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- PDB-5lzn: -TIP microtubule-binding domain -

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Basic information

Entry
Database: PDB / ID: 5lzn
Title-TIP microtubule-binding domain
ComponentsCalmodulin-regulated spectrin-associated protein 3
KeywordsSTRUCTURAL PROTEIN / -TIP / microtubule
Function / homology
Function and homology information


regulation of organelle organization / zonula adherens maintenance / microtubule minus-end / microtubule minus-end binding / protein transport along microtubule / regulation of Golgi organization / microtubule anchoring / establishment or maintenance of microtubule cytoskeleton polarity / cilium movement / epithelial cell-cell adhesion ...regulation of organelle organization / zonula adherens maintenance / microtubule minus-end / microtubule minus-end binding / protein transport along microtubule / regulation of Golgi organization / microtubule anchoring / establishment or maintenance of microtubule cytoskeleton polarity / cilium movement / epithelial cell-cell adhesion / zonula adherens / negative regulation of microtubule depolymerization / establishment of epithelial cell apical/basal polarity / motile cilium / embryo development ending in birth or egg hatching / regulation of focal adhesion assembly / spectrin binding / regulation of microtubule polymerization / axoneme / cytoplasmic microtubule organization / regulation of microtubule cytoskeleton organization / regulation of cell migration / ciliary basal body / microtubule cytoskeleton organization / neuron projection development / microtubule cytoskeleton / actin filament binding / in utero embryonic development / calmodulin binding / centrosome / cytoplasm
Similarity search - Function
CKK domain / CAMSAP, spectrin and Ca2+/calmodulin-binding region / Spectrin-binding region of Ca2+-Calmodulin / CKK domain / Calmodulin-regulated spectrin-associated protein / CKK domain superfamily / Microtubule-binding calmodulin-regulated spectrin-associated / CKK domain profile. / Microtubule-binding calmodulin-regulated spectrin-associated / Calmodulin-regulated spectrin-associated protein-like, Calponin-homology domain ...CKK domain / CAMSAP, spectrin and Ca2+/calmodulin-binding region / Spectrin-binding region of Ca2+-Calmodulin / CKK domain / Calmodulin-regulated spectrin-associated protein / CKK domain superfamily / Microtubule-binding calmodulin-regulated spectrin-associated / CKK domain profile. / Microtubule-binding calmodulin-regulated spectrin-associated / Calmodulin-regulated spectrin-associated protein-like, Calponin-homology domain / CAMSAP CH domain / PRC-barrel-like superfamily / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / Ubiquitin-like (UB roll) / Roll / Alpha Beta
Similarity search - Domain/homology
Calmodulin-regulated spectrin-associated protein 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsStangier, M.M. / Steinmetz, M.O.
Funding support Switzerland, 2items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
SystemsX.ch Switzerland
CitationJournal: Nat Struct Mol Biol / Year: 2017
Title: A structural model for microtubule minus-end recognition and protection by CAMSAP proteins.
Authors: Joseph Atherton / Kai Jiang / Marcel M Stangier / Yanzhang Luo / Shasha Hua / Klaartje Houben / Jolien J E van Hooff / Agnel-Praveen Joseph / Guido Scarabelli / Barry J Grant / Anthony J ...Authors: Joseph Atherton / Kai Jiang / Marcel M Stangier / Yanzhang Luo / Shasha Hua / Klaartje Houben / Jolien J E van Hooff / Agnel-Praveen Joseph / Guido Scarabelli / Barry J Grant / Anthony J Roberts / Maya Topf / Michel O Steinmetz / Marc Baldus / Carolyn A Moores / Anna Akhmanova /
Abstract: CAMSAP and Patronin family members regulate microtubule minus-end stability and localization and thus organize noncentrosomal microtubule networks, which are essential for cell division, polarization ...CAMSAP and Patronin family members regulate microtubule minus-end stability and localization and thus organize noncentrosomal microtubule networks, which are essential for cell division, polarization and differentiation. Here, we found that the CAMSAP C-terminal CKK domain is widely present among eukaryotes and autonomously recognizes microtubule minus ends. Through a combination of structural approaches, we uncovered how mammalian CKK binds between two tubulin dimers at the interprotofilament interface on the outer microtubule surface. In vitro reconstitution assays combined with high-resolution fluorescence microscopy and cryo-electron tomography suggested that CKK preferentially associates with the transition zone between curved protofilaments and the regular microtubule lattice. We propose that minus-end-specific features of the interprotofilament interface at this site serve as the basis for CKK's minus-end preference. The steric clash between microtubule-bound CKK and kinesin motors explains how CKK protects microtubule minus ends against kinesin-13-induced depolymerization and thus controls the stability of free microtubule minus ends.
History
DepositionSep 30, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 4, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Nov 15, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.4Jan 17, 2024Group: 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: Calmodulin-regulated spectrin-associated protein 3


Theoretical massNumber of molelcules
Total (without water)13,5611
Polymers13,5611
Non-polymers00
Water1,20767
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.360, 96.360, 63.270
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-1318-

HOH

21A-1346-

HOH

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Components

#1: Protein Calmodulin-regulated spectrin-associated protein 3 / Protein Nezha


Mass: 13560.570 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Camsap3, Kiaa1543 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q80VC9
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 2.71 Å3/Da / Density % sol: 54.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 100 mM citric acid, pH 5, 1 M NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→68.14 Å / Num. obs: 29557 / % possible obs: 100 % / Redundancy: 25.5 % / Net I/σ(I): 23.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UGJ

1ugj


Resolution: 1.4→68.14 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.967 / SU B: 3.207 / SU ML: 0.051 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.051 / ESU R Free: 0.051 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1916 1469 5 %RANDOM
Rwork0.162 ---
obs0.1636 28088 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 140.22 Å2 / Biso mean: 44.873 Å2 / Biso min: 18.77 Å2
Baniso -1Baniso -2Baniso -3
1-1.34 Å2-0 Å20 Å2
2--1.34 Å2-0 Å2
3----2.69 Å2
Refinement stepCycle: final / Resolution: 1.4→68.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms894 0 0 67 961
Biso mean---45.5 -
Num. residues----111
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.019916
X-RAY DIFFRACTIONr_bond_other_d0.0020.02851
X-RAY DIFFRACTIONr_angle_refined_deg1.3251.9551233
X-RAY DIFFRACTIONr_angle_other_deg0.92331977
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3045111
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.91923.09542
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.2415169
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.29157
X-RAY DIFFRACTIONr_chiral_restr0.0870.2135
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021001
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02194
X-RAY DIFFRACTIONr_rigid_bond_restr2.15831767
X-RAY DIFFRACTIONr_sphericity_free41.676551
X-RAY DIFFRACTIONr_sphericity_bonded29.96651764
LS refinement shellResolution: 1.4→1.436 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.564 97 -
Rwork0.546 2047 -
all-2144 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -21.7898 Å / Origin y: -6.1609 Å / Origin z: -11.9588 Å
111213212223313233
T0.0013 Å2-0.0002 Å20.0017 Å2-0.0054 Å20.0029 Å2--0.0536 Å2
L0.3123 °2-0.1023 °20.1359 °2-0.2965 °20.1941 °2--0.276 °2
S0.0127 Å °0.0004 Å °-0.0502 Å °-0.0094 Å °-0.015 Å °0.0425 Å °0.0017 Å °-0.011 Å °0.0023 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1122 - 1134
2X-RAY DIFFRACTION1A1135 - 1155
3X-RAY DIFFRACTION1A1156 - 1236

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