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- PDB-5vjc: TOG-tubulin binding specificity promotes microtubule dynamics and... -

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Basic information

Entry
Database: PDB / ID: 5vjc
TitleTOG-tubulin binding specificity promotes microtubule dynamics and mitotic spindle formation
ComponentsProtein mini spindles
KeywordsCELL CYCLE / TOG / HEAT Repeat / Tubulin
Function / homology
Function and homology information


establishment or maintenance of neuroblast polarity / bicoid mRNA localization / microtubule plus end polymerase / pronuclear fusion / oocyte microtubule cytoskeleton organization / establishment or maintenance of microtubule cytoskeleton polarity / mitotic spindle elongation / microtubule plus-end / female meiotic nuclear division / positive regulation of microtubule nucleation ...establishment or maintenance of neuroblast polarity / bicoid mRNA localization / microtubule plus end polymerase / pronuclear fusion / oocyte microtubule cytoskeleton organization / establishment or maintenance of microtubule cytoskeleton polarity / mitotic spindle elongation / microtubule plus-end / female meiotic nuclear division / positive regulation of microtubule nucleation / microtubule plus-end binding / endoplasmic reticulum organization / oogenesis / microtubule polymerization / establishment of mitotic spindle orientation / centrosome duplication / cytoplasmic microtubule organization / tubulin binding / mitotic spindle organization / axon guidance / spindle / kinetochore / spindle pole / mitotic cell cycle / microtubule binding / centrosome / cytoplasm
Similarity search - Function
XMAP215 family / : / XMAP215/Dis1/CLASP, TOG domain / CLASP N-terminal domain / CLASP N terminal / TOG domain / TOG / HEAT repeat profile. / HEAT, type 2 / Leucine-rich Repeat Variant ...XMAP215 family / : / XMAP215/Dis1/CLASP, TOG domain / CLASP N-terminal domain / CLASP N terminal / TOG domain / TOG / HEAT repeat profile. / HEAT, type 2 / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Protein mini spindles
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsByrnes, A.E. / Slep, K.C.
Funding support United States, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM008570 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM094415 United States
March of DimesFY11-434 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)F31-GM115107 United States
American Heart Association15PRE25380004 United States
CitationJournal: J. Cell Biol. / Year: 2017
Title: TOG-tubulin binding specificity promotes microtubule dynamics and mitotic spindle formation.
Authors: Byrnes, A.E. / Slep, K.C.
History
DepositionApr 19, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 2017Provider: repository / Type: Initial release
Revision 1.1May 31, 2017Group: Data collection / Database references
Revision 1.2Jun 21, 2017Group: Database references / Refinement description / Category: citation / software
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _software.classification
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 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

Downloads & links

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Assembly

Deposited unit
A: Protein mini spindles
B: Protein mini spindles


Theoretical massNumber of molelcules
Total (without water)62,6132
Polymers62,6132
Non-polymers00
Water4,972276
1
A: Protein mini spindles


Theoretical massNumber of molelcules
Total (without water)31,3061
Polymers31,3061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Protein mini spindles


Theoretical massNumber of molelcules
Total (without water)31,3061
Polymers31,3061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.256, 80.035, 146.771
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Protein mini spindles


Mass: 31306.404 Da / Num. of mol.: 2 / Fragment: UNP residues 1141-1411
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: msps, CG5000 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9VEZ3
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 276 / 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: 2.5 Å3/Da / Density % sol: 50.76 % / Description: Needles
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 26% PEG 3350 and 0.15 M Sodium Tartrate Dibasic Dihydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03319 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Oct 17, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03319 Å / Relative weight: 1
ReflectionResolution: 2→29.3 Å / Num. obs: 43212 / % possible obs: 95.6 % / Redundancy: 2 % / CC1/2: 0.992 / Rmerge(I) obs: 0.028 / Net I/σ(I): 17.7
Reflection shellResolution: 2→2.07 Å / Redundancy: 2 % / Rmerge(I) obs: 0.401 / Mean I/σ(I) obs: 2 / Num. unique obs: 4251 / CC1/2: 0.73 / % possible all: 86

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHENIX1.9_1692phasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OF3

2of3


Resolution: 2→29.327 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 23.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2217 1858 4.5 %
Rwork0.1871 --
obs0.1887 41311 95.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→29.327 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4110 0 0 276 4386
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084177
X-RAY DIFFRACTIONf_angle_d0.9995634
X-RAY DIFFRACTIONf_dihedral_angle_d15.3061592
X-RAY DIFFRACTIONf_chiral_restr0.041648
X-RAY DIFFRACTIONf_plane_restr0.004720
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0001-2.05410.35041330.27162686X-RAY DIFFRACTION86
2.0541-2.11460.25821270.24252771X-RAY DIFFRACTION89
2.1146-2.18280.29371290.22972824X-RAY DIFFRACTION90
2.1828-2.26080.2781350.21012928X-RAY DIFFRACTION93
2.2608-2.35130.25471430.19592975X-RAY DIFFRACTION95
2.3513-2.45820.21691410.19993026X-RAY DIFFRACTION96
2.4582-2.58770.23411430.19073071X-RAY DIFFRACTION97
2.5877-2.74980.22741470.19563097X-RAY DIFFRACTION98
2.7498-2.96190.23951490.19543136X-RAY DIFFRACTION99
2.9619-3.25960.2511460.19393143X-RAY DIFFRACTION99
3.2596-3.73050.22781520.17733200X-RAY DIFFRACTION100
3.7305-4.69690.17211530.15783229X-RAY DIFFRACTION100
4.6969-29.32970.20281600.18033367X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 43.4976 Å / Origin y: 33.6188 Å / Origin z: 92.2321 Å
111213212223313233
T0.158 Å2-0.0163 Å2-0.0226 Å2-0.184 Å2-0.0259 Å2--0.1993 Å2
L0.6897 °2-0.0306 °2-0.2262 °2-0.5993 °20.0871 °2--0.5972 °2
S-0.0187 Å °-0.0872 Å °0.1557 Å °-0.032 Å °-0.0221 Å °0.0653 Å °0.0095 Å °-0.0284 Å °-0.0001 Å °
Refinement TLS groupSelection details: all

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