[English] 日本語
Yorodumi
- PDB-2b1e: The structures of exocyst subunit Exo70p and the Exo84p C-termina... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2b1e
TitleThe structures of exocyst subunit Exo70p and the Exo84p C-terminal domains reveal a common motif
ComponentsExocyst complex component EXO70
KeywordsENDOCYTOSIS/EXOCYTOSIS / tethering complex / exocyst / ENDOCYTOSIS-EXOCYTOSIS COMPLEX
Function / homology
Function and homology information


exocyst assembly / exocyst localization / exocyst / prospore membrane / incipient cellular bud site / cellular bud tip / Golgi to plasma membrane transport / cellular bud neck / mating projection tip / vesicle docking involved in exocytosis ...exocyst assembly / exocyst localization / exocyst / prospore membrane / incipient cellular bud site / cellular bud tip / Golgi to plasma membrane transport / cellular bud neck / mating projection tip / vesicle docking involved in exocytosis / exocytosis / Rho protein signal transduction / transport vesicle / phosphatidylinositol-4,5-bisphosphate binding / small GTPase binding / protein transport / plasma membrane / cytoplasm
Similarity search - Function
Tetracycline Repressor; domain 2 - #60 / 5 helical Cullin repeat like - #30 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1150 / Exocyst complex component Exo70 / Exocyst complex component Exo70 N-terminal / Exocyst complex subunit Exo70, C-terminal / Exocyst complex component Exo70 / Exo70 exocyst complex subunit C-terminal / 5 helical Cullin repeat like / Cullin repeat-like-containing domain superfamily ...Tetracycline Repressor; domain 2 - #60 / 5 helical Cullin repeat like - #30 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1150 / Exocyst complex component Exo70 / Exocyst complex component Exo70 N-terminal / Exocyst complex subunit Exo70, C-terminal / Exocyst complex component Exo70 / Exo70 exocyst complex subunit C-terminal / 5 helical Cullin repeat like / Cullin repeat-like-containing domain superfamily / Monooxygenase / Tetracycline Repressor; domain 2 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Exocyst complex component EXO70
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsDong, G. / Hutagalung, A.H. / Fu, C. / Novick, P. / Reinisch, K.M.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2005
Title: The structures of exocyst subunit Exo70p and the Exo84p C-terminal domains reveal a common motif
Authors: Dong, G. / Hutagalung, A.H. / Fu, C. / Novick, P. / Reinisch, K.M.
History
DepositionSep 15, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 1, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Exocyst complex component EXO70


Theoretical massNumber of molelcules
Total (without water)64,8041
Polymers64,8041
Non-polymers00
Water4,702261
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.846, 60.605, 223.131
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Exocyst complex component EXO70 / Exocyst complex protein of 70 kDa


Mass: 64803.809 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P19658
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 261 / 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: 2.38 Å3/Da / Density % sol: 46.39 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 3000, lithium sulfate, sodium cloride, dithiothreitol, L-cysteine, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 8-BM / Wavelength: 0.9792, 0.9794, 0.9611
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 18, 2005
RadiationMonochromator: Si 111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97921
20.97941
30.96111
ReflectionResolution: 2→20 Å / Num. all: 39711 / Num. obs: 39711 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2→2.07 Å / % possible all: 96.6

-
Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2→20 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.25 3785 RANDOM
Rwork0.221 --
all0.263 37604 -
obs0.223 37604 -
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4310 0 0 261 4571

+
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