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- PDB-4qmj: The XMAP215 family drives microtubule polymerization using a stru... -

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Basic information

Entry
Database: PDB / ID: 4qmj
TitleThe XMAP215 family drives microtubule polymerization using a structurally diverse TOG array
ComponentsCytoskeleton-associated protein 5
KeywordsPROTEIN BINDING / TOG DOMAIN
Function / homology
Function and homology information


microtubule plus end polymerase / establishment or maintenance of microtubule cytoskeleton polarity / RNA transport / positive regulation of microtubule nucleation / microtubule plus-end binding / centrosome cycle / microtubule depolymerization / spindle organization / microtubule polymerization / centrosome duplication ...microtubule plus end polymerase / establishment or maintenance of microtubule cytoskeleton polarity / RNA transport / positive regulation of microtubule nucleation / microtubule plus-end binding / centrosome cycle / microtubule depolymerization / spindle organization / microtubule polymerization / centrosome duplication / ribonucleoprotein complex binding / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / Resolution of Sister Chromatid Cohesion / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / mitotic spindle organization / RHO GTPases Activate Formins / kinetochore / spindle pole / Separation of Sister Chromatids / Regulation of PLK1 Activity at G2/M Transition / microtubule binding / cadherin binding / cell division / centrosome / nucleolus / protein-containing complex / membrane / plasma membrane / cytosol / 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
Cytoskeleton-associated protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.498 Å
AuthorsFox, J.C. / Howard, A.E. / Currie, J.D. / Rogers, S.L. / Slep, K.C.
CitationJournal: Mol.Biol.Cell / Year: 2014
Title: The XMAP215 family drives microtubule polymerization using a structurally diverse TOG array.
Authors: Fox, J.C. / Howard, A.E. / Currie, J.D. / Rogers, S.L. / Slep, K.C.
History
DepositionJun 16, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 3, 2014Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytoskeleton-associated protein 5


Theoretical massNumber of molelcules
Total (without water)27,1091
Polymers27,1091
Non-polymers00
Water86548
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.125, 79.125, 68.499
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Cytoskeleton-associated protein 5 / Colonic and hepatic tumor overexpressed gene protein / Ch-TOG


Mass: 27109.215 Da / Num. of mol.: 1 / Fragment: TOG domain 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: chTOG, CKAP5, KIAA0097 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / References: UniProt: Q14008
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 1.98 Å3/Da / Density % sol: 37.8 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10 mg/ml protein was added to an equal volume of a mother liquor containing 27.5% PEG 4000, 100 mM Tris pH 7.5, and 70 mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97926 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 21, 2011
RadiationMonochromator: double crystal - liquid nitrogen cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.498→50 Å / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Rsym value: 0.095 / Net I/σ(I): 19.9
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 3.3 / Rsym value: 0.497 / % possible all: 99.7

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Processing

Software
NameVersionClassification
SERGUIdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.498→27.975 Å / SU ML: 0.31 / σ(F): 0.26 / Phase error: 24.82 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2757 789 10 %Random 10%
Rwork0.2083 ---
all0.2151 7889 --
obs0.2151 7889 99.03 %-
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.759 Å2 / ksol: 0.37 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.4394 Å20 Å2-0 Å2
2--2.4394 Å20 Å2
3----4.8788 Å2
Refinement stepCycle: LAST / Resolution: 2.498→27.975 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1790 0 0 48 1838
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081817
X-RAY DIFFRACTIONf_angle_d1.2012452
X-RAY DIFFRACTIONf_dihedral_angle_d16.227706
X-RAY DIFFRACTIONf_chiral_restr0.079285
X-RAY DIFFRACTIONf_plane_restr0.006313
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4985-2.65490.29411250.20791127X-RAY DIFFRACTION97
2.6549-2.85970.30361290.23861165X-RAY DIFFRACTION99
2.8597-3.14710.33241280.24711144X-RAY DIFFRACTION99
3.1471-3.60170.28861320.22161185X-RAY DIFFRACTION100
3.6017-4.53460.25751330.17521202X-RAY DIFFRACTION100
4.5346-27.97670.24521420.20471277X-RAY DIFFRACTION100

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