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- PDB-7wek: Crystal structure of the mouse Wdr47 NTD in complex with the WBR ... -

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Basic information

Entry
Database: PDB / ID: 7wek
TitleCrystal structure of the mouse Wdr47 NTD in complex with the WBR motif form Camsap3.
Components
  • WBR motif form Calmodulin-regulated spectrin-associated protein 3
  • WD repeat-containing protein 47
KeywordsPROTEIN BINDING / LisH motif containing protein
Function / homology
Function and homology information


regulation of organelle organization / detection of hot stimulus involved in thermoception / zonula adherens maintenance / anterior commissure morphogenesis / microtubule minus-end / cerebral cortex radial glia-guided migration / protein transport along microtubule / microtubule anchoring / regulation of Golgi organization / microtubule minus-end binding ...regulation of organelle organization / detection of hot stimulus involved in thermoception / zonula adherens maintenance / anterior commissure morphogenesis / microtubule minus-end / cerebral cortex radial glia-guided migration / protein transport along microtubule / microtubule anchoring / regulation of Golgi organization / microtubule minus-end binding / establishment or maintenance of microtubule cytoskeleton polarity / cilium movement / epithelial cell-cell adhesion / zonula adherens / corpus callosum development / neuronal stem cell population maintenance / negative regulation of microtubule depolymerization / establishment of epithelial cell apical/basal polarity / embryo development ending in birth or egg hatching / neural precursor cell proliferation / regulation of focal adhesion assembly / motile cilium / spectrin binding / motor behavior / regulation of microtubule polymerization / axoneme / regulation of microtubule cytoskeleton organization / regulation of cell migration / adult locomotory behavior / locomotory behavior / brain development / cerebral cortex development / autophagy / microtubule cytoskeleton organization / neuron projection development / actin filament binding / microtubule cytoskeleton / growth cone / in utero embryonic development / microtubule / calmodulin binding / neuron projection / ciliary basal body / axon / neuronal cell body / dendrite / centrosome / protein-containing complex binding / cytoplasm
Similarity search - Function
WD repeat-containing protein 47 / 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 / : ...WD repeat-containing protein 47 / 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 / : / LisH-like dimerisation domain / Calmodulin-regulated spectrin-associated protein-like, Calponin-homology domain / CAMSAP CH domain / C-terminal to LisH motif. / CTLH, C-terminal LisH motif / C-terminal to LisH (CTLH) motif profile. / Lissencephaly type-1-like homology motif / LIS1 homology (LisH) motif profile. / LIS1 homology motif / PRC-barrel-like superfamily / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / WD domain, G-beta repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Calmodulin-regulated spectrin-associated protein 3 / WD repeat-containing protein 47
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.21 Å
AuthorsRen, J.Q. / Li, D. / Feng, W.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: Cell Rep / Year: 2022
Title: Intertwined Wdr47-NTD dimer recognizes a basic-helical motif in Camsap proteins for proper central-pair microtubule formation.
Authors: Ren, J. / Li, D. / Liu, J. / Liu, H. / Yan, X. / Zhu, X. / Feng, W.
History
DepositionDec 23, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 30, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: WD repeat-containing protein 47
B: WD repeat-containing protein 47
C: WBR motif form Calmodulin-regulated spectrin-associated protein 3
D: WBR motif form Calmodulin-regulated spectrin-associated protein 3


Theoretical massNumber of molelcules
Total (without water)73,5334
Polymers73,5334
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11920 Å2
ΔGint-99 kcal/mol
Surface area28280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.077, 105.318, 155.972
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein WD repeat-containing protein 47 / Neuronal enriched MAP interacting protein / Nemitin


Mass: 33550.934 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Wdr47, Kiaa0893 / Production host: Escherichia (bacteria) / References: UniProt: Q8CGF6
#2: Protein/peptide WBR motif form Calmodulin-regulated spectrin-associated protein 3 / Marshalin / Protein Nezha


Mass: 3215.610 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) / References: UniProt: Q80VC9

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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: 3.24 Å3/Da / Density % sol: 62.05 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1M Tris-HCl, 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 19, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.2→30 Å / Num. obs: 16169 / % possible obs: 99.8 % / Redundancy: 6.7 % / CC1/2: 0.994 / CC star: 0.999 / Net I/σ(I): 18.3
Reflection shellResolution: 3.2→3.31 Å / Mean I/σ(I) obs: 1.148 / Num. unique obs: 1569 / CC1/2: 0.664 / CC star: 0.893

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7WEJ

7wej


Resolution: 3.21→24.18 Å / SU ML: 0.48 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 34.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3135 1609 10 %
Rwork0.2712 14473 -
obs0.2754 16082 99.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 240.53 Å2 / Biso min: 28.94 Å2
Refinement stepCycle: final / Resolution: 3.21→24.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4227 0 0 0 4227
Num. residues----547
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.21-3.310.3473136121594
3.31-3.431451305100
3.43-3.570.35491440.34361300100
3.57-3.730.39211450.34731302100
3.73-3.930.331460.3151321100
4.17-4.490.30821460.25181320100
4.49-4.940.27091460.25671311100
4.94-5.650.32091480.2681330100
5.65-7.090.33341510.32211362100

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