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- PDB-5vny: Crystal structure of DM14-3 domain of Lgd -

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Basic information

Entry
Database: PDB / ID: 5vny
TitleCrystal structure of DM14-3 domain of Lgd
ComponentsLethal (2) giant discs 1, isoform B
KeywordsENDOCYTOSIS / PROTEIN BINDING / ESCRT
Function / homology
Function and homology information


positive regulation of intralumenal vesicle formation / cytoplasmic side of apical plasma membrane / Sealing of the nuclear envelope (NE) by ESCRT-III / imaginal disc-derived wing vein morphogenesis / sensory organ precursor cell division / wing disc morphogenesis / compound eye development / female germ-line stem cell asymmetric division / phosphatidylinositol phosphate binding / sensory organ development ...positive regulation of intralumenal vesicle formation / cytoplasmic side of apical plasma membrane / Sealing of the nuclear envelope (NE) by ESCRT-III / imaginal disc-derived wing vein morphogenesis / sensory organ precursor cell division / wing disc morphogenesis / compound eye development / female germ-line stem cell asymmetric division / phosphatidylinositol phosphate binding / sensory organ development / endosome transport via multivesicular body sorting pathway / apicolateral plasma membrane / endosomal transport / negative regulation of Notch signaling pathway / mitotic cytokinesis / Notch signaling pathway / intracellular protein transport / DNA-binding transcription repressor activity, RNA polymerase II-specific / cell cortex / endosome membrane / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / regulation of transcription by RNA polymerase II / nucleus / cytoplasm / cytosol
Similarity search - Function
Domain of unknown function DM14 / Freud, C2 domain / Coiled-coil and C2 domain-containing protein 1 / Coiled-coil and C2 domain-containing protein 1, DM14 domain / Repeats in fly CG4713, worm Y37H9A.3 and human FLJ20241. / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain profile. / C2 domain superfamily
Similarity search - Domain/homology
Lethal (2) giant discs 1, isoform B / Coiled-coil and C2 domain-containing protein 1-like
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.101 Å
AuthorsMcMillan, B.J. / Blacklow, S.C.
CitationJournal: Cell Rep / Year: 2017
Title: Structural Basis for Regulation of ESCRT-III Complexes by Lgd.
Authors: McMillan, B.J. / Tibbe, C. / Drabek, A.A. / Seegar, T.C.M. / Blacklow, S.C. / Klein, T.
History
DepositionMay 1, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 2017Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lethal (2) giant discs 1, isoform B


Theoretical massNumber of molelcules
Total (without water)7,4261
Polymers7,4261
Non-polymers00
Water2,126118
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.670, 29.670, 139.110
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-578-

HOH

21A-589-

HOH

31A-612-

HOH

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Components

#1: Protein Lethal (2) giant discs 1, isoform B


Mass: 7426.284 Da / Num. of mol.: 1 / Fragment: DM14-3 domain (UNP residues 359-423)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: l(2)gd1, CG4713, Dmel_CG4713 / Production host: Escherichia coli (E. coli) / References: UniProt: M9NEZ0, UniProt: Q9VKJ9*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / Source method: isolated from a natural source / Formula: H2O

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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: 2.06 Å3/Da / Density % sol: 40.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 30% PEG2000 MME, Tris, pH 8.0

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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: Jun 19, 2015
RadiationMonochromator: Cryo-cooled double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.1→50 Å / Num. obs: 46405 / % possible obs: 96.4 % / Redundancy: 5.8 % / CC1/2: 0.998 / Rsym value: 0.073 / Net I/σ(I): 11.61
Reflection shellResolution: 1.1→1.13 Å / CC1/2: 0.608 / Rsym value: 0.962

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.101→34.778 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.99
RfactorNum. reflection% reflection
Rfree0.1782 3554 7.68 %
Rwork0.1697 --
obs0.1703 46256 96.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.101→34.778 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms514 0 0 118 632
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006524
X-RAY DIFFRACTIONf_angle_d0.897705
X-RAY DIFFRACTIONf_dihedral_angle_d17.431208
X-RAY DIFFRACTIONf_chiral_restr0.06772
X-RAY DIFFRACTIONf_plane_restr0.00895
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1007-1.11580.3373790.3307972X-RAY DIFFRACTION56
1.1158-1.13170.28661060.31461253X-RAY DIFFRACTION70
1.1317-1.14860.27731250.26631587X-RAY DIFFRACTION89
1.1486-1.16660.24031420.25991663X-RAY DIFFRACTION94
1.1666-1.18570.22171460.24451797X-RAY DIFFRACTION99
1.1857-1.20610.23321480.23121723X-RAY DIFFRACTION99
1.2061-1.22810.21571500.22221786X-RAY DIFFRACTION100
1.2281-1.25170.19561450.20781773X-RAY DIFFRACTION100
1.2517-1.27720.19331490.20791763X-RAY DIFFRACTION100
1.2772-1.3050.19611480.19761775X-RAY DIFFRACTION100
1.305-1.33540.20441470.19371746X-RAY DIFFRACTION100
1.3354-1.36880.19641450.19311766X-RAY DIFFRACTION100
1.3688-1.40580.18791530.19131816X-RAY DIFFRACTION100
1.4058-1.44710.20261560.18491752X-RAY DIFFRACTION100
1.4471-1.49380.1621450.17061770X-RAY DIFFRACTION100
1.4938-1.54720.18321500.16161795X-RAY DIFFRACTION100
1.5472-1.60920.17241430.15671757X-RAY DIFFRACTION100
1.6092-1.68240.15771490.151773X-RAY DIFFRACTION100
1.6824-1.77110.16921480.15021792X-RAY DIFFRACTION100
1.7711-1.88210.18331480.15491781X-RAY DIFFRACTION100
1.8821-2.02740.14761420.15261745X-RAY DIFFRACTION100
2.0274-2.23140.16811510.15721791X-RAY DIFFRACTION100
2.2314-2.55420.15491510.14611765X-RAY DIFFRACTION100
2.5542-3.21760.17851420.15781798X-RAY DIFFRACTION100
3.2176-34.79490.16941460.16291763X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 18.2458 Å / Origin y: 26.5643 Å / Origin z: 60.2038 Å
111213212223313233
T0.0991 Å20.0003 Å20.0021 Å2-0.1454 Å2-0.0126 Å2--0.1149 Å2
L0.0289 °20.0119 °20.0588 °2-0.0669 °2-0.0353 °2--0.1477 °2
S-0.0126 Å °0.0798 Å °0.028 Å °0.0034 Å °-0.0018 Å °0.0516 Å °-0.0413 Å °-0.0448 Å °0.0079 Å °
Refinement TLS groupSelection details: all

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