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- PDB-2qk0: Structural Basis of Microtubule Plus End Tracking by XMAP215, CLI... -

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Basic information

Entry
Database: PDB / ID: 2qk0
TitleStructural Basis of Microtubule Plus End Tracking by XMAP215, CLIP-170 and EB1
ComponentsCAP-Gly domain-containing linker protein 1
KeywordsPROTEIN BINDING / CLIP-170 / Cap-Gly domain / microtubule plus end / +TIP
Function / homology
Function and homology information


microtubule plus-end binding / microtubule bundle formation / intermediate filament / RHO GTPases activate IQGAPs / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / cytoplasmic microtubule organization / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / positive regulation of microtubule polymerization / ruffle ...microtubule plus-end binding / microtubule bundle formation / intermediate filament / RHO GTPases activate IQGAPs / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / cytoplasmic microtubule organization / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / positive regulation of microtubule polymerization / ruffle / Resolution of Sister Chromatid Cohesion / tubulin binding / RHO GTPases Activate Formins / cytoplasmic vesicle membrane / kinetochore / Separation of Sister Chromatids / microtubule cytoskeleton / mitotic cell cycle / cell cortex / microtubule binding / microtubule / centrosome / zinc ion binding / identical protein binding / nucleus / cytosol
Similarity search - Function
CLIP1, zinc knuckle / CLIP1 zinc knuckle / CAP Gly-rich-like domain / CAP-Gly domain signature. / CAP Gly-rich domain / CAP Gly-rich domain superfamily / CAP-Gly domain / CAP-Gly domain profile. / CAP_GLY / SH3 type barrels. ...CLIP1, zinc knuckle / CLIP1 zinc knuckle / CAP Gly-rich-like domain / CAP-Gly domain signature. / CAP Gly-rich domain / CAP Gly-rich domain superfamily / CAP-Gly domain / CAP-Gly domain profile. / CAP_GLY / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
CAP-Gly domain-containing linker protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsSlep, K.C. / Vale, R.D.
CitationJournal: Mol.Cell / Year: 2007
Title: Structural Basis of Microtubule Plus End Tracking by XMAP215, CLIP-170, and EB1.
Authors: Slep, K.C. / Vale, R.D.
History
DepositionJul 9, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CAP-Gly domain-containing linker protein 1


Theoretical massNumber of molelcules
Total (without water)8,2431
Polymers8,2431
Non-polymers00
Water1,18966
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)27.242, 42.533, 51.806
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsCLIP-170 is a homodimer formed via a large central coiled coil region not included in this construct. This construct embodies only Cap-Gly domain 1.

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Components

#1: Protein CAP-Gly domain-containing linker protein 1 / Restin / Cytoplasmic linker protein 170 alpha-2 / CLIP-170 / Reed-Sternberg intermediate filament- ...Restin / Cytoplasmic linker protein 170 alpha-2 / CLIP-170 / Reed-Sternberg intermediate filament-associated protein / Cytoplasmic linker protein 1


Mass: 8243.236 Da / Num. of mol.: 1 / Fragment: Cap-Gly domain 1 / Mutation: L124M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CLIP1, CYLN1, RSN / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 pLysS / References: UniProt: P30622
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 1.82 Å3/Da / Density % sol: 32.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 1.2 M Sodium malonate, 100 mM Glycine, 1.1 mM Lanthanum chloride, Protein concentration 15 mg/ml, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.97964, 1.12713
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 23, 2002
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979641
21.127131
Reflection

Χ2: 1 / D res high: 2 Å / D res low: 50 Å

IDAv σ(I) over netINumberRmerge(I) obsNum. obs% possible obs
127.6320080.048789999.7
237.6288770.046785599.4
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squared
4.315098.910.0280.964
3.424.3199.610.0341.008
2.993.4210010.0440.964
2.712.9910010.0570.955
2.522.7110010.0641.004
2.372.5299.910.0671.046
2.252.3799.710.0641.004
2.152.2510010.0750.987
2.072.1598.910.0770.99
22.0710010.0921.026
4.315099.520.030.976
3.424.3198.720.0361.016
2.993.4299.720.0430.956
2.712.9999.620.0530.999
2.522.7199.920.0550.994
2.372.5299.120.0570.983
2.252.3799.220.0581.022
2.152.2599.720.0641.018
2.072.1598.520.0711.024
22.0799.920.0791.05
ReflectionResolution: 2→50 Å / Num. obs: 7855 / % possible obs: 99.4 % / Rmerge(I) obs: 0.046 / Rsym value: 4.6 / Χ2: 1.004 / Net I/σ(I): 37.6
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.079 / Mean I/σ(I) obs: 15 / Num. unique all: 810 / Rsym value: 7.9 / Χ2: 1.05 / % possible all: 99.9

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Phasing

PhasingMethod: MAD
Phasing dm shellResolution: 2→500.01 Å / Delta phi final: 0.213 / FOM : 0.229 / Reflection: 7778

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
CNSrefinement
REFMACrefinement
PDB_EXTRACT2data extraction
Blu-Icedata collection
RefinementMethod to determine structure: MAD / Resolution: 2→32.88 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.233 814 10.3 %Random 10%
Rwork0.173 ---
obs-7778 98.8 %-
Solvent computationBsol: 51.033 Å2
Displacement parametersBiso mean: 11.085 Å2
Baniso -1Baniso -2Baniso -3
1-1.007 Å20 Å20 Å2
2---0.46 Å20 Å2
3----0.548 Å2
Refinement stepCycle: LAST / Resolution: 2→32.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms572 0 0 66 638
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.2041.5
X-RAY DIFFRACTIONc_scbond_it2.2762
X-RAY DIFFRACTIONc_mcangle_it1.6372
X-RAY DIFFRACTIONc_scangle_it3.3252.5
LS refinement shellResolution: 2→2.07 Å
RfactorNum. reflection% reflection
Rfree0.213 92 -
Rwork0.162 --
obs-793 98 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param

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