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- PDB-6m3q: Crystal structure of AnkB/beta4-spectrin complex -

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Basic information

Entry
Database: PDB / ID: 6m3q
TitleCrystal structure of AnkB/beta4-spectrin complex
Components
  • Ankyrin-2
  • Spectrin beta chain
KeywordsSTRUCTURAL PROTEIN / PROTEIN BINDING
Function / homology
Function and homology information


Interaction between L1 and Ankyrins / protein localization to T-tubule / atrial cardiac muscle cell to AV node cell communication / SA node cell to atrial cardiac muscle cell communication / regulation of calcium ion transmembrane transporter activity / positive regulation of calcium ion transmembrane transporter activity / NCAM signaling for neurite out-growth / reproductive process / spectrin / protein localization to M-band ...Interaction between L1 and Ankyrins / protein localization to T-tubule / atrial cardiac muscle cell to AV node cell communication / SA node cell to atrial cardiac muscle cell communication / regulation of calcium ion transmembrane transporter activity / positive regulation of calcium ion transmembrane transporter activity / NCAM signaling for neurite out-growth / reproductive process / spectrin / protein localization to M-band / clustering of voltage-gated sodium channels / protein localization to endoplasmic reticulum / positive regulation of potassium ion transmembrane transporter activity / T-tubule organization / SA node cell action potential / regulation of peptidyl-serine phosphorylation / membrane depolarization during SA node cell action potential / COPI-mediated anterograde transport / protein localization to organelle / paranodal junction assembly / phosphorylation-dependent protein binding / RAF/MAP kinase cascade / central nervous system projection neuron axonogenesis / regulation of SA node cell action potential / regulation of atrial cardiac muscle cell action potential / cell body fiber / positive regulation of cation channel activity / atrial cardiac muscle cell action potential / axon initial segment / sarcoplasmic reticulum calcium ion transport / cardiac conduction / paranode region of axon / cytoskeletal anchor activity / atrial septum development / positive regulation of potassium ion transport / costamere / axon hillock / node of Ranvier / actin filament capping / ventricular cardiac muscle cell action potential / positive regulation of multicellular organism growth / regulation of cardiac muscle cell contraction / response to methylmercury / positive regulation of calcium ion transport / regulation of release of sequestered calcium ion into cytosol / regulation of ventricular cardiac muscle cell membrane repolarization / regulation of cardiac muscle contraction by calcium ion signaling / protein localization to cell surface / fertilization / M band / adult walking behavior / Interaction between L1 and Ankyrins / A band / negative regulation of heart rate / ankyrin binding / spectrin binding / adult behavior / cortical actin cytoskeleton / transmission of nerve impulse / regulation of heart rate by cardiac conduction / regulation of calcium ion transport / intercalated disc / regulation of cardiac muscle contraction / phosphatase binding / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / COPI-mediated anterograde transport / regulation of sodium ion transport / T-tubule / regulation of heart rate / axonogenesis / cell projection / protein localization to plasma membrane / sensory perception of sound / phospholipid binding / sarcolemma / regulation of protein stability / protein localization / structural constituent of cytoskeleton / intracellular calcium ion homeostasis / PML body / recycling endosome / Z disc / nuclear matrix / endocytosis / actin filament binding / protein-macromolecule adaptor activity / protein transport / cell junction / actin binding / ATPase binding / actin cytoskeleton organization / postsynaptic membrane / basolateral plasma membrane / transmembrane transporter binding / lysosome / protein stabilization / cytoskeleton / early endosome / neuron projection / apical plasma membrane
Similarity search - Function
Pleckstrin homology domain, spectrin-type / Pleckstrin homology domain 9 / Pleckstrin homology domain / Spectrin, beta subunit / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #60 / Ankyrin, UPA domain / UPA domain / Domain present in ZO-1 and Unc5-like netrin receptors / ZU5 domain / ZU5 domain ...Pleckstrin homology domain, spectrin-type / Pleckstrin homology domain 9 / Pleckstrin homology domain / Spectrin, beta subunit / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #60 / 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 / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. / Actinin-type actin-binding domain, conserved site / Spectrin/alpha-actinin / Spectrin repeats / Death domain profile. / Calponin homology domain / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / Calponin homology (CH) domain / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / Ankyrin repeats (many copies) / Death-like domain superfamily / Ankyrin repeat / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / 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 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Spectrin beta chain / Ankyrin-2 / Spectrin beta chain
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.436 Å
AuthorsLi, J. / Chen, K. / Zhu, R. / Zhang, M.
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-2
F: Spectrin beta chain


Theoretical massNumber of molelcules
Total (without water)90,1102
Polymers90,1102
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1940 Å2
ΔGint-11 kcal/mol
Surface area37470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.900, 110.485, 131.675
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 Ankyrin-2 / / ANK-2 / Ankyrin-B / Brain ankyrin / Non-erythroid ankyrin


Mass: 53232.395 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ANK2, ANKB / Production host: Escherichia coli (E. coli) / References: UniProt: Q01484
#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: 2.76 Å3/Da / Density % sol: 55.37 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 7.5
Details: 25% w/v pentaerythritol propoxylate 629 (17/8 PO/OH), 50 mM magnesium chloride and 0.1 M HEPES, pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97799 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97799 Å / Relative weight: 1
ReflectionResolution: 3.4→50 Å / Num. obs: 14141 / % possible obs: 99.5 % / Redundancy: 6.7 % / Biso Wilson estimate: 62.23 Å2 / Rmerge(I) obs: 0.255 / Rpim(I) all: 0.106 / Rrim(I) all: 0.277 / Χ2: 1.799 / Net I/σ(I): 4.4 / Num. measured all: 94782
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.4-3.466.20.7676860.6610.3250.8351.56698.4
3.46-3.526.10.6326800.6530.2710.691.58597.4
3.52-3.596.20.5446860.7310.2330.5931.92999.7
3.59-3.6660.5186910.7930.230.5692.11199.1
3.66-3.745.80.5396820.7270.2440.5941.74798.6
3.74-3.836.30.6556890.7860.2810.7151.61899.9
3.83-3.926.80.6817050.8620.2820.7381.647100
3.92-4.036.90.5746980.9010.2350.6211.766100
4.03-4.156.80.4897200.9010.2020.531.873100
4.15-4.286.90.3466820.9580.1420.3742.028100
4.28-4.446.90.3077090.9570.1260.3332.21799.9
4.44-4.6170.3026890.9610.1230.3272.01100
4.61-4.827.20.2417090.9780.0970.261.87100
4.82-5.087.20.2297100.9680.0920.2471.796100
5.08-5.47.20.247230.9790.0960.2591.675100
5.4-5.817.20.2456990.9720.0980.2641.572100
5.81-6.47.10.2367340.9670.0950.2551.586100
6.4-7.327.10.1627200.9870.0650.1751.708100
7.32-9.216.80.0887410.9960.0360.0951.911100
9.21-506.30.0477880.9980.020.0511.76598.1

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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: 3.436→35.357 Å / SU ML: 0.51 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.18
RfactorNum. reflection% reflection
Rfree0.3071 667 4.75 %
Rwork0.2522 --
obs0.2548 14056 98.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 242.21 Å2 / Biso mean: 63.1711 Å2 / Biso min: 20.27 Å2
Refinement stepCycle: final / Resolution: 3.436→35.357 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5445 0 0 0 5445
Num. residues----754
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055550
X-RAY DIFFRACTIONf_angle_d1.0647584
X-RAY DIFFRACTIONf_chiral_restr0.05915
X-RAY DIFFRACTIONf_plane_restr0.008984
X-RAY DIFFRACTIONf_dihedral_angle_d15.4973300
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.4361-3.70120.36241240.3098245592
3.7012-4.07320.37951410.2974265399
4.0732-4.66140.29591150.24432721100
4.6614-5.86850.26161410.22942709100
5.8685-35.3570.28011460.22292851100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.42661.3710.14484.2453-1.17222.968-0.4634-0.81720.0411-0.22270.3113-0.42870.041-0.45580.01920.35040.0899-0.11020.4187-0.07590.350228.204-24.622-8.921
23.5001-1.00330.54630.86710.17162.17180.02550.1505-0.50290.06390.048-0.10780.250.2063-0.0740.42940.03560.02260.29850.03830.208618.506-18.316-22.137
31.1070.00040.28061.19750.46533.5711-0.0566-0.28520.3320.02660.01070.1126-0.0381-0.57030.05170.27140.05840.03870.37410.02640.2792-3.947-5.919-20.652
40.7132-0.92-0.29716.00581.73771.84930.1524-0.35160.2735-0.2423-0.14590.2797-0.5255-0.0650.00540.75870.0821-0.04490.7177-0.04320.441123.71722.0887.923
52.6207-0.354-1.69090.71530.85881.6708-0.18320.1803-0.37840.0444-0.0252-1.11550.41630.1848-0.30650.48730.1582-0.01280.5483-0.09150.970651.804-27.035-12.909
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN E AND RESID 954:993 )E954 - 993
2X-RAY DIFFRACTION2( CHAIN E AND RESID 994:1157 )E994 - 1157
3X-RAY DIFFRACTION3( CHAIN E AND RESID 1158:1458 )E1158 - 1458
4X-RAY DIFFRACTION4( CHAIN F AND RESID 1584:1762 )F1584 - 1762
5X-RAY DIFFRACTION5( CHAIN F AND RESID 1763:1897 )F1763 - 1897

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