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- PDB-3frv: Structure of Human CHMP3 (residues 1-150) -

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Basic information

Entry
Database: PDB / ID: 3frv
TitleStructure of Human CHMP3 (residues 1-150)
ComponentsCharged multivesicular body protein 3
KeywordsPROTEIN TRANSPORT / ESCRT / ESCRT-III / 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 / Translation of Replicase and Assembly of the Replication Transcription Complex / cytoplasmic vesicle / 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 / MOLECULAR REPLACEMENT / Resolution: 3.7 Å
AuthorsHill, C.P. / Schubert, H.L. / McCullough, J. / 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


Theoretical massNumber of molelcules
Total (without water)17,4091
Polymers17,4091
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)111.484, 111.484, 30.567
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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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: 17408.699 Da / Num. of mol.: 1 / Fragment: UNP residues 1 - 150
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CGI-149, CHMP3, NEDF, VPS24 / Plasmid: pGST / 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: 3.15 Å3/Da / Density % sol: 60.95 %
Crystal growTemperature: 286 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 16% PEG 3350, 100 mM HEPES, 200mM Proline, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 286K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 25, 2008 / Details: Verimax HR
RadiationMonochromator: verimax HR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 3.7→25 Å / Num. all: 2586 / Num. obs: 2451 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 101 Å2 / Rmerge(I) obs: 0.63 / Net I/σ(I): 18.3
Reflection shellResolution: 3.7→3.83 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.553 / Mean I/σ(I) obs: 2.2 / % possible all: 99.2

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Processing

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

2gd5


Resolution: 3.7→25 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: rigid body only - against anisotropically adjusted Fs by PHASER.
RfactorNum. reflectionSelection details
Rfree0.375 109 5%
Rwork0.435 --
obs0.41 2448 -
all-2448 -
Refinement stepCycle: LAST / Resolution: 3.7→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1053 0 0 0 1053

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