[English] 日本語
Yorodumi
- PDB-8v2s: CHMP1B/IST1 dsDNA bound copolymer -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8v2s
TitleCHMP1B/IST1 dsDNA bound copolymer
Components
  • Charged multivesicular body protein 1b
  • IST1 homolog
KeywordsDNA BINDING PROTEIN / nucleic acid binding
Function / homology
Function and homology information


MIT domain binding / multivesicular body-lysosome fusion / amphisome membrane / vesicle fusion with vacuole / ESCRT III complex disassembly / late endosome to lysosome transport / ESCRT III complex / kinetochore microtubule / endosome transport via multivesicular body sorting pathway / cytoskeleton-dependent cytokinesis ...MIT domain binding / multivesicular body-lysosome fusion / amphisome membrane / vesicle fusion with vacuole / ESCRT III complex disassembly / late endosome to lysosome transport / ESCRT III complex / kinetochore microtubule / endosome transport via multivesicular body sorting pathway / cytoskeleton-dependent cytokinesis / collateral sprouting / regulation of centrosome duplication / nuclear membrane reassembly / positive regulation of collateral sprouting / multivesicular body sorting pathway / Sealing of the nuclear envelope (NE) by ESCRT-III / membrane coat / midbody abscission / membrane fission / plasma membrane repair / late endosome to vacuole transport / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / multivesicular body membrane / multivesicular body assembly / regulation of mitotic spindle assembly / Flemming body / mitotic metaphase chromosome alignment / nucleus organization / viral budding via host ESCRT complex / endoplasmic reticulum-Golgi intermediate compartment / positive regulation of proteolysis / autophagosome membrane / autophagosome maturation / nuclear pore / multivesicular body / viral budding from plasma membrane / establishment of protein localization / kinetochore / autophagy / azurophil granule lumen / protein localization / protein transport / nuclear envelope / midbody / endosome membrane / cadherin binding / protein domain specific binding / lysosomal membrane / cell division / intracellular membrane-bounded organelle / centrosome / Neutrophil degranulation / protein-containing complex binding / chromatin / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Vacuolar protein sorting-associated protein Ist1 / Vacuolar protein sorting-associated protein IST1-like / Regulator of Vps4 activity in the MVB pathway / Snf7 family / Snf7
Similarity search - Domain/homology
IST1 homolog / Charged multivesicular body protein 1b
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.72 Å
AuthorsTalledge, N. / Laughlin, T.G. / Alian, A.
Funding support United States, 6items
OrganizationGrant numberCountry
National Institutes of Health/Office of the DirectorS10OD020054 United States
National Institutes of Health/Office of the Director1S10OD021741 United States
National Institutes of Health/Office of the Director1S10OD021596-01 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1DP2GM110772-01 United States
Howard Hughes Medical Institute (HHMI) United States
Chan Zuckerberg Initiative United States
CitationJournal: To Be Published
Title: ESCRT-III Assembles Around Mis-segregated DNA to Engage NoCut
Authors: Talledge, N. / Glover, J. / McCullough, J. / Alian, A. / Sadler, J.B.A. / Dempsey, N. / Laughlin, T.G. / Nguyen, H.C. / Wenzel, D. / Lalonde, M.S. / Ventimiglia, L.N. / LaJoie, D. / Iwasa, J. ...Authors: Talledge, N. / Glover, J. / McCullough, J. / Alian, A. / Sadler, J.B.A. / Dempsey, N. / Laughlin, T.G. / Nguyen, H.C. / Wenzel, D. / Lalonde, M.S. / Ventimiglia, L.N. / LaJoie, D. / Iwasa, J. / Starling, T. / Padilla-Parra, S. / Ullman, K.S. / Frost, A. / Sundquist, W.I. / Martin-Serrano, J.
History
DepositionNov 23, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Charged multivesicular body protein 1b
B: IST1 homolog


Theoretical massNumber of molelcules
Total (without water)61,9052
Polymers61,9052
Non-polymers00
Water00
1
A: Charged multivesicular body protein 1b
B: IST1 homolog
x 96


Theoretical massNumber of molelcules
Total (without water)5,942,857192
Polymers5,942,857192
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation95
identity operation1_555x,y,z1

-
Components

#1: Protein Charged multivesicular body protein 1b


Mass: 22108.355 Da / Num. of mol.: 1 / Mutation: M136V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CHMP1B / Plasmid: pET28a(+) / Details (production host): 6xHIS-SUMO_CHMP1B / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q7LBR1
#2: Protein IST1 homolog / hIST1 / Charged multivesicular body protein 8 / CHMP8 / Putative MAPK-activating protein PM28


Mass: 39796.402 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IST1, KIAA0174 / Plasmid: pET28c(+) / Details (production host): 6xHIS-SUMO_IST1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P53990
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

-
Sample preparation

Component
IDNameTypeDetailsEntity IDParent-IDSource
1CHMP1B/IST1 copolymer bound to a 60-mer oligonucleotide of ssDNACOMPLEXComplex assembly formed my mixing protein and oligonucleotide at a 1:20 molar ratio (protein to base) by dialysis into physiological buffer conditionsall0RECOMBINANT
2Charged multivesicular body protein 1B (CHMP1B)COMPLEXCHMP1B component of the nucleic acid templated helical assembly#11RECOMBINANT
3Increased sodium tolerance 1 (IST1)COMPLEXIST1 component of the nucleic acid templated assembly#21RECOMBINANT
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
11NO
210.220762 MDaYES
310.397494 MDaYES
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Homo sapiens (human)9606
32Homo sapiens (human)9606
43Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-IDPlasmid
21Escherichia coli BL21(DE3) (bacteria)469008pET28
32Escherichia coli BL21(DE3) (bacteria)469008pET28
43Escherichia coli BL21(DE3) (bacteria)469008pET28
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMTris HydrochlorideTris-HCl1
2125 mMSodium ChlorideNaCl1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Sample is at 16 micromolar protein concentration.
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R0.6/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 292.15 K

-
Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 1800 nm / Nominal defocus min: 800 nm / Calibrated defocus min: 100 nm / Calibrated defocus max: 4000 nm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: OTHER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1
EM imaging opticsEnergyfilter name: TFS Selectris / Energyfilter slit width: 10 eV

-
Processing

EM software
IDNameVersionCategory
1cryoSPARC4.2.1particle selection
2EPU3.4image acquisition
4cryoSPARC4.2.1CTF correction
7ISOLDE1.6.0model fitting
9ISOLDE1.6.0model refinement
10cryoSPARC4.2.1initial Euler assignment
11cryoSPARCV4.2.1final Euler assignment
12cryoSPARC4.2.1classification
13cryoSPARC4.2.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 3.025 ° / Axial rise/subunit: 2.72 Å / Axial symmetry: C1
Particle selectionNum. of particles selected: 511337
3D reconstructionResolution: 2.72 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 451289 / Algorithm: FOURIER SPACE / Num. of class averages: 10 / Symmetry type: HELICAL
Atomic model buildingProtocol: OTHER / Space: REAL
Atomic model building

3D fitting-ID: 1 / Source name: PDB / Type: experimental model

IDPDB-IDPdb chain-IDAccession codeChain-IDDetailsInitial refinement model-ID
16TZ4

6tz4

A6TZ4AIsolated CHMP1B monomer for each biological unit used as initial model1
23FRR

3frr

B3FRRBIsolated IST1 monomer for each biological unit used as initial model2

+
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