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- PDB-5j45: Crystal structure of Shrub, fly ortholog of SNF7/CHMP4B -

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Basic information

Entry
Database: PDB / ID: 5j45
TitleCrystal structure of Shrub, fly ortholog of SNF7/CHMP4B
ComponentsGH13992p
KeywordsTRANSPORT PROTEIN / ESCRT / polymerization / membrane
Function / homology
Function and homology information


Endosomal Sorting Complex Required For Transport (ESCRT) / Sealing of the nuclear envelope (NE) by ESCRT-III / fusome / Macroautophagy / contractile ring / female germ-line stem cell asymmetric division / ESCRT III complex / proximal dendrite / endosome transport via multivesicular body sorting pathway / late endosome to vacuole transport via multivesicular body sorting pathway ...Endosomal Sorting Complex Required For Transport (ESCRT) / Sealing of the nuclear envelope (NE) by ESCRT-III / fusome / Macroautophagy / contractile ring / female germ-line stem cell asymmetric division / ESCRT III complex / proximal dendrite / endosome transport via multivesicular body sorting pathway / late endosome to vacuole transport via multivesicular body sorting pathway / vesicle budding from membrane / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / dendrite morphogenesis / neuron remodeling / mitotic cytokinesis / multivesicular body / cytoplasmic side of plasma membrane / autophagy / midbody / symbiont entry into host cell / neuronal cell body
Similarity search - Function
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.758 Å
AuthorsMcMillan, B.J. / Blacklow, S.C.
CitationJournal: Cell Rep / Year: 2016
Title: Electrostatic Interactions between Elongated Monomers Drive Filamentation of Drosophila Shrub, a Metazoan ESCRT-III Protein.
Authors: McMillan, B.J. / Tibbe, C. / Jeon, H. / Drabek, A.A. / Klein, T. / Blacklow, S.C.
History
DepositionMar 31, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2016Group: Database references
Revision 1.2Aug 17, 2016Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GH13992p


Theoretical massNumber of molelcules
Total (without water)14,7551
Polymers14,7551
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)29.767, 29.767, 174.311
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein GH13992p / Shrub


Mass: 14754.847 Da / Num. of mol.: 1 / Fragment: UNP residues 18-143
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: shrb, Vps32, CG8055, Dmel_CG8055 / Production host: Escherichia coli (E. coli) / Variant (production host): BL21 PLysS / References: UniProt: Q8T0Q4

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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: 2.67 Å3/Da / Density % sol: 53.9 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 17% v/v PEG10K, 0.1 M NH4CH3CO2, and 100 mM Bis-Tris pH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.758→50 Å / Num. obs: 3869 / % possible obs: 98.1 % / Redundancy: 3.1 % / Biso Wilson estimate: 85.75 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 15.9
Reflection shellHighest resolution: 2.758 Å

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Processing

Software
NameVersionClassification
PHENIXdev_1951refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementResolution: 2.758→43.578 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 33.76
RfactorNum. reflection% reflection
Rfree0.2688 378 9.97 %
Rwork0.2161 --
obs0.2212 3792 97.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.758→43.578 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms890 0 0 0 890
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003892
X-RAY DIFFRACTIONf_angle_d0.5831188
X-RAY DIFFRACTIONf_dihedral_angle_d16.838363
X-RAY DIFFRACTIONf_chiral_restr0.029140
X-RAY DIFFRACTIONf_plane_restr0.002154
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7575-3.15640.34031270.31991093X-RAY DIFFRACTION94
3.1564-3.97640.31881230.25311155X-RAY DIFFRACTION99
3.9764-43.58320.23631280.18641166X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.3759-0.0502-2.51798.8149-0.63765.07490.65940.16791.93912.12710.98541.1379-1.98471.919-1.23210.72910.09210.22721.5153-0.0611.226644.817431.586811.4296
27.4271-0.0652-3.73253.5697-0.56446.29270.69810.37881.55910.498-0.361-0.1682-1.8968-0.4321-0.36280.64480.03060.08310.95780.18360.893961.039333.0018-2.0185
37.0255-0.9444-0.9112.76430.33884.4174-0.2255-0.6682-0.925-0.1132-0.0881-0.4696-0.23410.36040.34730.60.0642-0.04930.88550.07490.854671.173227.6879-8.9581
47.24532.6149-4.6859-1.5098-0.2486-1.05650.101-0.13220.60830.25790.1449-0.05020.1546-0.0895-0.2490.60810.05790.08131.52480.25251.008729.203823.08410.773
52.75460.91062.41842.20140.50136.95790.09822.0735-0.8067-1.37670.29660.06160.7882-0.7189-0.4710.98090.08070.17491.24260.01591.1351-4.619615.42923.6749
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 18:22)
2X-RAY DIFFRACTION2(chain A and resid 23:38)
3X-RAY DIFFRACTION3(chain A and resid 39:72)
4X-RAY DIFFRACTION4(chain A and resid 73:107)
5X-RAY DIFFRACTION5(chain A and resid 108:121)

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