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- PDB-3jc1: Electron cryo-microscopy of the IST1-CHMP1B ESCRT-III copolymer -

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Basic information

Entry
Database: PDB / ID: 3jc1
TitleElectron cryo-microscopy of the IST1-CHMP1B ESCRT-III copolymer
Components
  • Charged multivesicular body protein 1b
  • Increased Sodium Tolerance 1 (IST1)
KeywordsLIPID BINDING PROTEIN / ESCRT-III / IST1 / CHMP1B / membrane tubulation / helical filament
Function / homology
Function and homology information


MIT domain binding / 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 ...MIT domain binding / 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 / collateral sprouting / regulation of centrosome duplication / nuclear membrane reassembly / positive regulation of collateral sprouting / multivesicular body sorting pathway / Sealing of the nuclear envelope (NE) by ESCRT-III / membrane coat / midbody abscission / membrane fission / plasma membrane repair / 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 / intracellular protein localization / nuclear envelope / protein transport / 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: 4 Å
AuthorsMcCullough, J. / Clippinger, A.K. / Talledge, N. / Skowyra, M.L. / Saunders, M.G. / Naismith, T.V. / Colf, L.A. / Afonine, P. / Arthur, C. / Sundquist, W.I. ...McCullough, J. / Clippinger, A.K. / Talledge, N. / Skowyra, M.L. / Saunders, M.G. / Naismith, T.V. / Colf, L.A. / Afonine, P. / Arthur, C. / Sundquist, W.I. / Hanson, P.I. / Frost, A.
CitationJournal: Science / Year: 2015
Title: Structure and membrane remodeling activity of ESCRT-III helical polymers.
Authors: John McCullough / Amy K Clippinger / Nathaniel Talledge / Michael L Skowyra / Marissa G Saunders / Teresa V Naismith / Leremy A Colf / Pavel Afonine / Christopher Arthur / Wesley I Sundquist ...Authors: John McCullough / Amy K Clippinger / Nathaniel Talledge / Michael L Skowyra / Marissa G Saunders / Teresa V Naismith / Leremy A Colf / Pavel Afonine / Christopher Arthur / Wesley I Sundquist / Phyllis I Hanson / Adam Frost /
Abstract: The endosomal sorting complexes required for transport (ESCRT) proteins mediate fundamental membrane remodeling events that require stabilizing negative membrane curvature. These include endosomal ...The endosomal sorting complexes required for transport (ESCRT) proteins mediate fundamental membrane remodeling events that require stabilizing negative membrane curvature. These include endosomal intralumenal vesicle formation, HIV budding, nuclear envelope closure, and cytokinetic abscission. ESCRT-III subunits perform key roles in these processes by changing conformation and polymerizing into membrane-remodeling filaments. Here, we report the 4 angstrom resolution cryogenic electron microscopy reconstruction of a one-start, double-stranded helical copolymer composed of two different human ESCRT-III subunits, charged multivesicular body protein 1B (CHMP1B) and increased sodium tolerance 1 (IST1). The inner strand comprises "open" CHMP1B subunits that interlock in an elaborate domain-swapped architecture and is encircled by an outer strand of "closed" IST1 subunits. Unlike other ESCRT-III proteins, CHMP1B and IST1 polymers form external coats on positively curved membranes in vitro and in vivo. Our analysis suggests how common ESCRT-III filament architectures could stabilize different degrees and directions of membrane curvature.
History
DepositionNov 9, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2015Group: Database references
Revision 1.2Jul 18, 2018Group: Author supporting evidence / Data collection
Category: em_image_scans / em_single_particle_entity / em_software
Item: _em_software.image_processing_id / _em_software.name
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _struct_ref_seq_dif.details

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Structure visualization

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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
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Structure viewerMolecule:
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Assembly

Deposited unit
Aa: Increased Sodium Tolerance 1 (IST1)
Ab: Charged multivesicular body protein 1b
Ac: Increased Sodium Tolerance 1 (IST1)
Ad: Charged multivesicular body protein 1b
Ae: Increased Sodium Tolerance 1 (IST1)
Af: Charged multivesicular body protein 1b
Ag: Increased Sodium Tolerance 1 (IST1)
Ah: Charged multivesicular body protein 1b
Ai: Increased Sodium Tolerance 1 (IST1)
Aj: Charged multivesicular body protein 1b
Ak: Increased Sodium Tolerance 1 (IST1)
Al: Charged multivesicular body protein 1b
Am: Increased Sodium Tolerance 1 (IST1)
An: Charged multivesicular body protein 1b
Ao: Increased Sodium Tolerance 1 (IST1)
Ap: Charged multivesicular body protein 1b
Aq: Increased Sodium Tolerance 1 (IST1)
Ar: Charged multivesicular body protein 1b
As: Increased Sodium Tolerance 1 (IST1)
At: Charged multivesicular body protein 1b
Au: Increased Sodium Tolerance 1 (IST1)
Av: Charged multivesicular body protein 1b
Aw: Increased Sodium Tolerance 1 (IST1)
Ax: Charged multivesicular body protein 1b
Ay: Increased Sodium Tolerance 1 (IST1)
Az: Charged multivesicular body protein 1b
Ba: Increased Sodium Tolerance 1 (IST1)
Bb: Charged multivesicular body protein 1b
Bc: Increased Sodium Tolerance 1 (IST1)
Bd: Charged multivesicular body protein 1b
Be: Increased Sodium Tolerance 1 (IST1)
Bf: Charged multivesicular body protein 1b
Bg: Increased Sodium Tolerance 1 (IST1)
Bh: Charged multivesicular body protein 1b
Bi: Increased Sodium Tolerance 1 (IST1)
Bj: Charged multivesicular body protein 1b
Bk: Increased Sodium Tolerance 1 (IST1)
Bl: Charged multivesicular body protein 1b
Bm: Increased Sodium Tolerance 1 (IST1)
Bn: Charged multivesicular body protein 1b
Bo: Increased Sodium Tolerance 1 (IST1)
Bp: Charged multivesicular body protein 1b
Bq: Increased Sodium Tolerance 1 (IST1)
Br: Charged multivesicular body protein 1b
Bs: Increased Sodium Tolerance 1 (IST1)
Bt: Charged multivesicular body protein 1b
Bu: Increased Sodium Tolerance 1 (IST1)
Bv: Charged multivesicular body protein 1b
Bw: Increased Sodium Tolerance 1 (IST1)
Bx: Charged multivesicular body protein 1b
By: Increased Sodium Tolerance 1 (IST1)
Bz: Charged multivesicular body protein 1b
Ca: Increased Sodium Tolerance 1 (IST1)
Cb: Charged multivesicular body protein 1b
Cc: Increased Sodium Tolerance 1 (IST1)
Cd: Charged multivesicular body protein 1b
Ce: Increased Sodium Tolerance 1 (IST1)
Cf: Charged multivesicular body protein 1b
Cg: Increased Sodium Tolerance 1 (IST1)
Ch: Charged multivesicular body protein 1b
Ci: Increased Sodium Tolerance 1 (IST1)
Cj: Charged multivesicular body protein 1b
Ck: Increased Sodium Tolerance 1 (IST1)
Cl: Charged multivesicular body protein 1b
Cm: Increased Sodium Tolerance 1 (IST1)
Cn: Charged multivesicular body protein 1b
Co: Increased Sodium Tolerance 1 (IST1)
Cp: Charged multivesicular body protein 1b


Theoretical massNumber of molelcules
Total (without water)1,321,65668
Polymers1,321,65668
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
SymmetryHelical symmetry: (Circular symmetry: 1 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 34 / Rise per n subunits: 2.96 Å / Rotation per n subunits: 21.06 °)

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Components

#1: Protein ...
Increased Sodium Tolerance 1 (IST1) / hIST1 / Putative MAPK-activating protein PM28


Mass: 20934.514 Da / Num. of mol.: 34 / Fragment: N-terminal domain (UNP residues 6-187)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IST1, KIAA0174 / Plasmid: PGEX-2T-TEV / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) RIPL / References: UniProt: P53990
#2: 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 / Vps46-2 / hVps46-2


Mass: 17937.719 Da / Num. of mol.: 34 / Fragment: UNP residues 4-163
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: C18orf2, CHMP1B / Plasmid: PGEX-2T-TEV / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) RIPL / References: UniProt: Q7LBR1

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Experimental details

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Experiment

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

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Sample preparation

Component
IDNameTypeParent-ID
1IST1-NTD and CHMP1B double-stranded helical filamentCOMPLEX0
2IST11
3CHMP1B1
Buffer solutionName: 25 mM Tris, pH 8.0, 25 mM sodium chloride / pH: 8 / Details: 25 mM Tris, pH 8.0, 25 mM sodium chloride
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: Quantifoil R2/2 200 Mesh (glow-discharged) holey carbon grids
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 K
Details: Deposited 3.5 uL sample, blotted 3-6 seconds (0 mm offset), and plunged into liquid ethane (VITROBOT MARK III).
Method: Deposited 3.5 uL sample, blotted 3-6 seconds (0 mm offset)

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company /
Model: Tecnai F20 / Image courtesy: FEI Company
EM imaging

Date: Jun 1, 2013 / Electron source: FIELD EMISSION GUN / Illumination mode: FLOOD BEAM / Mode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 600 nm / Specimen-ID: 1

IDAccelerating voltage (kV)ModelCs (mm)Nominal magnification (X)Specimen holder type
1300FEI TITAN KRIOS259000FEI TITAN KRIOS AUTOGRID HOLDER
2200FEI TECNAI F20250000GATAN LIQUID NITROGEN
3300JEOL 3200FSC3.459000JEOL 3200FSC CRYOHOLDER
Image recordingElectron dose: 20 e/Å2 / Film or detector model: KODAK SO-163 FILM

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Processing

EM software
IDNameVersionCategory
1CTFFIND3CTF correction
2Cootmodel fitting
3MDFFmodel fitting
4NAMDmodel fitting
5Rosettamodel fitting
6UCSF Chimeramodel fitting
7EMAN23D reconstruction
8IHRSR3D reconstruction
9RELION3D reconstruction
10SPIDER3D reconstruction
CTF correctionDetails: CTFFIND3
Helical symmertyAngular rotation/subunit: 21.06 ° / Axial rise/subunit: 2.96 Å / Axial symmetry: C1
3D reconstructionMethod: Iterative Helical Real Space Reconstruction (IHRSR) / Resolution: 4 Å / Num. of particles: 188713 / Nominal pixel size: 1.22 Å / Actual pixel size: 1.22 Å
Details: Modified version of IHRSR algorithms as implemented in SPIDER was used to determine the helical symmetry. 3D reconstructions were performed using RELION.
Symmetry type: HELICAL
Atomic model buildingSpace: REAL / Target criteria: Molprobity validation, cross-correlation
Details: DETAILS--IST1 starting model (3FRR) was idealized in Rosetta, then relaxed while the structure was constrained. Iterative loop building was used.
Atomic model buildingPDB-ID: 3FRR

3frr


Accession code: 3FRR / Source name: PDB / Type: experimental model
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms92106 0 0 0 92106

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