediated signal transduction / negative regulation of Rho protein signal transduction / establishment of cell polarity / Neutrophil degranulation / GTPase activator activity / cell cortex / plasma membrane / cytoplasm
Similarity search - Function
: / PhoX homologous domain, present in p47phox and p40phox. / PX domain / Phox homology / PX domain superfamily / Rho GTPase-activating protein domain / RhoGAP domain / Rho GTPase-activating proteins domain profile. / GTPase-activator protein for Rho-like GTPases / Rho GTPase activation protein ...: / PhoX homologous domain, present in p47phox and p40phox. / PX domain / Phox homology / PX domain superfamily / Rho GTPase-activating protein domain / RhoGAP domain / Rho GTPase-activating proteins domain profile. / GTPase-activator protein for Rho-like GTPases / Rho GTPase activation protein / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily
Similarity search - Domain/homology
GTPase-activating protein BEM3 / Uncharacterized protein YMR124W
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.547 Å
AuthorsWang, J. / Li, L. / Ming, Z.H. / Wu, L.J. / Yan, L.M.
CitationJournal: To Be Published
Title: Structural basis and functional analysis epo1-bem3p complex for bud growth
Authors: Wang, J.
History
DepositionJan 8, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 28, 2021Provider: repository / Type: Initial release
Revision 1.1May 29, 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

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Uncharacterized protein YMR124W
B: Uncharacterized protein YMR124W
C: GTPase-activating protein BEM3
D: Uncharacterized protein YMR124W
E: Uncharacterized protein YMR124W
F: GTPase-activating protein BEM3


Theoretical massNumber of molelcules
Total (without water)112,3056
Polymers112,3056
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: immunoprecipitation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)119.405, 119.405, 144.575
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

-
Components

#1: Protein
Uncharacterized protein YMR124W


Mass: 22375.828 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: YMR124W, YM8564.06 / Production host: Escherichia coli (E. coli) / References: UniProt: P39523
#2: Protein GTPase-activating protein BEM3 / Bud emergence protein 3


Mass: 11400.604 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: BEM3, YPL115C, LPH12C / Production host: Escherichia coli (E. coli) / References: UniProt: P32873

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.39 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.6 M Ammonium sulfate, 0.1 M MES, pH 6.5, 10% 1,4-Dioxane

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9789 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 3.547→46.032 Å / Num. obs: 13161 / % possible obs: 99.9 % / Redundancy: 18 % / Rmerge(I) obs: 0.431 / Net I/σ(I): 10.31
Reflection shellResolution: 3.95→4.23 Å / Rmerge(I) obs: 0.961 / Num. unique obs: 1249

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
AutoSolphasing
RefinementMethod to determine structure: MAD / Resolution: 3.547→46.032 Å / SU ML: 0.68 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 46.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.398 674 5.12 %
Rwork0.3397 12487 -
obs0.3427 13161 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 383.6 Å2 / Biso mean: 122.3199 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 3.547→46.032 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4661 0 0 0 4661
Num. residues----566
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.547-3.82020.41431160.3898243599
3.8202-4.20440.38291340.35062445100
4.2044-4.81230.41071510.34992468100
4.8123-6.06070.44921410.38832496100
6.0607-460.37191320.30192643100

+
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