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- EMDB-9005: CryoEM reconstruction of IST1-CHMP1B copolymer filament bound to ... -

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Basic information

Entry
Database: EMDB / ID: EMD-9005
TitleCryoEM reconstruction of IST1-CHMP1B copolymer filament bound to ssDNA at 2.9 Angstrom resolution
Map data
SampleHelical assembly of IST1 and CHMP1B protein bound to ssDNA:
IST1 homolog / Charged multivesicular body protein 1b
Function / homology
Function and homology information


viral capsid secondary envelopment / MIT domain binding / abscission / ESCRT III complex disassembly / ESCRT III complex / cytoskeleton-dependent cytokinesis / endosome transport via multivesicular body sorting pathway / midbody abscission / regulation of centrosome duplication / membrane coat ...viral capsid secondary envelopment / MIT domain binding / abscission / ESCRT III complex disassembly / ESCRT III complex / cytoskeleton-dependent cytokinesis / endosome transport via multivesicular body sorting pathway / midbody abscission / regulation of centrosome duplication / membrane coat / positive regulation of collateral sprouting / multivesicular body assembly / late endosome to vacuole transport / nucleus organization / regulation of mitotic spindle assembly / Flemming body / mitotic metaphase plate congression / viral release from host cell / viral budding via host ESCRT complex / mitotic nuclear membrane reassembly / positive regulation of proteolysis / late endosome membrane / multivesicular body / endoplasmic reticulum-Golgi intermediate compartment / establishment of protein localization / nuclear envelope / azurophil granule lumen / protein transport / midbody / protein localization / endosome membrane / cadherin binding / centrosome / cell division / protein domain specific binding / intracellular membrane-bounded organelle / protein-containing complex binding / neutrophil degranulation / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / cytosol
Vacuolar protein sorting-associated protein IST1-like / Vacuolar protein sorting-associated protein Ist1 / Snf7 family
IST1 homolog / Charged multivesicular body protein 1b
Biological speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsTalledge N / Frost A / McCullough J
Funding support United States, 8 items
OrganizationGrant numberCountry
National Institutes of Health/Office of the DirectorS10OD020054 United States
National Institutes of Health/Office of the Director1S10OD021596-01 United States
National Institutes of Health/Office of the Director1S10OD021741 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)3P50GM082545-07S1 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1DP2GM110772-01 United States
American Asthma Foundation United States
Howard Hughes Medical Institute (HHMI) United States
Chan Zuckerberg Biohub United States
CitationJournal: Biorxiv / Year: 2018
Title: The ESCRT-III proteins IST1 and CHMP1B assemble around nucleic acids
Authors: Talledge N / McCullough J / Wenzel DM / Nguyen HC / Lalonde M / Bajorek M / Skalicky JJ / Frost A / Sundquist WI
Validation ReportSummary, Full report, XML, About validation report
History
DepositionJul 29, 2018-
Header (metadata) releaseAug 15, 2018-
Map releaseAug 15, 2018-
UpdateNov 20, 2019-
Current statusNov 20, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.025
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6e8g
  • Surface level: 0.025
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6e8g
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_9005.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 400 pix.
= 335.2 Å
0.84 Å/pix.
x 400 pix.
= 335.2 Å
0.84 Å/pix.
x 400 pix.
= 335.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.838 Å
Density
Contour LevelBy AUTHOR: 0.025 / Movie #1: 0.025
Minimum - Maximum-0.06302304 - 0.12529045
Average (Standard dev.)0.0009589213 (±0.007936976)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 335.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8380.8380.838
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z335.200335.200335.200
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ300300300
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.0630.1250.001

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Supplemental data

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Half map: Half map 2

Fileemd_9005_half_map_1.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: Half map 1

Fileemd_9005_half_map_2.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire Helical assembly of IST1 and CHMP1B protein bound to ssDNA

EntireName: Helical assembly of IST1 and CHMP1B protein bound to ssDNA
Number of components: 3

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Component #1: protein, Helical assembly of IST1 and CHMP1B protein bound to ssDNA

ProteinName: Helical assembly of IST1 and CHMP1B protein bound to ssDNA
Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli BL21(DE3) (bacteria) / Strain: BL21(DE3) RIPL
Source (natural)Location in cell: cytoplasm

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Component #2: protein, IST1 homolog

ProteinName: IST1 homolog / Number of Copies: 36 / Recombinant expression: No
MassTheoretical: 40.024711 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli BL21(DE3) (bacteria)

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Component #3: protein, Charged multivesicular body protein 1b

ProteinName: Charged multivesicular body protein 1b / Number of Copies: 36 / Recombinant expression: No
MassTheoretical: 22.140354 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli BL21(DE3) (bacteria)

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Experimental details

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Sample preparation

SpecimenSpecimen state: Filament / Method: cryo EM
Helical parametersAxial symmetry: C1 (asymmetric) / Delta z: 3.17 Å / Delta phi: 21.16 %deg;
Sample solutionpH: 8
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Temperature: 292.15 K / Humidity: 100 %
Details: 0 mm offset with 10 sec wait time and 2-4 sec blot.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 62 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 29000.0 X (nominal) / Cs: 2.6 mm / Imaging mode: BRIGHT FIELD
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 2980

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Image processing

ProcessingMethod: helical reconstruction
3D reconstructionSoftware: RELION / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF
Euler angles: Initial consensus auto refinement procedure was performed with RELION. Helical symmetry was imposed and refined during the initial assignment and a 310 Angstrom spherical mask was used ...Euler angles: Initial consensus auto refinement procedure was performed with RELION. Helical symmetry was imposed and refined during the initial assignment and a 310 Angstrom spherical mask was used during the refinement.
FSC plot (resolution estimation)

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Atomic model buiding

Modeling #1Refinement space: REAL / Overall bvalue: 52.5
Output model

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