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- EMDB-20589: CryoEM reconstruction of membrane-bound ESCRT-III filament compos... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-20589 | ||||||||||||||||||
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Title | CryoEM reconstruction of membrane-bound ESCRT-III filament composed of CHMP1B+IST1 (left-handed) | ||||||||||||||||||
![]() | RELION postprocessed map with helical symmetry applied to the entire map | ||||||||||||||||||
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![]() | membrane remodeling / membrane-bound protein filament / ESCRT-III / LIPID BINDING PROTEIN | ||||||||||||||||||
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 / endoplasmic reticulum-Golgi intermediate compartment / autophagosome maturation / 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: 3.1 Å | ||||||||||||||||||
![]() | Nguyen HC / Frost A | ||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Membrane constriction and thinning by sequential ESCRT-III polymerization. Authors: Henry C Nguyen / Nathaniel Talledge / John McCullough / Abhimanyu Sharma / Frank R Moss / Janet H Iwasa / Michael D Vershinin / Wesley I Sundquist / Adam Frost / ![]() Abstract: The endosomal sorting complexes required for transport (ESCRTs) mediate diverse membrane remodeling events. These typically require ESCRT-III proteins to stabilize negatively curved membranes; ...The endosomal sorting complexes required for transport (ESCRTs) mediate diverse membrane remodeling events. These typically require ESCRT-III proteins to stabilize negatively curved membranes; however, recent work has indicated that certain ESCRT-IIIs also participate in positive-curvature membrane-shaping reactions. ESCRT-IIIs polymerize into membrane-binding filaments, but the structural basis for negative versus positive membrane remodeling by these proteins remains poorly understood. To learn how certain ESCRT-IIIs shape positively curved membranes, we determined structures of human membrane-bound CHMP1B-only, membrane-bound CHMP1B + IST1, and IST1-only filaments by cryo-EM. Our structures show how CHMP1B first polymerizes into a single-stranded helical filament, shaping membranes into moderate-curvature tubules. Subsequently, IST1 assembles a second strand on CHMP1B, further constricting the membrane tube and reducing its diameter nearly to the fission point. Each step of constriction thins the underlying bilayer, lowering the barrier to membrane fission. Our structures reveal how a two-component, sequential polymerization mechanism drives membrane tubulation, constriction and bilayer thinning. | ||||||||||||||||||
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 | ![]() | 40.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 26.4 KB 26.4 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 12.5 KB | Display | ![]() |
Images | ![]() | 57.5 KB | ||
Masks | ![]() | 166.4 MB | ![]() | |
Filedesc metadata | ![]() | 6.2 KB | ||
Others | ![]() ![]() ![]() ![]() ![]() ![]() | 131.8 MB 131.6 MB 131.7 MB 131.6 MB 131.6 MB 131.7 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6tz5MC ![]() 6tz4C ![]() 6tz9C ![]() 6tzaC C: citing same article ( M: atomic model generated by this map |
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Similar structure data | |
EM raw data | ![]() Data size: 26.8 Data #1: copolymer_LH_job1415.mrcs [picked particles - multiframe - processed]) |
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Links
EMDB pages | ![]() ![]() |
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Map
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Annotation | RELION postprocessed map with helical symmetry applied to the entire map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.22 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
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Density Histograms |
-Additional map: RELION Refine3D filtered map with no symmetry applied (C1 map)
File | emd_20589_additional_1.map | ||||||||||||
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Annotation | RELION Refine3D filtered map with no symmetry applied (C1 map) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: RELION Refine3D filtered map with no symmetry applied (C1 map)
File | emd_20589_additional_2.map | ||||||||||||
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Annotation | RELION Refine3D filtered map with no symmetry applied (C1 map) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: RELION Refine3D unfiltered half map1 with no symmetry...
File | emd_20589_additional_3.map | ||||||||||||
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Annotation | RELION Refine3D unfiltered half map1 with no symmetry applied (C1 half1 map) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: RELION Refine3D unfiltered half map2 with no symmetry...
File | emd_20589_additional_4.map | ||||||||||||
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Annotation | RELION Refine3D unfiltered half map2 with no symmetry applied (C1 half2 map) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: RELION Refine3D unfiltered half map1 with helical symmetry...
File | emd_20589_half_map_1.map | ||||||||||||
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Annotation | RELION Refine3D unfiltered half map1 with helical symmetry imposed on the central 40% | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: RELION Refine3D unfiltered half map2 with helical symmetry...
File | emd_20589_half_map_2.map | ||||||||||||
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Annotation | RELION Refine3D unfiltered half map2 with helical symmetry imposed on the central 40% | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : membrane-bound ESCRT-III copolymer filament composed of CHMP1B an...
Entire | Name: membrane-bound ESCRT-III copolymer filament composed of CHMP1B and IST1 |
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Components |
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-Supramolecule #1: membrane-bound ESCRT-III copolymer filament composed of CHMP1B an...
Supramolecule | Name: membrane-bound ESCRT-III copolymer filament composed of CHMP1B and IST1 type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: Charged multivesicular body protein 1b
Macromolecule | Name: Charged multivesicular body protein 1b / type: protein_or_peptide / ID: 1 / Number of copies: 34 / 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 |
-Macromolecule #2: IST1 homolog
Macromolecule | Name: IST1 homolog / type: protein_or_peptide / ID: 2 / Number of copies: 34 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 21.574281 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MLGSGFKAER LRVNLRLVIN RLKLLEKKKT ELAQKARKEI ADYLAAGKDE RARIRVEHII REDYLVEAME ILELYCDLLL ARFGLIQSM KELDSGLAES VSTLIWAAPR LQSEVAELKI VADQLCAKYS KEYGKLCRTN QIGTVNDRLM HKLSVEAPPK I LVERYLIE IAKNYNVPYE PDSVVMAEAP P UniProtKB: IST1 homolog |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | helical reconstruction |
Aggregation state | helical array |
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Sample preparation
Buffer | pH: 7.4 |
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Grid | Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Details: unspecified |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 292 K / Instrument: FEI VITROBOT MARK III Details: Grids were blotted with Whatman No. 1 filter paper for 4-8 seconds with a 0 mm offset at 19C and 100 percent humidity before plunging into liquid ethane. |
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Electron microscopy
Microscope | FEI POLARA 300 |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 44.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Tecnai Polara / Image courtesy: FEI Company |