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- PDB-7s7j: Structure of Human SPASTIN-IST1 complex. -

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Basic information

Entry
Database: PDB / ID: 7s7j
TitleStructure of Human SPASTIN-IST1 complex.
Components
  • IST1 homolog
  • Spastin
KeywordsPROTEIN TRANSPORT / cytokinesis / MIT / AAA-ATPase
Function / homology
Function and homology information


cytokinetic process / microtubule-severing ATPase / microtubule severing ATPase activity / viral capsid secondary envelopment / microtubule severing / MIT domain binding / endoplasmic reticulum tubular network / positive regulation of microtubule depolymerization / abscission / ESCRT III complex disassembly ...cytokinetic process / microtubule-severing ATPase / microtubule severing ATPase activity / viral capsid secondary envelopment / microtubule severing / MIT domain binding / endoplasmic reticulum tubular network / positive regulation of microtubule depolymerization / abscission / ESCRT III complex disassembly / cytoskeleton-dependent cytokinesis / mitotic nuclear membrane reassembly / collateral sprouting / nuclear membrane reassembly / Sealing of the nuclear envelope (NE) by ESCRT-III / positive regulation of collateral sprouting / membrane fission / exit from mitosis / multivesicular body assembly / microtubule bundle formation / anterograde axonal transport / mitotic spindle disassembly / protein hexamerization / Flemming body / axonal transport of mitochondrion / beta-tubulin binding / positive regulation of cytokinesis / positive regulation of proteolysis / mitotic cytokinesis / alpha-tubulin binding / viral release from host cell / endoplasmic reticulum-Golgi intermediate compartment / metabolic process / endoplasmic reticulum to Golgi vesicle-mediated transport / axon cytoplasm / isomerase activity / lipid droplet / axonogenesis / establishment of protein localization / protein homooligomerization / protein localization / spindle pole / azurophil granule lumen / protein transport / nuclear envelope / midbody / cytoplasmic vesicle / microtubule binding / nuclear membrane / microtubule / endosome / cadherin binding / protein domain specific binding / axon / cell division / intracellular membrane-bounded organelle / centrosome / chromatin / Neutrophil degranulation / protein-containing complex binding / endoplasmic reticulum membrane / perinuclear region of cytoplasm / ATP hydrolysis activity / extracellular exosome / extracellular region / nucleoplasm / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Spastin, chordate / Spastin / Vacuolar protein sorting-associated protein Ist1 / Regulator of Vps4 activity in the MVB pathway / Vacuolar protein sorting-associated protein IST1-like / Vps4 oligomerisation, C-terminal / MIT domain / Microtubule Interacting and Trafficking molecule domain / Vps4 C terminal oligomerisation domain / AAA ATPase, AAA+ lid domain ...Spastin, chordate / Spastin / Vacuolar protein sorting-associated protein Ist1 / Regulator of Vps4 activity in the MVB pathway / Vacuolar protein sorting-associated protein IST1-like / Vps4 oligomerisation, C-terminal / MIT domain / Microtubule Interacting and Trafficking molecule domain / Vps4 C terminal oligomerisation domain / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / IST1 homolog / Spastin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å
AuthorsSkalicky, J.J. / Sundquist, W.I.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM112080-01 United States
CitationJournal: Elife / Year: 2022
Title: Comprehensive analysis of the human ESCRT-III-MIT domain interactome reveals new cofactors for cytokinetic abscission.
Authors: Wenzel, D.M. / Mackay, D.R. / Skalicky, J.J. / Paine, E.L. / Miller, M.S. / Ullman, K.S. / Sundquist, W.I.
History
DepositionSep 16, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Spastin
B: IST1 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9356
Polymers12,5152
Non-polymers4204
Water2,018112
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance, NMR chemical shift mapping Fluorescense Polarization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2160 Å2
ΔGint-16 kcal/mol
Surface area6620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.614, 79.614, 36.331
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41
Space group name HallI4bw
Symmetry operation#1: x,y,z
#2: -y+1/2,x,z+3/4
#3: y+1/2,-x,z+3/4
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: -y+1,x+1/2,z+5/4
#7: y+1,-x+1/2,z+5/4
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11B-515-

HOH

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein Spastin / / Spastic paraplegia 4 protein


Mass: 9779.303 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SPAST, ADPSP, FSP2, KIAA1083, SPG4 / Plasmid: pCA528 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UBP0, microtubule-severing ATPase
#2: Protein/peptide IST1 homolog / hIST1 / Putative MAPK-activating protein PM28


Mass: 2735.975 Da / Num. of mol.: 1 / Fragment: UNP residues 342-364 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P53990

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Non-polymers , 5 types, 116 molecules

#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 112 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.39 Å3/Da / Density % sol: 48.55 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 40% v/v PEG 300, 100 mM Sodium cacodylate / Hydrochloric acid pH=6.5, 200 mM Calcium Acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.97946 Å
DetectorType: CS-PAD CXI-1 / Detector: PIXEL / Date: Mar 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.15→33.05 Å / Num. obs: 74704 / % possible obs: 94.18 % / Redundancy: 13.6 % / Biso Wilson estimate: 10.39 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.029 / Rrim(I) all: 0.107 / Net I/σ(I): 16.4
Reflection shellResolution: 1.15→1.17 Å / Redundancy: 12.3 % / Rmerge(I) obs: 1.647 / Mean I/σ(I) obs: 4 / Num. unique obs: 1425 / CC1/2: 0.865 / Χ2: 0.47 / % possible all: 72.2

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XDSdata scaling
PHENIX1.17.1_3660phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EAB

3eab


Resolution: 1.15→33.05 Å / SU ML: 0.0854 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.0478
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1572 3893 5.21 %
Rwork0.1486 70810 -
obs0.1491 74703 94.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.12 Å2
Refinement stepCycle: LAST / Resolution: 1.15→33.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms843 0 25 112 980
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071892
X-RAY DIFFRACTIONf_angle_d0.90751181
X-RAY DIFFRACTIONf_chiral_restr0.0561125
X-RAY DIFFRACTIONf_plane_restr0.0048152
X-RAY DIFFRACTIONf_dihedral_angle_d14.7277370
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.15-1.160.20311010.22591886X-RAY DIFFRACTION69.28
1.16-1.180.19251280.20422220X-RAY DIFFRACTION82.73
1.18-1.190.21851400.19422494X-RAY DIFFRACTION93.6
1.19-1.210.18441410.20182538X-RAY DIFFRACTION93.02
1.21-1.230.19581330.18892537X-RAY DIFFRACTION94.85
1.23-1.250.21471340.18512469X-RAY DIFFRACTION93.26
1.25-1.270.17021500.18112586X-RAY DIFFRACTION94.97
1.27-1.290.19211380.17692564X-RAY DIFFRACTION94.67
1.29-1.310.18791340.19432370X-RAY DIFFRACTION89.94
1.31-1.330.1891380.16582519X-RAY DIFFRACTION95.51
1.33-1.360.17941420.16182559X-RAY DIFFRACTION94.34
1.36-1.390.14551420.15812590X-RAY DIFFRACTION96.2
1.39-1.420.17371380.15222525X-RAY DIFFRACTION95.14
1.42-1.450.14571370.15752602X-RAY DIFFRACTION95.97
1.45-1.490.18531360.14942554X-RAY DIFFRACTION96.14
1.49-1.530.14751430.15292529X-RAY DIFFRACTION93.26
1.53-1.570.17631400.14642578X-RAY DIFFRACTION95.97
1.57-1.620.1271460.14082584X-RAY DIFFRACTION97.43
1.62-1.680.14931440.13812608X-RAY DIFFRACTION97.18
1.68-1.750.13261440.13662627X-RAY DIFFRACTION96.55
1.75-1.830.17391480.1352622X-RAY DIFFRACTION97.43
1.83-1.920.13331220.13762499X-RAY DIFFRACTION93.14
1.92-2.040.13581450.13572674X-RAY DIFFRACTION98.46
2.04-2.20.14381460.12782595X-RAY DIFFRACTION98.77
2.2-2.420.14091520.13182633X-RAY DIFFRACTION98.41
2.42-2.770.16281340.14052573X-RAY DIFFRACTION95.28
2.77-3.490.17241430.15042673X-RAY DIFFRACTION99.4
3.49-33.050.14721540.14892602X-RAY DIFFRACTION97.08
Refinement TLS params.Method: refined / Origin x: 10.109030952 Å / Origin y: 6.39695215232 Å / Origin z: 3.52068011107 Å
111213212223313233
T0.0493200529798 Å2-0.0104137232665 Å20.0043240693062 Å2-0.0485373520616 Å2-0.000925893561402 Å2--0.0735757832151 Å2
L2.06968115299 °2-0.237544652625 °20.113120317699 °2-1.86982191999 °2-0.212376243702 °2--1.41971088212 °2
S-0.0219840108965 Å °-0.0355577817924 Å °-0.100654540876 Å °0.0086124561455 Å °0.0263938337374 Å °0.00110388075118 Å °0.0457666473318 Å °-0.00642634069108 Å °-0.0125257770535 Å °
Refinement TLS groupSelection details: all

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