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- PDB-5y4d: Crystal Structure of AnkB Ankyrin Repeats in Complex with AnkR/An... -

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Basic information

Entry
Database: PDB / ID: 5y4d
TitleCrystal Structure of AnkB Ankyrin Repeats in Complex with AnkR/AnkB Chimeric Autoinhibition Segment
ComponentsAnkyrin-1,Ankyrin-2,Ankyrin-2
KeywordsPROTEIN BINDING / ANK REPEAT / PROTEIN-PROTEIN INTERACTION / STRUCTURAL PROTEIN / AUTO-INHIBITION
Function / homology
Function and homology information


protein localization to T-tubule / atrial cardiac muscle cell to AV node cell communication / SA node cell to atrial cardiac muscle cell communication / protein localization to M-band / T-tubule organization / SA node cell action potential / membrane depolarization during SA node cell action potential / paranodal junction assembly / protein localization to organelle / sarcoplasmic reticulum calcium ion transport ...protein localization to T-tubule / atrial cardiac muscle cell to AV node cell communication / SA node cell to atrial cardiac muscle cell communication / protein localization to M-band / T-tubule organization / SA node cell action potential / membrane depolarization during SA node cell action potential / paranodal junction assembly / protein localization to organelle / sarcoplasmic reticulum calcium ion transport / positive regulation of potassium ion import across plasma membrane / potassium channel activator activity / A band / regulation of atrial cardiac muscle cell action potential / channel activator activity / phosphorylation-dependent protein binding / atrial cardiac muscle cell action potential / regulation of SA node cell action potential / protein localization to endoplasmic reticulum / cytoskeletal anchor activity / atrial septum development / costamere / ventricular cardiac muscle cell action potential / regulation of ventricular cardiac muscle cell membrane repolarization / response to methylmercury / positive regulation of calcium ion transport / regulation of release of sequestered calcium ion into cytosol / M band / regulation of cardiac muscle cell contraction / protein localization to cell surface / regulation of cardiac muscle contraction by calcium ion signaling / Interaction between L1 and Ankyrins / spectrin binding / regulation of heart rate by cardiac conduction / regulation of calcium ion transport / intercalated disc / regulation of cardiac muscle contraction / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / COPI-mediated anterograde transport / T-tubule / regulation of heart rate / protein localization to plasma membrane / recycling endosome / sarcolemma / regulation of protein stability / structural constituent of cytoskeleton / Z disc / endocytosis / intracellular calcium ion homeostasis / intracellular protein localization / protein transport / ATPase binding / protein-macromolecule adaptor activity / basolateral plasma membrane / transmembrane transporter binding / postsynaptic membrane / early endosome / cytoskeleton / lysosome / neuron projection / protein stabilization / apical plasma membrane / positive regulation of gene expression / protein kinase binding / enzyme binding / signal transduction / mitochondrion / membrane / plasma membrane / cytosol
Similarity search - Function
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) / Ankyrin repeat / Death domain profile. ...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) / Ankyrin repeat / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / Death-like domain superfamily / Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily
Similarity search - Domain/homology
Ankyrin 1, erythroid / Ankyrin-2
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsChen, K. / Li, J. / Wang, C. / Wei, Z. / Zhang, M.
CitationJournal: Elife / Year: 2017
Title: Autoinhibition of ankyrin-B/G membrane target bindings by intrinsically disordered segments from the tail regions.
Authors: Chen, K. / Li, J. / Wang, C. / Wei, Z. / Zhang, M.
History
DepositionAug 3, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 13, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Sep 17, 2025Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_validate_close_contact / struct_conn

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ankyrin-1,Ankyrin-2,Ankyrin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,98811
Polymers78,0271
Non-polymers96110
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Heterodimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1720 Å2
ΔGint-120 kcal/mol
Surface area29060 Å2
Unit cell
Length a, b, c (Å)179.787, 179.787, 227.098
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Ankyrin-1,Ankyrin-2,Ankyrin-2 / ANK-2 / Ankyrin-B / Brain ankyrin / Non-erythroid ankyrin


Mass: 78026.922 Da / Num. of mol.: 1
Fragment: UNP RESIDUES 1577-1613,UNP RESIDUES 3707-3718,UNP RESIDUES 28-693
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Homo sapiens (human)
Gene: Ank1, ANK2 / Production host: Escherichia coli (E. coli) / References: UniProt: D3Z5M4, UniProt: Q01484
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
Has protein modificationN

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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: 4.53 Å3/Da / Density % sol: 72.83 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 4 M ammonium acetate, 0.1 M Bis-Tris propane (pH 7.0)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 1, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 20949 / % possible obs: 97.6 % / Redundancy: 5.3 % / Biso Wilson estimate: 92.57 Å2 / Rmerge(I) obs: 0.103 / Χ2: 1.993 / Net I/σ(I): 9.3 / Num. measured all: 111753
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
3.3-3.365.50.72110251.436198.9
3.36-3.425.40.6510451.466198.9
3.42-3.485.40.51810521.535198.6
3.48-3.555.40.41610431.557198.4
3.55-3.635.40.32710401.545198.9
3.63-3.725.40.28710541.622198.5
3.72-3.815.40.24310651.797198.4
3.81-3.915.40.18510491.755198.3
3.91-4.035.40.1810401.813198.4
4.03-4.165.40.14710421.971198.1
4.16-4.315.40.12610482.011198.1
4.31-4.485.40.11210512.101197.9
4.48-4.685.40.10610442.066197.9
4.68-4.935.30.10310552.336197.7
4.93-5.245.30.10610452.442197.6
5.24-5.645.30.10710422.38197.1
5.64-6.215.30.09810552.178196.7
6.21-7.15.10.06610522.242196.2
7.1-8.945.10.04710452.836195.5
8.94-504.90.04310572.971191.8

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.22data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RLV

4rlv


Resolution: 3.3→42.806 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 0.9 / Phase error: 27.83
RfactorNum. reflection% reflection
Rfree0.229 1980 9.46 %
Rwork0.1834 --
obs0.1878 20932 97.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 194.51 Å2 / Biso mean: 102.7773 Å2 / Biso min: 44.73 Å2
Refinement stepCycle: final / Resolution: 3.3→42.806 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5019 0 50 0 5069
Biso mean--141.2 --
Num. residues----695
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075138
X-RAY DIFFRACTIONf_angle_d1.0117016
X-RAY DIFFRACTIONf_chiral_restr0.054859
X-RAY DIFFRACTIONf_plane_restr0.008910
X-RAY DIFFRACTIONf_dihedral_angle_d6.8893048
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.2978-3.38020.30641370.27171358149599
3.3802-3.47160.3151470.24911344149199
3.4716-3.57370.28661370.21651357149499
3.5737-3.6890.2591420.20651342148499
3.689-3.82070.24661400.18711362150298
3.8207-3.97360.24091430.18141348149198
3.9736-4.15430.24721430.17791352149598
4.1543-4.37310.22681360.16621355149198
4.3731-4.64680.19831410.16811345148698
4.6468-5.00510.24521440.1661365150998
5.0051-5.50780.25011430.19481344148797
5.5078-6.30270.25151390.2231365150497
6.3027-7.93240.22021450.17771350149596
7.9324-42.80920.17421430.1541365150893

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