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- PDB-3frt: The structure of human CHMP3 (residues 8 - 222). -

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Basic information

Entry
Database: PDB / ID: 3frt
TitleThe structure of human CHMP3 (residues 8 - 222).
ComponentsCharged multivesicular body protein 3
KeywordsPROTEIN TRANSPORT / ESCRT / ESCRT-111 / CHMP / Ist1 / Coiled coil / Cytoplasm / Lipoprotein / Membrane / Myristate / Phosphoprotein / Transport
Function / homology
Function and homology information


regulation of endosome size / multivesicular body-lysosome fusion / amphisome membrane / suppression of viral release by host / vesicle fusion with vacuole / late endosome to lysosome transport / ESCRT III complex / kinetochore microtubule / endosome transport via multivesicular body sorting pathway / regulation of centrosome duplication ...regulation of endosome size / multivesicular body-lysosome fusion / amphisome membrane / suppression of viral release by host / vesicle fusion with vacuole / late endosome to lysosome transport / ESCRT III complex / kinetochore microtubule / endosome transport via multivesicular body sorting pathway / regulation of centrosome duplication / nuclear membrane reassembly / Sealing of the nuclear envelope (NE) by ESCRT-III / multivesicular body sorting pathway / 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 assembly / phosphatidylcholine binding / multivesicular body membrane / regulation of mitotic spindle assembly / Translation of Replicase and Assembly of the Replication Transcription Complex / regulation of early endosome to late endosome transport / molecular function inhibitor activity / mitotic metaphase chromosome alignment / Macroautophagy / nucleus organization / positive regulation of cytokinesis / ubiquitin-specific protease binding / viral budding via host ESCRT complex / viral release from host cell / autophagosome membrane / protein polymerization / autophagosome maturation / Pyroptosis / nuclear pore / phosphatidylinositol-4,5-bisphosphate binding / multivesicular body / Endosomal Sorting Complex Required For Transport (ESCRT) / viral budding from plasma membrane / HCMV Late Events / macroautophagy / Late endosomal microautophagy / Budding and maturation of HIV virion / kinetochore / autophagy / late endosome / protein transport / cytoplasmic vesicle / Translation of Replicase and Assembly of the Replication Transcription Complex / midbody / early endosome / lysosomal membrane / apoptotic process / extracellular exosome / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Charged multivesicular body protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4 Å
AuthorsSchubert, H.L. / McCullough, J. / Hill, C.P. / Sundquist, W.I.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2009
Title: Structural basis for ESCRT-III protein autoinhibition.
Authors: Bajorek, M. / Schubert, H.L. / McCullough, J. / Langelier, C. / Eckert, D.M. / Stubblefield, W.M. / Uter, N.T. / Myszka, D.G. / Hill, C.P. / Sundquist, W.I.
History
DepositionJan 8, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 30, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Charged multivesicular body protein 3
B: Charged multivesicular body protein 3


Theoretical massNumber of molelcules
Total (without water)49,4012
Polymers49,4012
Non-polymers00
Water00
1
A: Charged multivesicular body protein 3


Theoretical massNumber of molelcules
Total (without water)24,7011
Polymers24,7011
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Charged multivesicular body protein 3


Theoretical massNumber of molelcules
Total (without water)24,7011
Polymers24,7011
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.472, 131.514, 48.508
Angle α, β, γ (deg.)90.00, 108.06, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Charged multivesicular body protein 3 / Chromatin-modifying protein 3 / Vacuolar protein-sorting-associated protein 24 / hVps24 / ...Chromatin-modifying protein 3 / Vacuolar protein-sorting-associated protein 24 / hVps24 / Neuroendocrine differentiation factor


Mass: 24700.600 Da / Num. of mol.: 2 / Fragment: UNP residues 8-222
Source method: isolated from a genetically manipulated source
Details: N-term GST / Source: (gene. exp.) Homo sapiens (human) / Gene: CGI-149, CHMP3, NEDF, VPS24 / Plasmid: pGEX / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)codon+RIL / References: UniProt: Q9Y3E7

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45.06 %
Crystal growTemperature: 286 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 10-22% PEG 6000 0.1 M Hepes, pH 7.0-8.0, VAPOR DIFFUSION, SITTING DROP, temperature 286K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97607 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 27, 2008
Details: flat mirror (vertical), single crystal Si(iii) bent (horizonatal)
RadiationMonochromator: Side scattering bent cube-root I-beam single crystal; asymmetric cut 4.965 degs
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97607 Å / Relative weight: 1
ReflectionResolution: 4→30 Å / Num. obs: 2950 / % possible obs: 78.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 111 Å2 / Rmerge(I) obs: 0.16 / Rsym value: 0.185 / Net I/σ(I): 9.33
Reflection shellResolution: 4→4.14 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.439 / Mean I/σ(I) obs: 2.92 / Num. unique all: 164 / Rsym value: 0.259 / % possible all: 78.7

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Processing

Software
NameClassification
MAR345dtbdata collection
PHASERphasing
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2GD5

2gd5


Resolution: 4→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: rigid body only - against anisotropically adjusted Fs by PHASER.
RfactorNum. reflectionSelection details
Rfree0.436 126 5%
Rwork0.383 --
all0.388 2808 -
obs0.388 2808 -
Refinement stepCycle: LAST / Resolution: 4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2270 0 0 0 2270

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