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- EMDB-42934: Focused classification of dsDNA nucleic acid density from in vitr... -

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Basic information

Entry
Database: EMDB / ID: EMD-42934
TitleFocused classification of dsDNA nucleic acid density from in vitro CHMP1B/IST1 copolymer filaments - Class2
Map dataRefined sharpened map
Sample
  • Complex: CHMP1B/IST1 copolymer bound to a 60-mer oligonucleotide of ssDNA
    • Complex: Charged multivesicular body protein 1B (CHMP1B)
      • Protein or peptide: Charged multivesicular body protein 1B (CHMP1B)
    • Complex: Increased sodium tolerance 1 (IST1)
      • Protein or peptide: Increased sodium tolerance 1 (IST1)
Keywordsnucleic acid binding / DNA BINDING PROTEIN
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 / cytoskeleton-dependent cytokinesis ...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 / cytoskeleton-dependent cytokinesis / endosome transport via multivesicular body sorting pathway / collateral sprouting / regulation of centrosome duplication / 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 / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / multivesicular body membrane / multivesicular body assembly / 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 / protein transport / protein localization / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.99 Å
AuthorsTalledge N / Laughlin TG / Alian A / McCullough J
Funding support United States, 6 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
Howard Hughes Medical Institute (HHMI) United States
Chan Zuckerberg Initiative United States
CitationJournal: To Be Published
Title: ESCRT-III Assembles Around Mis-segregated DNA to Engage NoCut
Authors: Talledge N / Glover J / McCullough J / Alian A / Sadler JBA / Dempsey N / Laughlin TG / Nguyen HC / Wenzel D / Lalonde MS / Ventimiglia LN / LaJoie D / Iwasa J / Starling T / Padilla-Parra S ...Authors: Talledge N / Glover J / McCullough J / Alian A / Sadler JBA / Dempsey N / Laughlin TG / Nguyen HC / Wenzel D / Lalonde MS / Ventimiglia LN / LaJoie D / Iwasa J / Starling T / Padilla-Parra S / Ullman KS / Frost A / Sundquist WI / Martin-Serrano J
History
DepositionNov 23, 2023-
Header (metadata) releaseNov 27, 2024-
Map releaseNov 27, 2024-
UpdateNov 27, 2024-
Current statusNov 27, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_42934.png

Downloads & links

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Map

FileDownload / File: emd_42934.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRefined sharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.89 Å/pix.
x 400 pix.
= 357.44 Å		0.89 Å/pix.
x 400 pix.
= 357.44 Å		0.89 Å/pix.
x 400 pix.
= 357.44 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8936 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.25505817 - 0.59230065
Average (Standard dev.)0.0074172174 (±0.036512654)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 357.44 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_42934_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Refined map

Fileemd_42934_additional_1.map
AnnotationRefined map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Refined half map B

Fileemd_42934_half_map_1.map
AnnotationRefined half map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Refined half map A

Fileemd_42934_half_map_2.map
AnnotationRefined half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : CHMP1B/IST1 copolymer bound to a 60-mer oligonucleotide of ssDNA

EntireName: CHMP1B/IST1 copolymer bound to a 60-mer oligonucleotide of ssDNA
Components
  • Complex: CHMP1B/IST1 copolymer bound to a 60-mer oligonucleotide of ssDNA
    • Complex: Charged multivesicular body protein 1B (CHMP1B)
      • Protein or peptide: Charged multivesicular body protein 1B (CHMP1B)
    • Complex: Increased sodium tolerance 1 (IST1)
      • Protein or peptide: Increased sodium tolerance 1 (IST1)

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Supramolecule #1: CHMP1B/IST1 copolymer bound to a 60-mer oligonucleotide of ssDNA

SupramoleculeName: CHMP1B/IST1 copolymer bound to a 60-mer oligonucleotide of ssDNA
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Complex assembly formed my mixing protein and oligonucleotide at a 1:20 molar ratio (protein to base) by dialysis into physiological buffer conditions
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 397.494 KDa

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Supramolecule #2: Charged multivesicular body protein 1B (CHMP1B)

SupramoleculeName: Charged multivesicular body protein 1B (CHMP1B) / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Details: CHMP1B component of the nucleic acid templated helical assembly
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: Increased sodium tolerance 1 (IST1)

SupramoleculeName: Increased sodium tolerance 1 (IST1) / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Details: IST1 component of the nucleic acid templated assembly
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Charged multivesicular body protein 1B (CHMP1B)

MacromoleculeName: Charged multivesicular body protein 1B (CHMP1B) / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MSNMEKHLFN LKFAAKELSR SAKKCDKEEK AEKAKIKKAI QKGNMEVARI HAENAIRQKN QAVNFLRMS ARVDAVAARV QTAVTMGKVT KSMAGVVKSM DATLKTMNLE KISALMDKFE H QFETLDVQ TQQMEDTVSS TTTLTTPQNQ VDMLLQEMAD EAGLDLNMEL ...String:
MSNMEKHLFN LKFAAKELSR SAKKCDKEEK AEKAKIKKAI QKGNMEVARI HAENAIRQKN QAVNFLRMS ARVDAVAARV QTAVTMGKVT KSMAGVVKSM DATLKTMNLE KISALMDKFE H QFETLDVQ TQQMEDTVSS TTTLTTPQNQ VDMLLQEMAD EAGLDLNMEL PQGQTGSVGT SV ASAEQDE LSQRLARLRD QV

UniProtKB: Charged multivesicular body protein 1b

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Macromolecule #2: Increased sodium tolerance 1 (IST1)

MacromoleculeName: Increased sodium tolerance 1 (IST1) / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MLGSGFKAER LRVNLRLVIN RLKLLEKKKT ELAQKARKEI ADYLAAGKDE RARIRVEHII REDYLVEAM EILELYCDLL LARFGLIQSM KELDSGLAES VSTLIWAAPR LQSEVAELKI V ADQLCAKY SKEYGKLCRT NQIGTVNDRL MHKLSVEAPP KILVERYLIE ...String:
MLGSGFKAER LRVNLRLVIN RLKLLEKKKT ELAQKARKEI ADYLAAGKDE RARIRVEHII REDYLVEAM EILELYCDLL LARFGLIQSM KELDSGLAES VSTLIWAAPR LQSEVAELKI V ADQLCAKY SKEYGKLCRT NQIGTVNDRL MHKLSVEAPP KILVERYLIE IAKNYNVPYE PD SVVMAEA PPGVETDLID VGFTDDVKKG GPGRGGSGGF TAPVGGPDGT VPMPMPMPMP SAN TPFSYP LPKGPSDFNG LPMGTYQAFP NIHPPQIPAT PPSYESVDDI NADKNISSAQ IVGP GPKPE ASAKLPSRPA DNYDNFVLPE LPSVPDTLPT ASAGASTSAS EDIDFDDLSR RFEEL KKKT

UniProtKB: IST1 homolog

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 8
Component:
ConcentrationFormulaName
50.0 mMTris-HClTris Hydrochloride
125.0 mMNaClSodium Chloride
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 292.15 K / Instrument: FEI VITROBOT MARK IV
DetailsSample is at 16 micromolar protein concentration.

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Electron microscopy

MicroscopeTFS GLACIOS
Specialist opticsEnergy filter - Name: TFS Selectris / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated defocus max: 4.0 µm / Calibrated defocus min: 0.1 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: OTHER / Cooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 3082034 / Details: dsDNA consensus helical map symmetry expanded
Startup modelType of model: OTHER
Details: Consensus reconstruction map included with this entry
Final reconstructionNumber classes used: 10 / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.99 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.2.1) / Number images used: 374113
Initial angle assignmentType: NOT APPLICABLE / Software - Name: cryoSPARC (ver. 4.2.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. V4.2.1)
Final 3D classificationNumber classes: 10 / Software - Name: cryoSPARC (ver. 4.2.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChainDetails

6tz4

chain_id: A, source_name: PDB, initial_model_type: experimental modelIsolated CHMP1B monomer for each biological unit used as initial model

3frr

chain_id: B, source_name: PDB, initial_model_type: experimental modelIsolated IST1 monomer for each biological unit used as initial model
RefinementSpace: REAL / Protocol: OTHER

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