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- EMDB-9005: CryoEM reconstruction of IST1-CHMP1B copolymer filament bound to ... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-9005 | |||||||||||||||||||||||||||
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Title | CryoEM reconstruction of IST1-CHMP1B copolymer filament bound to ssDNA at 2.9 Angstrom resolution | |||||||||||||||||||||||||||
![]() | Post processed map with imposed helical symmetry | |||||||||||||||||||||||||||
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![]() | ESCRT-III / CHMP1B / IST1 / ssDNA / DNA BINDING PROTEIN / PROTEIN FIBRIL | |||||||||||||||||||||||||||
Function / homology | ![]() viral capsid secondary envelopment / MIT domain binding / abscission / amphisome membrane / multivesicular body-lysosome fusion / vesicle fusion with vacuole / ESCRT III complex disassembly / late endosome to lysosome transport / ESCRT III complex / kinetochore microtubule ...viral capsid secondary envelopment / MIT domain binding / abscission / amphisome membrane / multivesicular body-lysosome fusion / 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 / regulation of centrosome duplication / collateral sprouting / nuclear membrane reassembly / positive regulation of collateral sprouting / Sealing of the nuclear envelope (NE) by ESCRT-III / midbody abscission / multivesicular body sorting pathway / membrane coat / plasma membrane repair / membrane fission / late endosome to vacuole transport / multivesicular body membrane / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / multivesicular body assembly / regulation of mitotic spindle assembly / Flemming body / mitotic metaphase chromosome alignment / nucleus organization / viral budding via host ESCRT complex / autophagosome membrane / positive regulation of proteolysis / autophagosome maturation / endoplasmic reticulum-Golgi intermediate compartment / viral release from host cell / nuclear pore / multivesicular body / viral budding from plasma membrane / establishment of protein localization / kinetochore / autophagy / nuclear envelope / azurophil granule lumen / protein localization / protein transport / midbody / endosome membrane / cadherin binding / protein domain specific binding / cell division / lysosomal membrane / 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 | |||||||||||||||||||||||||||
Biological species | ![]() | |||||||||||||||||||||||||||
Method | helical reconstruction / cryo EM / Resolution: 2.9 Å | |||||||||||||||||||||||||||
![]() | Talledge N / Frost A | |||||||||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 54 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 20.8 KB 20.8 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 14.2 KB | Display | ![]() |
Images | ![]() | 207.5 KB | ||
Filedesc metadata | ![]() | 6.9 KB | ||
Others | ![]() ![]() | 193.6 MB 193.6 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6e8gMC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Post processed map with imposed helical symmetry | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.838 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: Half map 2
File | emd_9005_half_map_1.map | ||||||||||||
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Annotation | Half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 1
File | emd_9005_half_map_2.map | ||||||||||||
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Annotation | Half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Helical assembly of IST1 and CHMP1B protein bound to ssDNA
Entire | Name: Helical assembly of IST1 and CHMP1B protein bound to ssDNA |
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Components |
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-Supramolecule #1: Helical assembly of IST1 and CHMP1B protein bound to ssDNA
Supramolecule | Name: Helical assembly of IST1 and CHMP1B protein bound to ssDNA type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: IST1 homolog
Macromolecule | Name: IST1 homolog / type: protein_or_peptide / ID: 1 / Number of copies: 36 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 40.024711 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: 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 |
-Macromolecule #2: Charged multivesicular body protein 1b
Macromolecule | Name: Charged multivesicular body protein 1b / type: protein_or_peptide / ID: 2 / Number of copies: 36 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 22.140354 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: 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 |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | helical reconstruction |
Aggregation state | filament |
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Sample preparation
Buffer | pH: 8 Component:
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Grid | Model: 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 | |||||||||
Vitrification | Cryogen 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
Microscope | FEI TITAN KRIOS |
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Image recording | Film 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 beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.6 mm / Nominal magnification: 29000 |
Sample stage | Specimen 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
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL / Overall B value: 52.5 |
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Output model | ![]() PDB-6e8g: |