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- PDB-3eab: Crystal structure of Spastin MIT in complex with ESCRT III -

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Basic information

Entry
Database: PDB / ID: 3eab
TitleCrystal structure of Spastin MIT in complex with ESCRT III
Components
  • CHMP1b
  • Spastin
KeywordsCELL CYCLE / Spastin / CHMP / MIT / ESCRT / Alternative splicing / ATP-binding / Cytoplasm / Disease mutation / Hereditary spastic paraplegia / Nucleotide-binding / Nucleus / Polymorphism
Function / homology
Function and homology information


cytokinetic process / microtubule-severing ATPase / microtubule severing ATPase activity / microtubule severing / endoplasmic reticulum tubular network / positive regulation of microtubule depolymerization / MIT domain binding / multivesicular body-lysosome fusion / amphisome membrane / vesicle fusion with vacuole ...cytokinetic process / microtubule-severing ATPase / microtubule severing ATPase activity / microtubule severing / endoplasmic reticulum tubular network / positive regulation of microtubule depolymerization / 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 / membrane coat / regulation of centrosome duplication / nuclear membrane reassembly / mitotic 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 / anterograde axonal transport / multivesicular body membrane / exit from mitosis / microtubule bundle formation / protein hexamerization / regulation of mitotic spindle assembly / mitotic spindle disassembly / mitotic metaphase chromosome alignment / nucleus organization / axonal transport of mitochondrion / positive regulation of cytokinesis / viral budding via host ESCRT complex / mitotic cytokinesis / autophagosome membrane / autophagosome maturation / endoplasmic reticulum to Golgi vesicle-mediated transport / alpha-tubulin binding / nuclear pore / beta-tubulin binding / multivesicular body / lipid droplet / axon cytoplasm / axonogenesis / viral budding from plasma membrane / establishment of protein localization / protein homooligomerization / kinetochore / autophagy / spindle pole / protein transport / cytoplasmic vesicle / midbody / nuclear membrane / microtubule binding / microtubule / endosome membrane / endosome / protein domain specific binding / axon / lysosomal membrane / cell division / centrosome / endoplasmic reticulum membrane / protein-containing complex binding / perinuclear region of cytoplasm / ATP hydrolysis activity / extracellular exosome / nucleoplasm / ATP binding / identical protein binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #440 / Spastin, chordate / Spastin / Phosphotransferase system, lactose/cellobiose-type IIA subunit / Vps4 oligomerisation, C-terminal / MIT domain / Microtubule Interacting and Trafficking molecule domain / : / Vps4 C terminal oligomerisation domain / Snf7 family ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #440 / Spastin, chordate / Spastin / Phosphotransferase system, lactose/cellobiose-type IIA subunit / Vps4 oligomerisation, C-terminal / MIT domain / Microtubule Interacting and Trafficking molecule domain / : / Vps4 C terminal oligomerisation domain / Snf7 family / Snf7 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / Helix non-globular / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Special / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Mainly Alpha
Similarity search - Domain/homology
cDNA, FLJ94734, Homo sapiens CHMP1.5 protein (CHMP1.5), mRNA / Charged multivesicular body protein 1b / Spastin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsYang, D. / Rimanchi, N. / Renvoise, B. / Lippincott-Schwartz, J. / Blackstone, C. / Hurley, J.H.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2008
Title: Structural basis for midbody targeting of spastin by the ESCRT-III protein CHMP1B.
Authors: Yang, D. / Rismanchi, N. / Renvoise, B. / Lippincott-Schwartz, J. / Blackstone, C. / Hurley, J.H.
History
DepositionAug 25, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

Downloads & links

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Assembly

Deposited unit
A: Spastin
B: Spastin
C: Spastin
D: Spastin
E: Spastin
F: Spastin
G: CHMP1b
H: CHMP1b
I: CHMP1b
J: CHMP1b
K: CHMP1b
L: CHMP1b


Theoretical massNumber of molelcules
Total (without water)94,41512
Polymers94,41512
Non-polymers00
Water00
1
A: Spastin
G: CHMP1b


Theoretical massNumber of molelcules
Total (without water)15,7362
Polymers15,7362
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2110 Å2
ΔGint-9 kcal/mol
Surface area7730 Å2
MethodPISA
2
B: Spastin
H: CHMP1b


Theoretical massNumber of molelcules
Total (without water)15,7362
Polymers15,7362
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2140 Å2
ΔGint-8 kcal/mol
Surface area7450 Å2
MethodPISA
3
C: Spastin
I: CHMP1b


Theoretical massNumber of molelcules
Total (without water)15,7362
Polymers15,7362
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2050 Å2
ΔGint-9 kcal/mol
Surface area7800 Å2
MethodPISA
4
D: Spastin
J: CHMP1b


Theoretical massNumber of molelcules
Total (without water)15,7362
Polymers15,7362
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1940 Å2
ΔGint-5 kcal/mol
Surface area7540 Å2
MethodPISA
5
E: Spastin
K: CHMP1b


Theoretical massNumber of molelcules
Total (without water)15,7362
Polymers15,7362
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2100 Å2
ΔGint-7 kcal/mol
Surface area7320 Å2
MethodPISA
6
F: Spastin
L: CHMP1b


Theoretical massNumber of molelcules
Total (without water)15,7362
Polymers15,7362
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint-9 kcal/mol
Surface area7190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.967, 95.493, 100.360
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
Spastin


Mass: 10314.937 Da / Num. of mol.: 6 / Fragment: UNP residues 112 to 196
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SPAST, KIAA1083, SPG4 / Production host: Escherichia coli (E. coli) / Strain (production host): Rossetta / References: UniProt: Q9UBP0
#2: Protein/peptide
CHMP1b


Mass: 5420.950 Da / Num. of mol.: 6 / Fragment: UNP residues 145 to 194
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: B2RA72, UniProt: Q7LBR1*PLUS

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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: 3.76 Å3/Da / Density % sol: 67.28 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 10% PEG 2000 MME, 0.2 M Ammonia Sulfate, 0.1 M Sodium Acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97920, 0.97934, 0.97166
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Feb 4, 2008
RadiationMonochromator: Si 220 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97921
20.979341
30.971661
ReflectionResolution: 2.3→50 Å / Num. obs: 59615 / % possible obs: 90.9 % / Biso Wilson estimate: 24.5 Å2
Reflection shellResolution: 2.3→2.38 Å / % possible all: 53.3

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Processing

Software
NameClassification
SOLVEphasing
CNSrefinement
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.5→47.65 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 58202.66 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.268 2438 5.1 %RANDOM
Rwork0.232 ---
obs0.232 48059 93.7 %-
all-50497 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.8832 Å2 / ksol: 0.345367 e/Å3
Displacement parametersBiso mean: 53.7 Å2
Baniso -1Baniso -2Baniso -3
1-12.76 Å20 Å20 Å2
2--0.94 Å20 Å2
3----13.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.44 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.5→47.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5977 0 0 0 5977
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d21.1
X-RAY DIFFRACTIONc_improper_angle_d2.63
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.383 362 5.5 %
Rwork0.315 6247 -
obs--78.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water.param

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