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

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Basic information

Entry
Database: PDB / ID: 4qmi
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 / MOLECULAR REPLACEMENT / Resolution: 1.9 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
Revision 1.2Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytoskeleton-associated protein 5
B: Cytoskeleton-associated protein 5


Theoretical massNumber of molelcules
Total (without water)53,4682
Polymers53,4682
Non-polymers00
Water6,485360
1
A: Cytoskeleton-associated protein 5


Theoretical massNumber of molelcules
Total (without water)26,7341
Polymers26,7341
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cytoskeleton-associated protein 5


Theoretical massNumber of molelcules
Total (without water)26,7341
Polymers26,7341
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.418, 74.293, 93.684
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 Cytoskeleton-associated protein 5 / Colonic and hepatic tumor overexpressed gene protein / Ch-TOG


Mass: 26734.055 Da / Num. of mol.: 2 / 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) / Strain (production host): Bl21 De3 Plyss / References: UniProt: Q14008
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 360 / 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: 2.1 Å3/Da / Density % sol: 41.33 %
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 28% PEG 4000, 100 mM Tris pH 7.5, and 125 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-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 7, 2011
RadiationMonochromator: double crystal - liquid nitrogen cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Rmerge(I) obs: 0.082 / Rsym value: 0.082 / Net I/σ(I): 22.9
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.428 / Mean I/σ(I) obs: 4.7 / Rsym value: 0.428 / % possible all: 100

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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: MOLECULAR REPLACEMENT / Resolution: 1.9→48.67 Å / SU ML: 0.2 / σ(F): 1.34 / Phase error: 19.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2153 1998 5.57 %Random 10%
Rwork0.1745 ---
all0.1767 35863 --
obs0.1767 35863 99.29 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.851 Å2 / ksol: 0.372 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.7368 Å20 Å2-0 Å2
2--5.7872 Å20 Å2
3----3.0504 Å2
Refinement stepCycle: LAST / Resolution: 1.9→48.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3541 0 0 360 3901
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073595
X-RAY DIFFRACTIONf_angle_d1.0684849
X-RAY DIFFRACTIONf_dihedral_angle_d14.4431397
X-RAY DIFFRACTIONf_chiral_restr0.066562
X-RAY DIFFRACTIONf_plane_restr0.006618
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9002-1.94770.28491280.21022169X-RAY DIFFRACTION91
1.9477-2.00040.27831410.20522410X-RAY DIFFRACTION100
2.0004-2.05920.27841410.18192383X-RAY DIFFRACTION100
2.0592-2.12570.23591420.17162407X-RAY DIFFRACTION100
2.1257-2.20170.18861410.16252393X-RAY DIFFRACTION100
2.2017-2.28980.21361430.16532415X-RAY DIFFRACTION100
2.2898-2.3940.21351420.16642423X-RAY DIFFRACTION100
2.394-2.52020.22221440.16612414X-RAY DIFFRACTION100
2.5202-2.67810.23091420.17262423X-RAY DIFFRACTION100
2.6781-2.88490.20981440.17212429X-RAY DIFFRACTION100
2.8849-3.17510.19291440.16542443X-RAY DIFFRACTION100
3.1751-3.63450.1781450.15652464X-RAY DIFFRACTION100
3.6345-4.57850.18641470.16332489X-RAY DIFFRACTION100
4.5785-48.6860.24391540.2082603X-RAY DIFFRACTION100

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