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- PDB-5vo5: Crystal structure of Lgd-Shrub complex, single chain fusion -

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Basic information

Entry
Database: PDB / ID: 5vo5
TitleCrystal structure of Lgd-Shrub complex, single chain fusion
ComponentsCoiled-coil and C2 domain-containing protein 1-like,GH13992p
KeywordsTRANSPORT PROTEIN / ESCRT
Function / homology
Function and homology information


positive regulation of intralumenal vesicle formation / cytoplasmic side of apical plasma membrane / Endosomal Sorting Complex Required For Transport (ESCRT) / Sealing of the nuclear envelope (NE) by ESCRT-III / imaginal disc-derived wing vein morphogenesis / sensory organ precursor cell division / fusome / Macroautophagy / wing disc morphogenesis / contractile ring ...positive regulation of intralumenal vesicle formation / cytoplasmic side of apical plasma membrane / Endosomal Sorting Complex Required For Transport (ESCRT) / Sealing of the nuclear envelope (NE) by ESCRT-III / imaginal disc-derived wing vein morphogenesis / sensory organ precursor cell division / fusome / Macroautophagy / wing disc morphogenesis / contractile ring / compound eye development / female germ-line stem cell asymmetric division / phosphatidylinositol phosphate binding / ESCRT III complex / sensory organ development / endosome transport via multivesicular body sorting pathway / late endosome to vacuole transport via multivesicular body sorting pathway / proximal dendrite / apicolateral plasma membrane / vesicle budding from membrane / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / endosomal transport / dendrite morphogenesis / neuron remodeling / mitotic cytokinesis / negative regulation of Notch signaling pathway / Notch signaling pathway / multivesicular body / intracellular protein transport / autophagy / DNA-binding transcription repressor activity, RNA polymerase II-specific / cytoplasmic side of plasma membrane / midbody / cell cortex / DNA-binding transcription factor activity, RNA polymerase II-specific / endosome membrane / RNA polymerase II cis-regulatory region sequence-specific DNA binding / symbiont entry into host cell / neuronal cell body / regulation of transcription by RNA polymerase II / nucleus / cytosol / cytoplasm
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. / Snf7 family / Snf7 / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain ...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. / Snf7 family / Snf7 / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain / C2 domain profile. / C2 domain superfamily
Similarity search - Domain/homology
Charged multivesicular body protein 4 / Coiled-coil and C2 domain-containing protein 1-like
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.004 Å
AuthorsMcMillan, B.J. / Seegar, T.C.M. / 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 2, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Coiled-coil and C2 domain-containing protein 1-like,GH13992p


Theoretical massNumber of molelcules
Total (without water)20,9071
Polymers20,9071
Non-polymers00
Water1,22568
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Coiled-coil and C2 domain-containing protein 1-like,GH13992p

A: Coiled-coil and C2 domain-containing protein 1-like,GH13992p


Theoretical massNumber of molelcules
Total (without water)41,8132
Polymers41,8132
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_657-x+1,y,-z+21
Buried area1470 Å2
ΔGint-13 kcal/mol
Surface area23290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.970, 26.990, 82.840
Angle α, β, γ (deg.)90.00, 125.95, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Coiled-coil and C2 domain-containing protein 1-like,GH13992p / Lethal giant disks protein / Shrub


Mass: 20906.725 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly)
Gene: l(2)gd1, lgd, CG4713, shrb, Vps32, CG8055, Dmel_CG8055
Production host: Escherichia coli (E. coli) / References: UniProt: Q9VKJ9, UniProt: Q8T0Q4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 2.62 Å3/Da / Density % sol: 53.02 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 18% PEG 3350 0.1 M sodium citrate pH 5.5 Cryopreserved using 20% glycerol, 25% PEG 3350, 0.1 M sodium citrate 5.4

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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: Feb 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.004→48.97 Å / Num. obs: 27084 / % possible obs: 97.36 % / Redundancy: 3.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.06595 / Net I/σ(I): 11.44
Reflection shellResolution: 2.004→2.076 Å / Redundancy: 3.6 % / Rmerge(I) obs: 1.549 / Mean I/σ(I) obs: 0.95 / Num. unique obs: 1428 / CC1/2: 0.365 / Rpim(I) all: 0.9336 / % possible all: 93.85

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5VNY, 5J45

5vny

5j45


Resolution: 2.004→48.967 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.44
RfactorNum. reflection% reflection
Rfree0.2688 2698 9.96 %
Rwork0.2404 --
obs0.2432 27084 95.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.004→48.967 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1408 0 0 68 1476
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0011420
X-RAY DIFFRACTIONf_angle_d0.3581899
X-RAY DIFFRACTIONf_dihedral_angle_d14.008910
X-RAY DIFFRACTIONf_chiral_restr0.03213
X-RAY DIFFRACTIONf_plane_restr0.002250
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0041-2.04060.37541310.37651192X-RAY DIFFRACTION88
2.0406-2.07980.39181360.36911262X-RAY DIFFRACTION91
2.0798-2.12230.37061440.36411313X-RAY DIFFRACTION99
2.1223-2.16840.38681420.34421284X-RAY DIFFRACTION97
2.1684-2.21880.3381450.33711277X-RAY DIFFRACTION93
2.2188-2.27430.36591440.32211272X-RAY DIFFRACTION93
2.2743-2.33580.36781370.30361261X-RAY DIFFRACTION94
2.3358-2.40460.38681490.30231306X-RAY DIFFRACTION97
2.4046-2.48220.29421420.27911287X-RAY DIFFRACTION94
2.4822-2.57090.30051450.26351275X-RAY DIFFRACTION98
2.5709-2.67380.31251490.28071344X-RAY DIFFRACTION96
2.6738-2.79550.2731410.26261258X-RAY DIFFRACTION96
2.7955-2.94280.21291380.25831293X-RAY DIFFRACTION95
2.9428-3.12720.27791380.25261256X-RAY DIFFRACTION93
3.1272-3.36860.2661460.24991319X-RAY DIFFRACTION97
3.3686-3.70750.23281430.20911300X-RAY DIFFRACTION98
3.7075-4.24370.24361360.19031284X-RAY DIFFRACTION95
4.2437-5.34560.25341470.19681323X-RAY DIFFRACTION95
5.3456-48.98150.21861450.20931280X-RAY DIFFRACTION96
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)
14.29051.1448-2.42881.9548-0.91093.2323-0.1181-2.5538-0.47450.5585-0.3852-0.17540.02691.98930.45510.51750.1208-0.03431.25110.25230.531323.93382.485716.0172
27.7145-3.5559-6.79245.06916.29069.4269-0.41760.555-0.69210.2383-0.24060.32021.4399-0.59150.62630.3901-0.0174-0.03950.2186-0.00460.44016.1942-1.90299.123
31.14420.09860.06721.2662-1.45216.05610.13950.2672-0.00340.191-0.0032-0.0581-1.34460.2444-0.10510.28340.0172-0.05030.28770.00620.317511.22580.578817.8226
44.4092.71182.28334.28263.12252.9828-0.56830.4616-0.2509-0.0288-0.47760.3405-1.5806-2.11350.93970.54050.2184-0.13990.8228-0.09490.61657.8694-4.51477.8448
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 76 )
2X-RAY DIFFRACTION2chain 'A' and (resid 77 through 112 )
3X-RAY DIFFRACTION3chain 'A' and (resid 113 through 174 )
4X-RAY DIFFRACTION4chain 'A' and (resid 175 through 190 )

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