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- PDB-7xce: Crystal structure of Ankyrin G in complex with neurofascin -

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Basic information

Entry
Database: PDB / ID: 7xce
TitleCrystal structure of Ankyrin G in complex with neurofascin
ComponentsNeurofascin,Ankyrin-3
KeywordsPROTEIN BINDING / CELL ADHESION / STRUCTURAL PROTEIN
Function / homology
Function and homology information


Schwann cell microvillus / regulation of protein targeting / positive regulation of sodium ion import across plasma membrane / Neurofascin interactions / positive regulation of cell communication by electrical coupling / positive regulation of membrane depolarization during cardiac muscle cell action potential / maintenance of protein location in plasma membrane / membrane assembly / protein localization to axon / clustering of voltage-gated sodium channels ...Schwann cell microvillus / regulation of protein targeting / positive regulation of sodium ion import across plasma membrane / Neurofascin interactions / positive regulation of cell communication by electrical coupling / positive regulation of membrane depolarization during cardiac muscle cell action potential / maintenance of protein location in plasma membrane / membrane assembly / protein localization to axon / clustering of voltage-gated sodium channels / protein binding involved in heterotypic cell-cell adhesion / protein localization to paranode region of axon / spectrin-associated cytoskeleton / establishment or maintenance of microtubule cytoskeleton polarity / regulation of potassium ion transport / paranodal junction assembly / magnesium ion homeostasis / protein localization to juxtaparanode region of axon / positive regulation of membrane potential / cell-cell adhesion mediator activity / negative regulation of delayed rectifier potassium channel activity / plasma membrane organization / paranodal junction / channel activator activity / phosphorylation-dependent protein binding / maintenance of protein location in cell / paranode region of axon / positive regulation of homotypic cell-cell adhesion / positive regulation of sodium ion transport / peripheral nervous system development / regulation of modification of postsynaptic structure / negative regulation of endocytosis / axon initial segment / costamere / anterograde axonal transport / cellular response to magnesium ion / Golgi to plasma membrane protein transport / node of Ranvier / Neutrophil degranulation / spectrin binding / neuromuscular junction development / axon development / transmission of nerve impulse / response to immobilization stress / mitotic cytokinesis / intercalated disc / sodium channel regulator activity / lateral plasma membrane / positive regulation of protein targeting to membrane / bicellular tight junction / neuronal action potential / cytoskeletal protein binding / myelination / T-tubule / axon cytoplasm / axonogenesis / axon guidance / basal plasma membrane / sarcoplasmic reticulum / protein localization to plasma membrane / establishment of protein localization / positive regulation of non-canonical NF-kappaB signal transduction / synapse organization / sarcolemma / cell-cell adhesion / brain development / neuromuscular junction / structural constituent of cytoskeleton / Z disc / protein-macromolecule adaptor activity / basolateral plasma membrane / transmembrane transporter binding / postsynaptic membrane / RNA polymerase II-specific DNA-binding transcription factor binding / cytoskeleton / lysosome / neuron projection / postsynapse / postsynaptic density / cadherin binding / protein domain specific binding / axon / synapse / dendrite / positive regulation of gene expression / regulation of transcription by RNA polymerase II / glutamatergic synapse / cell surface / signal transduction / nucleus / membrane / plasma membrane
Similarity search - Function
Neurofascin / Ankyrin-3, death domain / Neurofascin/L1/NrCAM, C-terminal domain / Bravo-like intracellular region / Ankyrin, UPA domain / UPA domain / : / Domain present in ZO-1 and Unc5-like netrin receptors / ZU5 domain / ZU5 domain ...Neurofascin / Ankyrin-3, death domain / Neurofascin/L1/NrCAM, C-terminal domain / Bravo-like intracellular region / Ankyrin, UPA domain / UPA domain / : / Domain present in ZO-1 and Unc5-like netrin receptors / ZU5 domain / ZU5 domain / ZU5 domain profile. / Ankyrin repeats (many copies) / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / Ankyrin repeat-containing domain / Immunoglobulin / Immunoglobulin domain / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Death-like domain superfamily / Ankyrin repeat / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Ankyrin repeats (3 copies) / Fibronectin type III / Fibronectin type III superfamily / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Mainly Alpha
Similarity search - Domain/homology
Ankyrin-3 / Neurofascin
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsHe, L. / Li, J. / Wang, C.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: J.Biol.Chem. / Year: 2022
Title: Crystal structure of Ankyrin-G in complex with a fragment of Neurofascin reveals binding mechanisms required for integrity of the axon initial segment.
Authors: He, L. / Jiang, W. / Li, J. / Wang, C.
History
DepositionMar 24, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 21, 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: Neurofascin,Ankyrin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8893
Polymers28,7011
Non-polymers1882
Water54030
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area440 Å2
ΔGint-18 kcal/mol
Surface area12230 Å2
Unit cell
Length a, b, c (Å)97.877, 97.877, 89.101
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Neurofascin,Ankyrin-3 / ANK-3 / Ankyrin-G


Mass: 28700.688 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The fusion protein of Neurofascin, Linker, and Ankyrin-3
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Nfasc, Ank3 / Production host: Escherichia coli (E. coli) / References: UniProt: P97685, UniProt: O70511
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.72 Å3/Da / Density % sol: 66.91 %
Crystal growTemperature: 289.2 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M ammonium acetate, 0.1 M Bis-Tris (pH 5.5), 17% w/v polyethylene glycol 10000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 15440 / % possible obs: 99.6 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.059 / Rrim(I) all: 0.137 / Χ2: 2.027 / Net I/σ(I): 8.1 / Num. measured all: 83059
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.5-2.545.60.9137600.7860.4191.0061.41799.9
2.54-2.595.60.7157480.8570.3280.7891.414100
2.59-2.645.60.6927650.870.3190.7631.455100
2.64-2.695.60.5937520.8930.2730.6541.421100
2.69-2.755.60.5117510.9340.2350.5641.55899.9
2.75-2.825.50.4717610.9610.2170.521.552100
2.82-2.895.50.4157600.9570.1920.4591.56199.9
2.89-2.965.50.3377590.9490.1560.3721.71499.9
2.96-3.055.50.2997560.9640.1380.331.79599.9
3.05-3.155.40.2367740.9720.110.2611.931100
3.15-3.265.40.1877580.9850.0880.2081.92100
3.26-3.395.40.167660.9850.0760.1782.09799.7
3.39-3.555.30.1217590.9910.0580.1342.0999.7
3.55-3.735.20.0997810.9910.0480.112.32199.7
3.73-3.975.10.087680.9940.0390.0892.33299.7
3.97-4.275.40.087850.9940.0380.0892.66599.7
4.27-4.75.40.0747850.9940.0350.0822.94599.6
4.7-5.385.30.0777860.9930.0370.0852.69899.5
5.38-6.785.20.0788040.9930.0380.0872.61199.1
6.78-504.70.068620.9940.0310.0683.20596.7

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Processing

Software
NameVersionClassification
PHENIXv1.18.2refinement
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5Y4E

5y4e


Resolution: 2.5→34.6 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 0.32 / Phase error: 22.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2333 744 4.83 %
Rwork0.1932 14667 -
obs0.1952 15411 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 115.15 Å2 / Biso mean: 50.9493 Å2 / Biso min: 28.42 Å2
Refinement stepCycle: final / Resolution: 2.5→34.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1801 0 11 30 1842
Biso mean--59.5 48.24 -
Num. residues----246
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.70.29741450.249728713016100
2.7-2.970.27651390.236728883027100
2.97-3.40.26951480.218929003048100
3.4-4.280.21451390.177629483087100
4.28-34.60.21081730.17133060323399

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