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- PDB-6tz4: CryoEM reconstruction of membrane-bound ESCRT-III filament compos... -

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Basic information

Entry
Database: PDB / ID: 6tz4
TitleCryoEM reconstruction of membrane-bound ESCRT-III filament composed of CHMP1B+IST1 (right-handed)
Components
  • Charged multivesicular body protein 1b
  • IST1 homolog
KeywordsLIPID BINDING PROTEIN / membrane remodeling / membrane-bound protein filament / ESCRT-III
Function / homology
Function and homology information


MIT domain binding / abscission / 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 ...MIT domain binding / abscission / 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 / 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 / plasma membrane repair / membrane coat / membrane fission / late endosome to vacuole transport / multivesicular body membrane / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / regulation of mitotic spindle assembly / multivesicular body assembly / Flemming body / mitotic metaphase chromosome alignment / nucleus organization / viral budding via host ESCRT complex / positive regulation of proteolysis / endoplasmic reticulum-Golgi intermediate compartment / 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: 3.2 Å
AuthorsNguyen, H.C. / Frost, A.
Funding support United States, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P50 AI150464 United States
National Institutes of Health/Office of the DirectorS10OD020054 United States
National Institutes of Health/Office of the DirectorS10OD021741 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
CitationJournal: Nat Struct Mol Biol / Year: 2020
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
DepositionAug 10, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
JB: Charged multivesicular body protein 1b
MB: IST1 homolog
A: Charged multivesicular body protein 1b
B: IST1 homolog
C: Charged multivesicular body protein 1b
D: IST1 homolog
E: Charged multivesicular body protein 1b
F: IST1 homolog
G: Charged multivesicular body protein 1b
H: IST1 homolog
I: Charged multivesicular body protein 1b
J: IST1 homolog
K: Charged multivesicular body protein 1b
L: IST1 homolog
M: Charged multivesicular body protein 1b
N: IST1 homolog
O: Charged multivesicular body protein 1b
P: IST1 homolog
Q: Charged multivesicular body protein 1b
R: IST1 homolog
S: Charged multivesicular body protein 1b
T: IST1 homolog
V: Charged multivesicular body protein 1b
W: IST1 homolog
X: Charged multivesicular body protein 1b
Y: IST1 homolog
Z: Charged multivesicular body protein 1b
AA: IST1 homolog
BA: Charged multivesicular body protein 1b
CA: IST1 homolog
DA: Charged multivesicular body protein 1b
EA: IST1 homolog
FA: Charged multivesicular body protein 1b
GA: IST1 homolog
HA: Charged multivesicular body protein 1b
IA: IST1 homolog
JA: Charged multivesicular body protein 1b
KA: IST1 homolog
LA: Charged multivesicular body protein 1b
MA: IST1 homolog
NA: Charged multivesicular body protein 1b
OA: IST1 homolog
PA: Charged multivesicular body protein 1b
QA: IST1 homolog
RA: Charged multivesicular body protein 1b
SA: IST1 homolog
TA: Charged multivesicular body protein 1b
UA: IST1 homolog
VA: Charged multivesicular body protein 1b
WA: IST1 homolog
XA: Charged multivesicular body protein 1b
YA: IST1 homolog
ZA: Charged multivesicular body protein 1b
AB: IST1 homolog
BB: Charged multivesicular body protein 1b
CB: IST1 homolog
DB: Charged multivesicular body protein 1b
EB: IST1 homolog
FB: Charged multivesicular body protein 1b
GB: IST1 homolog
HB: Charged multivesicular body protein 1b
IB: IST1 homolog
LB: Charged multivesicular body protein 1b
KB: IST1 homolog
NB: Charged multivesicular body protein 1b
OB: IST1 homolog
PB: Charged multivesicular body protein 1b
QB: IST1 homolog
RB: Charged multivesicular body protein 1b
SB: IST1 homolog
02: Charged multivesicular body protein 1b
01: IST1 homolog


Theoretical massNumber of molelcules
Total (without water)1,573,72772
Polymers1,573,72772
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_5551
SymmetryHelical symmetry: (Circular symmetry: 1 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 36 / Rise per n subunits: 2.96 Å / Rotation per n subunits: 20.02 °)

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Components

#1: Protein ...
Charged multivesicular body protein 1b / CHMP1.5 / Chromatin-modifying protein 1b / CHMP1b / Vacuolar protein sorting-associated protein 46- ...CHMP1.5 / Chromatin-modifying protein 1b / CHMP1b / Vacuolar protein sorting-associated protein 46-2 / hVps46-2


Mass: 22140.354 Da / Num. of mol.: 36 / Mutation: K37E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CHMP1B, C18orf2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7LBR1
#2: Protein ...
IST1 homolog / hIST1 / Putative MAPK-activating protein PM28


Mass: 21574.281 Da / Num. of mol.: 36 / Fragment: N-terminal domain (UNP residues 1-189)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IST1, KIAA0174 / Production host: Escherichia coli (E. coli) / References: UniProt: P53990

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: membrane-bound ESCRT-III copolymer filament composed of CHMP1B and IST1
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: unspecified
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 292 K
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 imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 44 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameCategory
2SerialEMimage acquisition
9PHENIXmodel refinement
10RELIONinitial Euler assignment
11RELIONfinal Euler assignment
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 20.02 ° / Axial rise/subunit: 2.96 Å / Axial symmetry: C1
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 61974 / Symmetry type: HELICAL

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