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- PDB-4d8o: Crystal Structure of the ankyrin-B ZU5-ZU5-UPA-DD tandem -

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Basic information

Entry
Database: PDB / ID: 4d8o
TitleCrystal Structure of the ankyrin-B ZU5-ZU5-UPA-DD tandem
ComponentsAnkyrin-2
KeywordsPROTEIN BINDING / ZU5 / UPA / death domain / supramodule
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 / regulation of calcium ion transmembrane transporter activity / positive regulation of calcium ion transmembrane transporter activity / protein localization to M-band / positive regulation of potassium ion transmembrane transporter activity / T-tubule organization / SA node cell action potential / membrane depolarization during SA node cell action potential ...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 / protein localization to M-band / positive regulation of potassium ion transmembrane transporter activity / T-tubule organization / SA node cell action potential / membrane depolarization during SA node cell action potential / protein localization to organelle / paranodal junction assembly / phosphorylation-dependent protein binding / regulation of SA node cell action potential / regulation of atrial cardiac muscle cell action potential / positive regulation of cation channel activity / atrial cardiac muscle cell action potential / protein localization to endoplasmic reticulum / sarcoplasmic reticulum calcium ion transport / cytoskeletal anchor activity / atrial septum development / positive regulation of potassium ion transport / ventricular cardiac muscle cell action potential / costamere / response to methylmercury / regulation of release of sequestered calcium ion into cytosol / positive regulation of calcium ion transport / regulation of ventricular cardiac muscle cell membrane repolarization / M band / regulation of cardiac muscle cell contraction / regulation of cardiac muscle contraction by calcium ion signaling / protein localization to cell surface / Interaction between L1 and Ankyrins / A band / 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 / regulation of protein stability / protein localization / recycling endosome / structural constituent of cytoskeleton / sarcolemma / Z disc / intracellular calcium ion homeostasis / endocytosis / protein transport / protein-macromolecule adaptor activity / ATPase binding / basolateral plasma membrane / postsynaptic membrane / transmembrane transporter binding / lysosome / early endosome / cytoskeleton / protein stabilization / neuron projection / apical plasma membrane / positive regulation of gene expression / protein kinase binding / enzyme binding / mitochondrion / plasma membrane / cytosol
Similarity search - Function
Immunoglobulin-like - #2660 / Chondroitinase Ac; Chain A, domain 3 - #30 / Ankyrin, UPA domain / UPA domain / Chondroitinase Ac; Chain A, domain 3 / Domain present in ZO-1 and Unc5-like netrin receptors / ZU5 domain / ZU5 domain / ZU5 domain profile. / Death Domain, Fas ...Immunoglobulin-like - #2660 / Chondroitinase Ac; Chain A, domain 3 - #30 / Ankyrin, UPA domain / UPA domain / Chondroitinase Ac; Chain A, domain 3 / Domain present in ZO-1 and Unc5-like netrin receptors / ZU5 domain / ZU5 domain / ZU5 domain profile. / Death Domain, Fas / Death Domain, Fas / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / Ankyrin repeats (many copies) / 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 / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.203 Å
AuthorsWei, Z. / Wang, C. / Yu, C. / Zhang, M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Structure of the ZU5-ZU5-UPA-DD tandem of ankyrin-B reveals interaction surfaces necessary for ankyrin function
Authors: Wang, C. / Yu, C. / Ye, F. / Wei, Z. / Zhang, M.
History
DepositionJan 11, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 28, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2013Group: Database references
Revision 1.2Aug 16, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software
Revision 1.4Nov 8, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ankyrin-2


Theoretical massNumber of molelcules
Total (without water)66,1371
Polymers66,1371
Non-polymers00
Water1,820101
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)75.674, 80.056, 94.988
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: 66136.508 Da / Num. of mol.: 1 / Fragment: residues 966-1535
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ANK2 / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q01484
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsA PART OF RESIDUES 1211-1219 IN Q01484 HAS BEEN DELETED. THE SEQUENCE OF RESIDUES 1220-1535 IS FROM ...A PART OF RESIDUES 1211-1219 IN Q01484 HAS BEEN DELETED. THE SEQUENCE OF RESIDUES 1220-1535 IS FROM ISOFORM 2 OF ANKYRIN-2 (Q01484-2).

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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: 2.18 Å3/Da / Density % sol: 43.45 % / Mosaicity: 0.312 °
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 18% PEG3350, 0.2M ammonium acetate, 5% n-Octyl-beta-D-glucoside, pH 7.5, vapor diffusion, hanging drop, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.98 Å
DetectorDetector: CCD / Date: Dec 18, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 29634 / % possible obs: 99.4 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.085 / Χ2: 1.187 / Net I/σ(I): 11.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.2-2.247.30.48314580.9871100
2.24-2.287.30.46514551.0781100
2.28-2.327.30.42814611.051100
2.32-2.377.30.35314731.0671100
2.37-2.427.30.30314821.0871100
2.42-2.487.30.27914631.1631100
2.48-2.547.20.23414661.1541100
2.54-2.617.20.19214721.2341100
2.61-2.697.20.17814841.2521100
2.69-2.777.20.14814671.3331100
2.77-2.877.10.13314711.2351100
2.87-2.997.10.11914891.2851100
2.99-3.126.90.10214801.2541100
3.12-3.296.60.09315061.35199.9
3.29-3.496.40.08214811.2971100
3.49-3.7660.07414951.276199.9
3.76-4.145.90.06715101.18199.6
4.14-4.745.50.06115101.175199.1
4.74-5.975.80.0615251.158199.5
5.97-505.20.06114861.157190.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.6.4_486refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3F59, 3G5B, 2YVI

3f59

3g5b

2yvi


Resolution: 2.203→36.887 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.24 / σ(F): 0 / Phase error: 25.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.245 1457 5.13 %RANDOM
Rwork0.2078 ---
obs0.2096 28402 95.26 %-
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.329 Å2 / ksol: 0.375 e/Å3
Displacement parametersBiso max: 154.8 Å2 / Biso mean: 57.1454 Å2 / Biso min: 25.29 Å2
Baniso -1Baniso -2Baniso -3
1-15.1816 Å2-0 Å2-0 Å2
2---6.4946 Å2-0 Å2
3----8.6869 Å2
Refinement stepCycle: LAST / Resolution: 2.203→36.887 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3989 0 0 101 4090
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054076
X-RAY DIFFRACTIONf_angle_d0.8745527
X-RAY DIFFRACTIONf_chiral_restr0.059631
X-RAY DIFFRACTIONf_plane_restr0.004715
X-RAY DIFFRACTIONf_dihedral_angle_d13.5211509
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.203-2.28180.29881410.25362435257689
2.2818-2.37310.29091220.23962524264690
2.3731-2.48110.29741450.23522589273493
2.4811-2.61190.30351410.23322636277794
2.6119-2.77550.29041490.22842698284796
2.7755-2.98970.26571630.23312707287097
2.9897-3.29040.24881620.22182815297799
3.2904-3.76610.28951530.201628162969100
3.7661-4.74330.17271440.17532870301499
4.7433-36.89180.23091370.20522855299295
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)
11.34051.6989-1.28931.4262-1.84713.88550.1385-0.2502-0.06190.1088-0.1579-0.01610.32970.26740.02090.43990.01050.03670.3420.00920.3158-28.2016-22.309934.5137
21.57450.0550.53491.3897-1.03862.37050.0373-0.1119-0.1427-0.12510.02240.15970.0887-0.1679-0.03320.3111-0.0445-0.01650.2955-0.01450.3435-38.6041-13.90073.6514
32.17891.6010.15222.70710.98691.927-0.08840.0954-0.0274-0.28540.19-0.1811-0.3410.2359-0.10270.3377-0.04490.05120.31520.0110.2964-7.1032-0.543224.0622
41.91041.38170.52744.5912.27291.8036-0.19530.23470.21410.38470.29130.28170.46020.3209-0.04740.5062-0.00680.03840.4596-0.10920.44411.1842-15.962721.3993
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and resseq 964:1124A964 - 1124
2X-RAY DIFFRACTION2chain A and resseq 1125:1289A1125 - 1289
3X-RAY DIFFRACTION3chain A and resseq 1290:1423A1290 - 1423
4X-RAY DIFFRACTION4chain A and resseq 1452:1529A1452 - 1529

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