[English] 日本語
Yorodumi
- PDB-4y5j: Drosophila melanogaster Mini spindles TOG3 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4y5j
TitleDrosophila melanogaster Mini spindles TOG3
ComponentsMINI SPINDLES TOG3
KeywordsPROTEIN BINDING / XMAP215 / TOG / microtubule polymerization
Function / homology
Function and homology information


establishment or maintenance of neuroblast polarity / bicoid mRNA localization / microtubule plus end polymerase / pronuclear fusion / oocyte microtubule cytoskeleton organization / establishment or maintenance of microtubule cytoskeleton polarity / mitotic spindle elongation / positive regulation of microtubule nucleation / female meiotic nuclear division / microtubule plus-end ...establishment or maintenance of neuroblast polarity / bicoid mRNA localization / microtubule plus end polymerase / pronuclear fusion / oocyte microtubule cytoskeleton organization / establishment or maintenance of microtubule cytoskeleton polarity / mitotic spindle elongation / positive regulation of microtubule nucleation / female meiotic nuclear division / microtubule plus-end / microtubule plus-end binding / endoplasmic reticulum organization / oogenesis / microtubule polymerization / establishment of mitotic spindle orientation / centrosome duplication / cytoplasmic microtubule organization / tubulin binding / mitotic spindle organization / axon guidance / kinetochore / spindle pole / spindle / mitotic cell cycle / microtubule binding / centrosome / perinuclear region of cytoplasm
Similarity search - Function
XMAP215 family / : / XMAP215/Dis1/CLASP, TOG domain / CLASP N-terminal domain / CLASP N terminal / TOG domain / TOG / HEAT repeat profile. / HEAT, type 2 / Leucine-rich Repeat Variant ...XMAP215 family / : / XMAP215/Dis1/CLASP, TOG domain / CLASP N-terminal domain / CLASP N terminal / TOG domain / TOG / HEAT repeat profile. / HEAT, type 2 / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Protein mini spindles
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.303 Å
AuthorsSlep, K.C. / Howard, A.E.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM008570 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM094415 United States
March of DimesFY14-247 United States
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Drosophila melanogaster Mini Spindles TOG3 Utilizes Unique Structural Elements to Promote Domain Stability and Maintain a TOG1- and TOG2-like Tubulin-binding Surface.
Authors: Howard, A.E. / Fox, J.C. / Slep, K.C.
History
DepositionFeb 11, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 18, 2015Group: Database references
Revision 1.2Apr 29, 2015Group: Database references
Revision 1.3Aug 23, 2017Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: citation / diffrn_detector ...citation / diffrn_detector / entity_src_gen / pdbx_struct_oper_list / struct_keywords
Item: _citation.journal_id_CSD / _diffrn_detector.type ..._citation.journal_id_CSD / _diffrn_detector.type / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
Revision 1.4Sep 20, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_audit_support / software / Item: _pdbx_audit_support.funding_organization
Revision 1.5Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Feb 28, 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: MINI SPINDLES TOG3


Theoretical massNumber of molelcules
Total (without water)27,3371
Polymers27,3371
Non-polymers00
Water2,072115
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.824, 49.824, 204.992
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number153
Space group name H-MP3212
Components on special symmetry positions
IDModelComponents
11A-937-

HOH

-
Components

#1: Protein MINI SPINDLES TOG3 / Mini spindles / isoform C


Mass: 27337.436 Da / Num. of mol.: 1 / Fragment: unp residues 582-825
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: msps, CG5000, Dmel_CG5000 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9VEZ3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.69 Å3/Da / Density % sol: 54.22 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: PEG4000, potassium phosphate monobasic

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97723 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 2, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97723 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 13396 / Num. obs: 13396 / % possible obs: 99.5 % / Redundancy: 10.8 % / Rsym value: 0.08 / Net I/σ(I): 33.4
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 8.9 % / Mean I/σ(I) obs: 5.1 / % possible all: 95

-
Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIXphasing
PHENIX(phenix.refine: 1.9_1692)refinement
Cootmodel building
HKL-2000data reduction
RefinementMethod to determine structure: SAD / Resolution: 2.303→34.165 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 24.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2409 1306 10.01 %Random selection
Rwork0.1762 ---
obs0.1827 13043 97.78 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.303→34.165 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1759 0 0 115 1874
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081787
X-RAY DIFFRACTIONf_angle_d1.0262411
X-RAY DIFFRACTIONf_dihedral_angle_d15.263677
X-RAY DIFFRACTIONf_chiral_restr0.041280
X-RAY DIFFRACTIONf_plane_restr0.004309
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3026-2.39470.28681400.20271244X-RAY DIFFRACTION94
2.3947-2.50370.25831410.19231250X-RAY DIFFRACTION96
2.5037-2.63560.28261380.19131257X-RAY DIFFRACTION96
2.6356-2.80070.25111440.19441289X-RAY DIFFRACTION98
2.8007-3.01680.25951460.18981292X-RAY DIFFRACTION99
3.0168-3.32020.27311550.1811334X-RAY DIFFRACTION99
3.3202-3.80010.22241430.17621324X-RAY DIFFRACTION100
3.8001-4.78560.21511510.15541343X-RAY DIFFRACTION100
4.7856-34.16910.22271480.16681404X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 14.6438 Å / Origin y: 20.8603 Å / Origin z: 110.2691 Å
111213212223313233
T0.2329 Å20.0684 Å20.0019 Å2-0.194 Å2-0.0089 Å2--0.2242 Å2
L0.698 °20.2715 °2-0.0125 °2-1.0208 °2-0.1477 °2--1.2958 °2
S0.0281 Å °0.0339 Å °0.057 Å °-0.1558 Å °-0.0022 Å °-0.0155 Å °0.0865 Å °-0.1047 Å °-0.0297 Å °
Refinement TLS groupSelection details: all

+
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