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- PDB-6ei6: CC2D1B coordinates ESRCT-III activity during the mitotic reformat... -

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Basic information

Entry
Database: PDB / ID: 6ei6
TitleCC2D1B coordinates ESRCT-III activity during the mitotic reformation of the nuclear envelope
ComponentsCoiled-coil and C2 domain-containing protein 1-like
KeywordsCYTOSOLIC PROTEIN / ESCRT protein regulator / nuclear envelope reformation / polymerization
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
DI(HYDROXYETHYL)ETHER / Coiled-coil and C2 domain-containing protein 1-like
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.461 Å
AuthorsVentimiglia, L.N. / Cuesta-Geijo, M.A. / Martinelli, N. / Caballe, A. / Macheboeuf, P. / Miguet, N. / Parnham, I.M. / Olmos, Y. / Carlton, J.G. / Weissehorn, W. / martin-Serrano, J.
CitationJournal: Dev. Cell / Year: 2018
Title: CC2D1B Coordinates ESCRT-III Activity during the Mitotic Reformation of the Nuclear Envelope.
Authors: Ventimiglia, L.N. / Cuesta-Geijo, M.A. / Martinelli, N. / Caballe, A. / Macheboeuf, P. / Miguet, N. / Parnham, I.M. / Olmos, Y. / Carlton, J.G. / Weissenhorn, W. / Martin-Serrano, J.
History
DepositionSep 18, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 10, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 19, 2018Group: Data collection / Database references / Structure summary
Category: citation / citation_author / entity
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name / _entity.formula_weight

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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
B: Coiled-coil and C2 domain-containing protein 1-like
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,26210
Polymers62,4832
Non-polymers7798
Water2,954164
1
A: Coiled-coil and C2 domain-containing protein 1-like
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6365
Polymers31,2421
Non-polymers3944
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Coiled-coil and C2 domain-containing protein 1-like
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6265
Polymers31,2421
Non-polymers3844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)87.410, 54.050, 97.900
Angle α, β, γ (deg.)90.00, 99.52, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 31241.717 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: l(2)gd1, lgd, CG4713 / Plasmid: pProEx-Htb / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9VKJ9
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 3.83 Å3/Da / Density % sol: 67.9 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M Bis-Tris pH 6.5, 15-25% PEG 3500 Mme, 200 mM ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 9, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.46→59.594 Å / Num. obs: 33151 / % possible obs: 98.85 % / Redundancy: 3.5 % / CC1/2: 0.995 / Rmerge(I) obs: 0.072 / Net I/av σ(I): 12 / Net I/σ(I): 6
Reflection shellResolution: 2.46→2.59 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 3.6 / CC1/2: 0.88 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
MOSFLMdata reduction
SCALAdata scaling
Auto-Rickshawphasing
RefinementMethod to determine structure: SAD / Resolution: 2.461→59.594 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 26.79
RfactorNum. reflection% reflection
Rfree0.2475 1613 4.9 %
Rwork0.205 --
obs0.2072 32922 99.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.461→59.594 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3963 0 42 164 4169
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014065
X-RAY DIFFRACTIONf_angle_d1.2165472
X-RAY DIFFRACTIONf_dihedral_angle_d4.2492496
X-RAY DIFFRACTIONf_chiral_restr0.06603
X-RAY DIFFRACTIONf_plane_restr0.006705
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.461-2.53340.35871390.28482579X-RAY DIFFRACTION99
2.5334-2.61520.31931120.26642597X-RAY DIFFRACTION99
2.6152-2.70870.31021120.25152627X-RAY DIFFRACTION99
2.7087-2.81710.31061560.2492555X-RAY DIFFRACTION100
2.8171-2.94530.28941180.25532617X-RAY DIFFRACTION100
2.9453-3.10060.31221310.24762605X-RAY DIFFRACTION100
3.1006-3.29490.25671370.23132604X-RAY DIFFRACTION99
3.2949-3.54920.2871270.21252610X-RAY DIFFRACTION100
3.5492-3.90630.22691490.19192595X-RAY DIFFRACTION99
3.9063-4.47140.18051310.16832648X-RAY DIFFRACTION99
4.4714-5.63280.22961510.17222604X-RAY DIFFRACTION99
5.6328-59.61160.21381500.17442668X-RAY DIFFRACTION98

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