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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 dataPost processed map with imposed helical symmetry
Sample
  • Complex: Helical assembly of IST1 and CHMP1B protein bound to ssDNA
    • Protein or peptide: IST1 homolog
    • Protein or peptide: Charged multivesicular body protein 1b
KeywordsESCRT-III / CHMP1B / IST1 / ssDNA / DNA BINDING PROTEIN / PROTEIN FIBRIL
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 / membrane coat / regulation of centrosome duplication / nuclear membrane reassembly / Sealing of the nuclear envelope (NE) by ESCRT-III / multivesicular body sorting pathway / positive regulation of collateral sprouting / 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 assembly / multivesicular body membrane / 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 / intracellular protein localization / nuclear envelope / protein transport / midbody / endosome membrane / cadherin binding / protein domain specific binding / lysosomal membrane / cell division / intracellular membrane-bounded organelle / centrosome / Neutrophil degranulation / chromatin / protein-containing complex binding / 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)
Methodhelical reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsTalledge N / Frost A
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 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
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)3P50GM082545-07S1 United States
Howard Hughes Medical Institute (HHMI) United States
American Asthma Foundation 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
History
DepositionJul 29, 2018-
Header (metadata) releaseAug 15, 2018-
Map releaseAug 15, 2018-
UpdateMar 13, 2024-
Current statusMar 13, 2024Processing 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
  • Download
  • 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

emd_9005.png

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)
AnnotationPost processed map with imposed helical symmetry
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

Histogram

Histogram (log scale)
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

Histogram

Histogram (log scale)

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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

Histogram

Histogram (log scale)

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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
Components
  • Complex: Helical assembly of IST1 and CHMP1B protein bound to ssDNA
    • Protein or peptide: IST1 homolog
    • Protein or peptide: Charged multivesicular body protein 1b

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

SupramoleculeName: Helical assembly of IST1 and CHMP1B protein bound to ssDNA
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human) / Location in cell: cytoplasm

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Macromolecule #1: IST1 homolog

MacromoleculeName: IST1 homolog / type: protein_or_peptide / ID: 1 / Number of copies: 36 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 40.024711 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MLGSGFKAER LRVNLRLVIN RLKLLEKKKT ELAQKARKEI ADYLAAGKDE RARIRVEHII REDYLVEAME ILELYCDLLL ARFGLIQSM KELDSGLAES VSTLIWAAPR LQSEVAELKI VADQLCAKYS KEYGKLCRTN QIGTVNDRLM HKLSVEAPPK I LVERYLIE ...String:
MLGSGFKAER LRVNLRLVIN RLKLLEKKKT ELAQKARKEI ADYLAAGKDE RARIRVEHII REDYLVEAME ILELYCDLLL ARFGLIQSM KELDSGLAES VSTLIWAAPR LQSEVAELKI VADQLCAKYS KEYGKLCRTN QIGTVNDRLM HKLSVEAPPK I LVERYLIE IAKNYNVPYE PDSVVMAEAP PGVETDLIDV GFTDDVKKGG PGRGGSGGFT APVGGPDGTV PMPMPMPMPM PS ANTPFSY PLPKGPSDFN GLPMGTYQAF PNIHPPQIPA TPPSYESVDD INADKNISSA QIVGPGPKPE ASAKLPSRPA DNY DNFVLP ELPSVPDTLP TASAGASTSA SEDIDFDDLS RRFEELKKKT

UniProtKB: IST1 homolog

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Macromolecule #2: Charged multivesicular body protein 1b

MacromoleculeName: Charged multivesicular body protein 1b / type: protein_or_peptide / ID: 2 / Number of copies: 36 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.140354 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MSNMEKHLFN LKFAAKELSR SAKKCDKEEK AEKAKIEKAI QKGNMEVARI HAENAIRQKN QAVNFLRMSA RVDAVAARVQ TAVTMGKVT KSMAGVVKSM DATLKTMNLE KISALMDKFE HQFETLDVQT QQMEDTMSST TTLTTPQNQV DMLLQEMADE A GLDLNMEL ...String:
MSNMEKHLFN LKFAAKELSR SAKKCDKEEK AEKAKIEKAI QKGNMEVARI HAENAIRQKN QAVNFLRMSA RVDAVAARVQ TAVTMGKVT KSMAGVVKSM DATLKTMNLE KISALMDKFE HQFETLDVQT QQMEDTMSST TTLTTPQNQV DMLLQEMADE A GLDLNMEL PQGQTGSVGT SVASAEQDEL SQRLARLRDQ V

UniProtKB: Charged multivesicular body protein 1b

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 8
Component:
ConcentrationFormulaName
125.0 mMNaClsodium chloride
25.0 mMC4H11NO3Tris
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 292.15 K / Instrument: FEI VITROBOT MARK III
Details: 0 mm offset with 10 sec wait time and 2-4 sec blot.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Frames/image: 3-32 / Number grids imaged: 1 / Number real images: 2980 / Average exposure time: 6.2 sec. / Average electron dose: 62.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.6 mm / Nominal magnification: 29000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionNumber classes used: 1
Applied symmetry - Helical parameters - Δz: 3.17 Å
Applied symmetry - Helical parameters - Δ&Phi: 21.16 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 101990
Segment selectionNumber selected: 224252 / Software - Name: RELION (ver. 2.1)
Software - details: Manual helix picking was used to determine the filaments helical path.
Details: Helical particle segments were selected using RELION manualpick and extracted using overlapping segments with an asymmetric unit of 17 subunits with a 3.0 Angstrom rise (51 Angstrom total).
Startup modelType of model: EMDB MAP
EMDB ID:

6461


Details: Low pass filter to 60 Angstrom
Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 2.1)
Details: 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 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL / Overall B value: 52.5
Output model

PDB-6e8g:
CryoEM reconstruction of IST1-CHMP1B copolymer filament bound to ssDNA at 2.9 Angstrom resolution

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