[English] 日本語
Yorodumi
- EMDB-3522: S. pombe microtubule copolymerized with GTP and Mal3-143 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-3522
TitleS. pombe microtubule copolymerized with GTP and Mal3-143
Map data
Sample
  • Complex: Microtubule decorated with Mal3
    • Protein or peptide: Tubulin beta chain
    • Protein or peptide: Microtubule integrity protein mal3
    • Protein or peptide: Tubulin alpha-1 chain
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
KeywordsSchizosaccharomyces pombe microtubules / structural protein
Function / homology
Function and homology information


mitotic spindle pole body duplication / dynein-driven meiotic oscillatory nuclear movement / post-anaphase array microtubule end / Platelet degranulation / nuclear migration involved in conjugation with cellular fusion / cortical microtubule / nuclear migration by microtubule mediated pushing forces / cell cortex of cell tip / karyogamy involved in conjugation with cellular fusion / mitotic spindle astral microtubule ...mitotic spindle pole body duplication / dynein-driven meiotic oscillatory nuclear movement / post-anaphase array microtubule end / Platelet degranulation / nuclear migration involved in conjugation with cellular fusion / cortical microtubule / nuclear migration by microtubule mediated pushing forces / cell cortex of cell tip / karyogamy involved in conjugation with cellular fusion / mitotic spindle astral microtubule / nuclear division / mitotic spindle midzone / mitotic spindle pole body / mitotic spindle elongation / protein localization to microtubule / nuclear microtubule / astral microtubule / microtubule plus-end / cytoskeletal anchor activity / attachment of mitotic spindle microtubules to kinetochore / microtubule plus-end binding / microtubule lateral binding / spindle midzone / intracellular distribution of mitochondria / ATPase activator activity / microtubule organizing center / regulation of microtubule polymerization or depolymerization / spindle assembly / cytoplasmic microtubule / cytoplasmic microtubule organization / spindle microtubule / molecular condensate scaffold activity / structural constituent of cytoskeleton / microtubule cytoskeleton organization / spindle / mitotic cell cycle / microtubule cytoskeleton / microtubule binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / microtubule / hydrolase activity / cell division / response to antibiotic / GTPase activity / GTP binding / metal ion binding / nucleus / cytoplasm / cytosol
Similarity search - Function
EB1, C-terminal / Microtubule-associated protein RP/EB / EB1, C-terminal domain superfamily / EB1-C terminal (EB1-C) domain profile. / EB1-like C-terminal motif / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / Alpha tubulin / Tubulin-beta mRNA autoregulation signal. ...EB1, C-terminal / Microtubule-associated protein RP/EB / EB1, C-terminal domain superfamily / EB1-C terminal (EB1-C) domain profile. / EB1-like C-terminal motif / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / Alpha tubulin / Tubulin-beta mRNA autoregulation signal. / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily
Similarity search - Domain/homology
Tubulin alpha-1 chain / Tubulin beta chain / Microtubule integrity protein mal3
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast) / Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.6 Å
Authorsvon Loeffelholz O / Moores C
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/L00190X/1 United Kingdom
CitationJournal: Nat Commun / Year: 2017
Title: Nucleotide- and Mal3-dependent changes in fission yeast microtubules suggest a structural plasticity view of dynamics.
Authors: Ottilie von Loeffelholz / Neil A Venables / Douglas Robert Drummond / Miho Katsuki / Robert Cross / Carolyn A Moores /
Abstract: Using cryo-electron microscopy, we characterize the architecture of microtubules assembled from Schizosaccharomyces pombe tubulin, in the presence and absence of their regulatory partner Mal3. Cryo- ...Using cryo-electron microscopy, we characterize the architecture of microtubules assembled from Schizosaccharomyces pombe tubulin, in the presence and absence of their regulatory partner Mal3. Cryo-electron tomography reveals that microtubules assembled from S. pombe tubulin have predominantly B-lattice interprotofilament contacts, with protofilaments skewed around the microtubule axis. Copolymerization with Mal3 favors 13 protofilament microtubules with reduced protofilament skew, indicating that Mal3 adjusts interprotofilament interfaces. A 4.6-Å resolution structure of microtubule-bound Mal3 shows that Mal3 makes a distinctive footprint on the S. pombe microtubule lattice and that unlike mammalian microtubules, S. pombe microtubules do not show the longitudinal lattice compaction associated with EB protein binding and GTP hydrolysis. Our results firmly support a structural plasticity view of microtubule dynamics in which microtubule lattice conformation is sensitive to a variety of effectors and differently so for different tubulins.
History
DepositionDec 1, 2016-
Header (metadata) releaseJan 11, 2017-
Map releaseDec 20, 2017-
UpdateMar 19, 2025-
Current statusMar 19, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.085
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.085
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-5mjs
  • Surface level: 0.085
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5mjs
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3522.png

Downloads & links

-
Map

FileDownload / File: emd_3522.map.gz / Format: CCP4 / Size: 9.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.39 Å/pix.
x 213 pix.
= 296.07 Å		1.39 Å/pix.
x 134 pix.
= 186.26 Å		1.39 Å/pix.
x 91 pix.
= 126.49 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 1.39 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.085 / Movie #1: 0.085
Minimum - Maximum-0.26938048 - 0.38003
Average (Standard dev.)0.017890109 (±0.04964143)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions13491213
Spacing91134213
CellA: 126.49 Å / B: 186.26 Å / C: 296.07 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.391.391.39
M x/y/z91134213
origin x/y/z0.0000.0000.000
length x/y/z126.490186.260296.070
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS91134213
D min/max/mean-0.2690.3800.018

-
Supplemental data

-
Sample components

-
Entire : Microtubule decorated with Mal3

EntireName: Microtubule decorated with Mal3
Components
  • Complex: Microtubule decorated with Mal3
    • Protein or peptide: Tubulin beta chain
    • Protein or peptide: Microtubule integrity protein mal3
    • Protein or peptide: Tubulin alpha-1 chain
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE

-
Supramolecule #1: Microtubule decorated with Mal3

SupramoleculeName: Microtubule decorated with Mal3 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Schizosaccharomyces pombe (fission yeast)

-
Macromolecule #1: Tubulin beta chain

MacromoleculeName: Tubulin beta chain / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843
Molecular weightTheoretical: 47.191031 KDa
Recombinant expressionOrganism: Schizosaccharomyces pombe (fission yeast)
SequenceString: MREIVHIQAG QCGNQVGAAF WSTIADEHGL DSAGIYHGTS EAQHERLNVY FNEAAGGKYV PRAVLVDLEP GTMDAVKSGK FGNLFRPDN IIYGQSGAGN IWAKGHYTEG AELADAVLDV VRREAEACDA LQGFQLTHSL GGGTGSGMGT LLLSKIREEY P DRMMATFS ...String:
MREIVHIQAG QCGNQVGAAF WSTIADEHGL DSAGIYHGTS EAQHERLNVY FNEAAGGKYV PRAVLVDLEP GTMDAVKSGK FGNLFRPDN IIYGQSGAGN IWAKGHYTEG AELADAVLDV VRREAEACDA LQGFQLTHSL GGGTGSGMGT LLLSKIREEY P DRMMATFS VAPAPKSSDT VVEPYNATLS MHQLVENSDE TFCIDNEALS SIFANTLKIK SPSYDDLNHL VSAVMAGVTT SF RFPGELN SDLRKLAVNM VPFPRLHFFM VGFAPLAAIG SSSFQAVSVP ELTQQMFDAN NMMVAADPRH GRYLTVAALF RGK VSMKEV DEQIRSVQTK NSAYFVEWIP DNVLKAVCSV PPKDLKMSAT FIGNSTSIQE IFRRLGDQFS AMFRRKAFLH WYTG EGMDE MEFTEAESNM NDLVSEYQQY QEAG

UniProtKB: Tubulin beta chain

-
Macromolecule #2: Microtubule integrity protein mal3

MacromoleculeName: Microtubule integrity protein mal3 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843
Molecular weightTheoretical: 16.6689 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSESRQELLA WINQVTSLGL TRIEDCGKGY AMIQIFDSIY QDIPLKKVNF ECNNEYQYIN NWKVLQQVFL KKGIDKVVDP ERLSRCKMQ DNLEFVQWAK RFWDQYYPGG DYDALARRGN RGPANTRVMN SSAGATGPSR RRQV

UniProtKB: Microtubule integrity protein mal3

-
Macromolecule #3: Tubulin alpha-1 chain

MacromoleculeName: Tubulin alpha-1 chain / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843
Molecular weightTheoretical: 49.813832 KDa
Recombinant expressionOrganism: Schizosaccharomyces pombe (fission yeast)
SequenceString: MREVISVHVG QAGVQIGNAC WELYCLEHGI GPDGFPTENS EVHKNNSYLN DGFGTFFSET GQGKFVPRSI YVDLEPNVID QVRTGPYKD LFHPEQMVTG KEDASNNYAR GHYTVGKEMI DSVLERIRRM ADNCSGLQGF LVFHSFGGGT GSGLGALLLE R LNMEYGKK ...String:
MREVISVHVG QAGVQIGNAC WELYCLEHGI GPDGFPTENS EVHKNNSYLN DGFGTFFSET GQGKFVPRSI YVDLEPNVID QVRTGPYKD LFHPEQMVTG KEDASNNYAR GHYTVGKEMI DSVLERIRRM ADNCSGLQGF LVFHSFGGGT GSGLGALLLE R LNMEYGKK SNLQFSVYPA PQVSTSVVEP YNSVLTTHAT LDNSDCTFMV DNEACYDICR RNLDIERPTY ENLNRLIAQV VS SITASLR FAGSLNVDLN EFQTNLVPYP RIHFPLVTYS PIVSAAKAFH ESNSVQEITN QCFEPYNQMV KCDPRTGRYM ATC LLYRGD VIPRDVQAAV TSIKSRRTIQ FVDWCPTGFK IGICYEPPQH VPGSGIAKVN RAVCMLSNTT SIAEAWSRLD HKFD LMYSK RAFVHWYVGE GMEEGEFSEA REDLAALERD YEEVGQDSM

UniProtKB: Tubulin alpha-1 chain

-
Macromolecule #4: GUANOSINE-5'-DIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-DIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 4 / Formula: GDP
Source (natural)Organism: Schizosaccharomyces pombe (fission yeast)
Molecular weightTheoretical: 443.201 Da
Chemical component information

ChemComp-GDP:
GUANOSINE-5'-DIPHOSPHATE / GDP, energy-carrying molecule*YM

-
Macromolecule #5: GUANOSINE-5'-TRIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 4 / Formula: GTP
Source (natural)Organism: Schizosaccharomyces pombe (fission yeast)
Molecular weightTheoretical: 523.18 Da
Chemical component information

ChemComp-GTP:
GUANOSINE-5'-TRIPHOSPHATE / GTP, energy-carrying molecule*YM

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statehelical array

-
Sample preparation

Concentration2 mg/mL
BufferpH: 6.5
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 40 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI POLARA 300
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

1jff

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: FREALIGN (ver. 8) / Number images used: 12763
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: SPIDER (ver. 14.18)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: FREALIGN (ver. 8) / Details: helical symmetry applied

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: BACKBONE TRACE
Output model

PDB-5mjs:
S. pombe microtubule copolymerized with GTP and Mal3-143

+
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