[English] 日本語
Yorodumi
- EMDB-3527: S. pombe microtubule decorated with Cut7 motor domain in the AMPP... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-3527
TitleS. pombe microtubule decorated with Cut7 motor domain in the AMPPNP state
Map data
Sample
  • Complex: Cut7 MTD decorated S. pombe microtubule stabilized with Epothilone-B
    • Complex: Alpha tubulin, Beta tubulin
      • Protein or peptide: Tubulin alpha-1 chain
      • Protein or peptide: Tubulin beta chain
    • Complex: Cut7
      • Protein or peptide: Kinesin-like protein cut7
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
  • Ligand: 7,11-DIHYDROXY-8,8,10,12,16-PENTAMETHYL-3-[1-METHYL-2-(2-METHYL-THIAZOL-4-YL)VINYL]-4,17-DIOXABICYCLO[14.1.0]HEPTADECANE-5,9-DIONE
KeywordsS. pombe / microtubule / kinesin-5 / Cut7 motor domain / motor protein
Function / homology
Function and homology information


mitotic spindle pole body duplication / Platelet degranulation / mitotic spindle formation (spindle phase one) / mitotic spindle elongation (spindle phase three) / Kinesins / initial mitotic spindle pole body separation / microtubule plus-end directed mitotic chromosome migration / nuclear migration by microtubule mediated pushing forces / meiotic spindle pole / meiotic spindle assembly ...mitotic spindle pole body duplication / Platelet degranulation / mitotic spindle formation (spindle phase one) / mitotic spindle elongation (spindle phase three) / Kinesins / initial mitotic spindle pole body separation / microtubule plus-end directed mitotic chromosome migration / nuclear migration by microtubule mediated pushing forces / meiotic spindle pole / meiotic spindle assembly / nuclear division / mitotic spindle midzone / mitotic spindle pole body / mitotic spindle elongation / mitotic spindle midzone assembly / spindle elongation / polar microtubule / astral microtubule / plus-end-directed microtubule motor activity / meiotic spindle / microtubule motor activity / minus-end-directed microtubule motor activity / microtubule associated complex / intracellular distribution of mitochondria / mitotic spindle assembly / cytoplasmic microtubule / cytoplasmic microtubule organization / spindle microtubule / kinetochore / structural constituent of cytoskeleton / microtubule cytoskeleton organization / spindle / mitotic 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 / ATP hydrolysis activity / ATP binding / metal ion binding / nucleus / cytoplasm / cytosol
Similarity search - Function
: / : / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain / Kinesin motor domain profile. / Kinesin motor, catalytic domain. ATPase. / Kinesin motor domain / Kinesin motor domain superfamily / Alpha tubulin ...: / : / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain / Kinesin motor domain profile. / Kinesin motor, catalytic domain. ATPase. / Kinesin motor domain / Kinesin motor domain superfamily / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Tubulin alpha-1 chain / Tubulin beta chain / Kinesin-like protein cut7
Similarity search - Component
Biological speciesSchizosaccharomyces pombe 972 (yeast) / Schizosaccharomyces pombe 972h-
Methodsingle particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsMoores CA / von Loeffelholz O
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilL00190X/1 United Kingdom
CitationJournal: J Mol Biol / Year: 2020
Title: Corrigendum to "Cryo-EM Structure (4.5 Å) of Yeast Kinesin-5-Microtubule Complex Reveals a Distinct Binding Footprint and Mechanism of Drug Resistance" [J. Mol. Biol. 431 (2019) 864-872] ...Title: Corrigendum to "Cryo-EM Structure (4.5 Å) of Yeast Kinesin-5-Microtubule Complex Reveals a Distinct Binding Footprint and Mechanism of Drug Resistance" [J. Mol. Biol. 431 (2019) 864-872] https://doi.org/10.1016/j.jmb.2019.01.011.
Authors: Ottilie von Loeffelholz / Alejandro Peña / Douglas Robert Drummond / Robert Cross / Carolyn Ann Moores /
History
DepositionDec 7, 2016-
Header (metadata) releaseJan 11, 2017-
Map releaseAug 8, 2018-
UpdateSep 20, 2023-
Current statusSep 20, 2023Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0811
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0811
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-5mlv
  • Surface level: 0.0811
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6s8m
  • Surface level: 0.0811
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6s8m
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3527.png

Downloads & links

-
Map

FileDownload / File: emd_3527.map.gz / Format: CCP4 / Size: 1.3 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 211 pix.
= 293.29 Å		1.39 Å/pix.
x 135 pix.
= 187.65 Å		1.39 Å/pix.
x 125 pix.
= 173.75 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: 0.0811 / Movie #1: 0.0811
Minimum - Maximum-0.26908487 - 0.4405258
Average (Standard dev.)0.015761957 (±0.045668256)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions135125211
Spacing125135211
CellA: 173.75 Å / B: 187.65 Å / C: 293.29 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.391.391.39
M x/y/z125135211
origin x/y/z0.0000.0000.000
length x/y/z173.750187.650293.290
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ380380380
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS125135211
D min/max/mean-0.2690.4410.016

-
Supplemental data

-
Additional map: #1

Fileemd_3527_additional.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: #1

Fileemd_3527_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : Cut7 MTD decorated S. pombe microtubule stabilized with Epothilone-B

EntireName: Cut7 MTD decorated S. pombe microtubule stabilized with Epothilone-B
Components
  • Complex: Cut7 MTD decorated S. pombe microtubule stabilized with Epothilone-B
    • Complex: Alpha tubulin, Beta tubulin
      • Protein or peptide: Tubulin alpha-1 chain
      • Protein or peptide: Tubulin beta chain
    • Complex: Cut7
      • Protein or peptide: Kinesin-like protein cut7
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
  • Ligand: 7,11-DIHYDROXY-8,8,10,12,16-PENTAMETHYL-3-[1-METHYL-2-(2-METHYL-THIAZOL-4-YL)VINYL]-4,17-DIOXABICYCLO[14.1.0]HEPTADECANE-5,9-DIONE

+
Supramolecule #1: Cut7 MTD decorated S. pombe microtubule stabilized with Epothilone-B

SupramoleculeName: Cut7 MTD decorated S. pombe microtubule stabilized with Epothilone-B
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3

+
Supramolecule #2: Alpha tubulin, Beta tubulin

SupramoleculeName: Alpha tubulin, Beta tubulin / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1, #3
Source (natural)Organism: Schizosaccharomyces pombe 972 (yeast)

+
Supramolecule #3: Cut7

SupramoleculeName: Cut7 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Schizosaccharomyces pombe 972 (yeast)

+
Macromolecule #1: Tubulin alpha-1 chain

MacromoleculeName: Tubulin alpha-1 chain / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Schizosaccharomyces pombe 972h-
Molecular weightTheoretical: 51.20318 KDa
Recombinant expressionOrganism: Schizosaccharomyces pombe
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 YEEVGQDSMD NEMYEADEEY

UniProtKB: Tubulin alpha-1 chain

+
Macromolecule #2: Kinesin-like protein cut7

MacromoleculeName: Kinesin-like protein cut7 / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Schizosaccharomyces pombe 972h-
Molecular weightTheoretical: 47.589062 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAPRVAPGGS QQFLGKQGLK AKNPVSTPNS HFRSASNPRK RREPPTIDTG YPDRSDTNSP TDHALHDENE TNINVVVRVR GRTDQEVRD NSSLAVSTSG AMGAELAIQS DPSSMLVTKT YAFDKVFGPE ADQLMLFENS VAPMLEQVLN GYNCTIFAYG Q TGTGKTYT ...String:
MAPRVAPGGS QQFLGKQGLK AKNPVSTPNS HFRSASNPRK RREPPTIDTG YPDRSDTNSP TDHALHDENE TNINVVVRVR GRTDQEVRD NSSLAVSTSG AMGAELAIQS DPSSMLVTKT YAFDKVFGPE ADQLMLFENS VAPMLEQVLN GYNCTIFAYG Q TGTGKTYT MSGDLSDSDG ILSEGAGLIP RALYQLFSSL DNSNQEYAVK CSYYELYNEE IRDLLVSEEL RKPARVFEDT SR RGNVVIT GIEESYIKNA GDGLRLLREG SHRRQVAATK CNDLSSRSHS IFTITLHRKV SSGMTDETNS LTINNNSDDL LRA SKLHMV DLAGSENIGR SGAENKRARE TGMINQSLLT LGRVINALVE KAHHIPYRES KLTRLLQDSL GGKTKTSMIV TVSS TNTNL EETISTLEYA ARAKSIRNKP QNNQLVF

UniProtKB: Kinesin-like protein cut7

+
Macromolecule #3: Tubulin beta chain

MacromoleculeName: Tubulin beta chain / type: protein_or_peptide / ID: 3 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Schizosaccharomyces pombe 972h-
Molecular weightTheoretical: 49.518359 KDa
Recombinant expressionOrganism: Schizosaccharomyces pombe
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 QEAGIDEGDE DYEIEEEKEP LEY

UniProtKB: Tubulin beta chain

+
Macromolecule #4: GUANOSINE-5'-TRIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 6 / Formula: GTP
Molecular weightTheoretical: 523.18 Da
Chemical component information

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

+
Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 6 / Formula: MG
Molecular weightTheoretical: 24.305 Da

+
Macromolecule #6: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / type: ligand / ID: 6 / Number of copies: 6 / Formula: ANP
Molecular weightTheoretical: 506.196 Da
Chemical component information

ChemComp-ANP:
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP, energy-carrying molecule analogue*YM

+
Macromolecule #7: GUANOSINE-5'-DIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-DIPHOSPHATE / type: ligand / ID: 7 / Number of copies: 6 / Formula: GDP
Molecular weightTheoretical: 443.201 Da
Chemical component information

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

+
Macromolecule #8: 7,11-DIHYDROXY-8,8,10,12,16-PENTAMETHYL-3-[1-METHYL-2-(2-METHYL-T...

MacromoleculeName: 7,11-DIHYDROXY-8,8,10,12,16-PENTAMETHYL-3-[1-METHYL-2-(2-METHYL-THIAZOL-4-YL)VINYL]-4,17-DIOXABICYCLO[14.1.0]HEPTADECANE-5,9-DIONE
type: ligand / ID: 8 / Number of copies: 6 / Formula: EPB
Molecular weightTheoretical: 507.683 Da
Chemical component information

ChemComp-EPB:
7,11-DIHYDROXY-8,8,10,12,16-PENTAMETHYL-3-[1-METHYL-2-(2-METHYL-THIAZOL-4-YL)VINYL]-4,17-DIOXABICYCLO[14.1.0]HEPTADECANE-5,9-DIONE

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statehelical array

-
Sample preparation

BufferpH: 6.5
Sugar embeddingMaterial: vitreous ice
VitrificationCryogen name: ETHANE

-
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: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: PDB ENTRY
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: FREALIGN
Details: reference was low-pass filtered to 8 Angstroms in the final round of alignment.
Number images used: 12543
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

+
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