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- EMDB-28696: CryoEM reconstruction of membrane-bound, right-handed CHMP1B+IST1... -

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Basic information

Entry
Database: EMDB / ID: EMD-28696
TitleCryoEM reconstruction of membrane-bound, right-handed CHMP1B+IST1 filament with brominated POPS probe
Map dataRight-handed, 18-subunit-per-turn, membrane-bound CHMP1B/IST1 with brominated POPS.Handedness
Sample
  • Complex: Helical copolymer of CHMP1B and IST1 bound to a lipid membrane nanotube
    • Protein or peptide: CHMP1B
    • Protein or peptide: IST1
Biological speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsMoss FR / Frost A
Funding support United States, 7 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM117593 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM137109 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM082545 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM110772 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM089740 United States
Howard Hughes Medical Institute (HHMI) United States
Chan Zuckerberg Initiative 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
DepositionOct 28, 2022-
Header (metadata) releaseJan 11, 2023-
Map releaseJan 11, 2023-
UpdateJan 25, 2023-
Current statusJan 25, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28696.png

Downloads & links

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Map

FileDownload / File: emd_28696.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRight-handed, 18-subunit-per-turn, membrane-bound CHMP1B/IST1 with brominated POPS.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 480 pix.
= 394.56 Å		0.82 Å/pix.
x 480 pix.
= 394.56 Å		0.82 Å/pix.
x 480 pix.
= 394.56 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.822 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.003
Minimum - Maximum-0.010532566 - 0.019910714
Average (Standard dev.)0.00015386811 (±0.001321116)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 394.56 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_28696_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Right-handed, 18-subunit-per-turn, membrane-bound CHMP1B/IST1 with brominated POPS. No...

Fileemd_28696_additional_1.map
AnnotationRight-handed, 18-subunit-per-turn, membrane-bound CHMP1B/IST1 with brominated POPS. No helical symmetry has been applied.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Additional map: RELION post-processed, right-handed, 18-subunit-per-turn, membrane-bound CHMP1B/IST1 with brominated...

Fileemd_28696_additional_2.map
AnnotationRELION post-processed, right-handed, 18-subunit-per-turn, membrane-bound CHMP1B/IST1 with brominated POPS.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Right-handed, 18-subunit-per-turn, membrane-bound CHMP1B/IST1 with brominated POPS. Half...

Fileemd_28696_half_map_1.map
AnnotationRight-handed, 18-subunit-per-turn, membrane-bound CHMP1B/IST1 with brominated POPS. Half 1.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Right-handed, 18-subunit-per-turn, membrane-bound CHMP1B/IST1 with brominated POPS. Half...

Fileemd_28696_half_map_2.map
AnnotationRight-handed, 18-subunit-per-turn, membrane-bound CHMP1B/IST1 with brominated POPS. Half 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 copolymer of CHMP1B and IST1 bound to a lipid membrane na...

EntireName: Helical copolymer of CHMP1B and IST1 bound to a lipid membrane nanotube
Components
  • Complex: Helical copolymer of CHMP1B and IST1 bound to a lipid membrane nanotube
    • Protein or peptide: CHMP1B
    • Protein or peptide: IST1

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Supramolecule #1: Helical copolymer of CHMP1B and IST1 bound to a lipid membrane na...

SupramoleculeName: Helical copolymer of CHMP1B and IST1 bound to a lipid membrane nanotube
type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: all
Details: The lipid nanotube contains a brominated analog of POPS
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: CHMP1B

MacromoleculeName: CHMP1B / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSNMEKHLFN LKFAAKELSR SAKKCDKEEK AEKAKIKKAI QKGNMEVARI HAENAIRQKN QAVNFLRMSA RVDAVAARVQ TAVTMGKVTK SMAGVVKSMD ATLKTMNLEK ISALMDKFEH QFETLDVQTQ QMEDTMSSTT TLTTPQNQVD MLLQEMADEA GLDLNMELPQ ...String:
MSNMEKHLFN LKFAAKELSR SAKKCDKEEK AEKAKIKKAI QKGNMEVARI HAENAIRQKN QAVNFLRMSA RVDAVAARVQ TAVTMGKVTK SMAGVVKSMD ATLKTMNLEK ISALMDKFEH QFETLDVQTQ QMEDTMSSTT TLTTPQNQVD MLLQEMADEA GLDLNMELPQ GQTGSVGTSV ASAEQDELSQ RLARLRDQV

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Macromolecule #2: IST1

MacromoleculeName: IST1 / type: protein_or_peptide / ID: 2 / Details: N-terminal domain / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MLGSGFKAER LRVNLRLVIN RLKLLEKKKT ELAQKARKEI ADYLAAGKDE RARIRVEHII REDYLVEAME ILELYCDLLL ARFGLIQSMK ELDSGLAESV STLIWAAPRL QSEVAELKIV ADQLCAKYSK EYGKLCRTNQ IGTVNDRLMH KLSVEAPP

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 292 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 105000
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 5060 / Average electron dose: 67.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Segment selectionNumber selected: 202716 / Software - Name: crYOLO
Startup modelType of model: INSILICO MODEL / In silico model: Featureless cylinder
Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 3.0.8)
Final reconstructionApplied symmetry - Helical parameters - Δz: 3.0 Å
Applied symmetry - Helical parameters - Δ&Phi: 19.99 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0.8) / Number images used: 16746
FSC plot (resolution estimation)

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