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- PDB-2e3i: Crystal structure of the CLIP-170 CAP-Gly domain 1 -

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Basic information

Entry
Database: PDB / ID: 2e3i
TitleCrystal structure of the CLIP-170 CAP-Gly domain 1
ComponentsRestin
KeywordsSTRUCTURAL PROTEIN / CAP-Gly / Cytoplasmic linker / tubulin binding
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 / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMaesaki, R. / Hakoshima, T.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Structural basis for tubulin recognition by cytoplasmic linker protein 170 and its autoinhibition
Authors: Mishima, M. / Maesaki, R. / Kasa, M. / Watanabe, T. / Fukata, M. / Kaibuchi, K. / Hakoshima, T.
History
DepositionNov 26, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 28, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 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

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Assembly

Deposited unit
A: Restin


Theoretical massNumber of molelcules
Total (without water)9,5051
Polymers9,5051
Non-polymers00
Water99155
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.298, 27.117, 30.508
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 9504.622 Da / Num. of mol.: 1 / Fragment: CAP-Gly domain 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CLIP-170 / Plasmid: pGEX6P / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P30622
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 1.94 Å3/Da / Density % sol: 36.66 %
Crystal growMethod: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Dec 15, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 5160 / % possible obs: 96.1 % / Rsym value: 0.041 / Net I/σ(I): 31.9
Reflection shellResolution: 2→2.1 Å / Mean I/σ(I) obs: 9.2 / Rsym value: 0.113 / % possible all: 91.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2E3H

2e3h


Resolution: 2→50 Å / σ(F): 2 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2585 255 -RANDOM
Rwork0.2352 ---
obs-5049 93 %-
Displacement parametersBiso mean: 17.6946 Å2
Baniso -1Baniso -2Baniso -3
1--0.63 Å20 Å20 Å2
2---1.927 Å20 Å2
3---2.557 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms612 0 0 55 667
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.4527
X-RAY DIFFRACTIONc_bond_d0.0127

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