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- PDB-6m3r: Crystal structure of AnkG/beta4-spectrin complex -

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Basic information

Entry
Database: PDB / ID: 6m3r
TitleCrystal structure of AnkG/beta4-spectrin complex
Components
  • Ankyrin-3
  • Spectrin beta chain
KeywordsSTRUCTURAL PROTEIN / PROTEIN BINDING
Function / homology
Function and homology information


Interaction between L1 and Ankyrins / regulation of protein targeting / positive regulation of sodium ion import across plasma membrane / 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 / NCAM signaling for neurite out-growth / protein localization to axon / spectrin ...Interaction between L1 and Ankyrins / regulation of protein targeting / positive regulation of sodium ion import across plasma membrane / 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 / NCAM signaling for neurite out-growth / protein localization to axon / spectrin / clustering of voltage-gated sodium channels / positive regulation of sodium ion transmembrane transporter activity / spectrin-associated cytoskeleton / establishment or maintenance of microtubule cytoskeleton polarity / regulation of potassium ion transport / COPI-mediated anterograde transport / magnesium ion homeostasis / positive regulation of membrane potential / central nervous system projection neuron axonogenesis / RAF/MAP kinase cascade / negative regulation of delayed rectifier potassium channel activity / plasma membrane organization / phosphorylation-dependent protein binding / positive regulation of cation channel activity / maintenance of protein location in cell / cell body fiber / cardiac conduction / positive regulation of homotypic cell-cell adhesion / paranode region of axon / positive regulation of sodium ion transport / Golgi to plasma membrane protein transport / axon hillock / negative regulation of endocytosis / actin filament capping / axon initial segment / costamere / cellular response to magnesium ion / anterograde axonal transport / positive regulation of multicellular organism growth / juxtaparanode region of axon / regulation of modification of postsynaptic structure / node of Ranvier / fertilization / adult walking behavior / ankyrin binding / negative regulation of heart rate / neuromuscular process / spectrin binding / neuromuscular junction development / axon development / transmission of nerve impulse / adult behavior / mitotic cytokinesis / response to immobilization stress / positive regulation of protein targeting to membrane / intercalated disc / bicellular tight junction / lateral plasma membrane / phosphatase binding / neuronal action potential / regulation of sodium ion transport / cytoskeletal protein binding / axon cytoplasm / T-tubule / axonogenesis / axon guidance / sarcoplasmic reticulum / basal plasma membrane / protein localization to plasma membrane / sensory perception of sound / establishment of protein localization / synapse organization / positive regulation of non-canonical NF-kappaB signal transduction / neuromuscular junction / sarcolemma / PML body / phospholipid binding / structural constituent of cytoskeleton / Z disc / nuclear matrix / intracellular protein localization / actin binding / protein-containing complex assembly / protein-macromolecule adaptor activity / basolateral plasma membrane / RNA polymerase II-specific DNA-binding transcription factor binding / transmembrane transporter binding / postsynaptic membrane / cytoskeleton / lysosome / postsynapse / neuron projection / postsynaptic density / cadherin binding / axon / neuronal cell body / synapse / dendrite / positive regulation of gene expression / regulation of transcription by RNA polymerase II
Similarity search - Function
Ankyrin-3, death domain / Pleckstrin homology domain, spectrin-type / Pleckstrin homology domain 9 / Pleckstrin homology domain / Spectrin, beta subunit / Ankyrin, UPA domain / UPA domain / : / Domain present in ZO-1 and Unc5-like netrin receptors / ZU5 domain ...Ankyrin-3, death domain / Pleckstrin homology domain, spectrin-type / Pleckstrin homology domain 9 / Pleckstrin homology domain / Spectrin, beta subunit / Ankyrin, UPA domain / UPA domain / : / Domain present in ZO-1 and Unc5-like netrin receptors / ZU5 domain / ZU5 domain / ZU5 domain profile. / Spectrin repeat / Spectrin repeat / Ankyrin repeats (many copies) / Spectrin/alpha-actinin / Spectrin repeats / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. / Actinin-type actin-binding domain, conserved site / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / Calponin homology domain / Calponin homology (CH) domain / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / Death-like domain superfamily / Ankyrin repeat / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / PH-like domain superfamily
Similarity search - Domain/homology
Spectrin beta chain / Ankyrin-3 / Spectrin beta chain
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.313 Å
AuthorsLi, J. / Chen, K. / Zhu, R. / Zhang, M.
Funding support Hong Kong, 1items
OrganizationGrant numberCountry
The University Grants Committee, Research Grants Council (RGC)16100517 Hong Kong
CitationJournal: J.Mol.Biol. / Year: 2020
Title: Structural Basis Underlying Strong Interactions between Ankyrins and Spectrins.
Authors: Li, J. / Chen, K. / Zhu, R. / Zhang, M.
History
DepositionMar 4, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: Ankyrin-3
F: Spectrin beta chain


Theoretical massNumber of molelcules
Total (without water)91,4382
Polymers91,4382
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1670 Å2
ΔGint-10 kcal/mol
Surface area37340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.591, 139.591, 211.317
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

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


Mass: 54560.531 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Ank3 / Production host: Escherichia coli (E. coli) / References: UniProt: O70511
#2: Protein Spectrin beta chain


Mass: 36877.199 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Sptbn4, Spnb4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8VIE5, UniProt: E9PX29*PLUS

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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: 6.5 Å3/Da / Density % sol: 81.08 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 8.5
Details: 0.8 M potassium sodium tartrate tetrahydrate, 0.1 M Tris, pH 8.5 and 0.5% w/v polyethylene glycol monomethyl ether 5,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 4.3→50 Å / Num. obs: 16538 / % possible obs: 99.9 % / Redundancy: 15.7 % / Biso Wilson estimate: 77.93 Å2 / Rmerge(I) obs: 0.159 / Rpim(I) all: 0.059 / Rrim(I) all: 0.142 / Χ2: 0.961 / Net I/σ(I): 2.2 / Num. measured all: 259971
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. unique obsCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
4.3-4.3716.18050.510.6021.013100
4.37-4.4515.88220.5970.5710.981100
4.45-4.5416.17890.6740.5370.975100
4.54-4.6315.88350.6990.4331.022100
4.63-4.7316.17890.7710.3640.988100
4.73-4.84168230.8070.3150.985100
4.84-4.9615.88210.8660.2460.9581000.994
4.96-5.116.18100.9120.2430.9961000.991
5.1-5.2516.38260.9090.1940.9721000.7950.819
5.25-5.4216.48130.9150.1830.9921000.7480.771
5.42-5.6116.28260.9390.1750.9871000.710.732
5.61-5.8315.98200.9430.1620.9631000.6510.672
5.83-6.115.98180.9650.1340.961000.5380.555
6.1-6.4215.68270.9620.1150.9521000.4580.472
6.42-6.8215.38400.9810.0820.9621000.3250.335
6.82-7.3514.88260.9880.0610.9441000.2350.243
7.35-8.0812.48310.9880.0410.93999.30.1420.148
8.08-9.2516.28450.9980.0210.95899.50.0850.088
9.25-11.6316.88580.9990.0140.89999.90.060.061
11.63-5014.89140.9990.0130.78199.50.0530.054

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4D8O, 3KBT

4d8o

3kbt


Resolution: 4.313→39.896 Å / SU ML: 0.74 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.9
RfactorNum. reflection% reflection
Rfree0.2952 763 4.83 %
Rwork0.2564 --
obs0.2583 15782 95.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 349.62 Å2 / Biso mean: 87.6322 Å2 / Biso min: 3.08 Å2
Refinement stepCycle: final / Resolution: 4.313→39.896 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4999 0 0 0 4999
Num. residues----711
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085091
X-RAY DIFFRACTIONf_angle_d1.316972
X-RAY DIFFRACTIONf_chiral_restr0.063857
X-RAY DIFFRACTIONf_plane_restr0.013904
X-RAY DIFFRACTIONf_dihedral_angle_d16.1163023
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
4.3133-4.64590.38061330.3291255782
4.6459-5.11260.34361560.27253068100
5.1126-5.85040.33031590.2743312499
5.8504-7.36330.32031600.2613312099
7.3633-39.8960.19161550.2008315096

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