[English] 日本語
Yorodumi
- PDB-7xce: Crystal structure of Ankyrin G in complex with neurofascin -

+
Open data


ID or keywords:

Loading...

-
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 / 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 / regulation of protein targeting / maintenance of protein location in plasma membrane / membrane assembly / protein localization to axon / clustering of voltage-gated sodium channels ...Schwann cell microvillus / 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 / regulation of protein targeting / 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 / positive regulation of sodium ion transmembrane transporter activity / protein localization to paranode region of axon / establishment or maintenance of microtubule cytoskeleton polarity / regulation of potassium ion transport / spectrin-associated cytoskeleton / magnesium ion homeostasis / paranodal junction assembly / phosphorylation-dependent protein binding / cell-cell adhesion mediator activity / positive regulation of membrane potential / protein localization to juxtaparanode region of axon / paranodal junction / plasma membrane organization / negative regulation of delayed rectifier potassium channel activity / positive regulation of cation channel activity / positive regulation of homotypic cell-cell adhesion / axon initial segment / maintenance of protein location in cell / Golgi to plasma membrane protein transport / paranode region of axon / positive regulation of sodium ion transport / peripheral nervous system development / negative regulation of endocytosis / node of Ranvier / costamere / anterograde axonal transport / cellular response to magnesium ion / Neutrophil degranulation / spectrin binding / neuromuscular junction development / axon development / transmission of nerve impulse / plasma membrane => GO:0005886 / neuronal action potential / mitotic cytokinesis / response to immobilization stress / positive regulation of protein targeting to membrane / intercalated disc / lateral plasma membrane / axon cytoplasm / T-tubule / myelination / cytoskeletal protein binding / axonogenesis / basal plasma membrane / sarcoplasmic reticulum / axon guidance / protein localization to plasma membrane / synapse organization / brain development / sarcolemma / neuromuscular junction / establishment of protein localization / structural constituent of cytoskeleton / cell-cell adhesion / Z disc / positive regulation of non-canonical NF-kappaB signal transduction / protein-macromolecule adaptor activity / postsynaptic membrane / basolateral plasma membrane / RNA polymerase II-specific DNA-binding transcription factor binding / transmembrane transporter binding / lysosome / cytoskeleton / neuron projection / cadherin binding / axon / protein domain specific binding / dendrite / synapse / positive regulation of gene expression / regulation of transcription by RNA polymerase II / cell surface / signal transduction / membrane / nucleus / plasma membrane
Similarity search - Function
Neurofascin / Ankyrin-3, death domain / Neurofascin/L1/NrCAM, C-terminal domain / Bravo-like intracellular region / Basigin-like / 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 / Basigin-like / Ankyrin, UPA domain / UPA domain / Domain present in ZO-1 and Unc5-like netrin receptors / ZU5 domain / ZU5 domain / ZU5 domain profile. / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / Ankyrin repeats (many copies) / Immunoglobulin / 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 / Ankyrin repeats (3 copies) / Fibronectin type-III domain profile. / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Fibronectin type III / Fibronectin type III superfamily / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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 / Sulfate


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 / Glycerol


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


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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more