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- PDB-4rly: Crystal Structure of AnkB Ankyrin Repeats (R1-R9) in Complex with... -

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Basic information

Entry
Database: PDB / ID: 4rly
TitleCrystal Structure of AnkB Ankyrin Repeats (R1-R9) in Complex with Nav1.2 Ankyrin Binding Domain
ComponentsNav1.2 - AnkB chimera
KeywordsSTRUCTURAL PROTEIN / ANK Repeat / Protein-protein interaction
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 / : / : / positive regulation of potassium ion transmembrane transporter activity / protein localization to M-band / 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 / : / : / positive regulation of potassium ion transmembrane transporter activity / protein localization to M-band / T-tubule organization / SA node cell action potential / membrane depolarization during SA node cell action potential / protein localization to organelle / paranodal junction assembly / sarcoplasmic reticulum calcium ion transport / regulation of atrial cardiac muscle cell action potential / atrial cardiac muscle cell action potential / phosphorylation-dependent protein binding / positive regulation of cation channel activity / intrinsic apoptotic signaling pathway in response to osmotic stress / nerve development / regulation of SA node cell action potential / protein localization to endoplasmic reticulum / cytoskeletal anchor activity / paranode region of axon / atrial septum development / dentate gyrus development / costamere / positive regulation of potassium ion transport / ventricular cardiac muscle cell action potential / response to methylmercury / cardiac muscle cell action potential involved in contraction / positive regulation of calcium ion transport / regulation of release of sequestered calcium ion into cytosol / regulation of ventricular cardiac muscle cell membrane repolarization / node of Ranvier / voltage-gated sodium channel complex / regulation of cardiac muscle cell contraction / protein localization to cell surface / M band / A band / Interaction between L1 and Ankyrins / regulation of cardiac muscle contraction by calcium ion signaling / voltage-gated sodium channel activity / sodium ion transport / spectrin binding / Phase 0 - rapid depolarisation / 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 / neuronal action potential / COPI-mediated anterograde transport / T-tubule / myelination / sodium ion transmembrane transport / regulation of heart rate / protein localization to plasma membrane / determination of adult lifespan / regulation of protein stability / sarcolemma / recycling endosome / structural constituent of cytoskeleton / memory / Z disc / intracellular calcium ion homeostasis / endocytosis / Sensory perception of sweet, bitter, and umami (glutamate) taste / intracellular protein localization / protein transport / nervous system development / presynaptic membrane / ATPase binding / protein-macromolecule adaptor activity / basolateral plasma membrane / neuron apoptotic process / cellular response to hypoxia / transmembrane transporter binding / postsynaptic membrane / cytoskeleton / early endosome / lysosome / calmodulin binding / neuron projection / protein stabilization / apical plasma membrane / axon / positive regulation of gene expression / protein kinase binding / glutamatergic synapse / enzyme binding / 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. / Voltage-gated Na+ ion channel, cytoplasmic domain / Cytoplasmic domain of voltage-gated Na+ ion channel / SCN5A-like, C-terminal IQ motif ...Ankyrin, UPA domain / UPA domain / : / Domain present in ZO-1 and Unc5-like netrin receptors / ZU5 domain / ZU5 domain / ZU5 domain profile. / Voltage-gated Na+ ion channel, cytoplasmic domain / Cytoplasmic domain of voltage-gated Na+ ion channel / SCN5A-like, C-terminal IQ motif / Sodium ion transport-associated / Voltage-gated sodium channel alpha subunit, inactivation gate / Sodium ion transport-associated / Voltage gated sodium channel, alpha subunit / Ankyrin repeats (many copies) / Death domain profile. / Voltage-gated cation channel calcium and sodium / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / Ankyrin repeat-containing domain / Short calmodulin-binding motif containing conserved Ile and Gln residues. / IQ motif, EF-hand binding site / IQ motif profile. / Voltage-dependent channel domain superfamily / 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 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Ion transport domain / Ion transport protein / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
Sodium channel Nav1.2 / Ankyrin-2 / Sodium channel protein type 2 subunit alpha
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5032 Å
AuthorsWei, Z. / Wang, C. / Zhang, M.
CitationJournal: Elife / Year: 2014
Title: Structural basis of diverse membrane target recognitions by ankyrins.
Authors: Wang, C. / Wei, Z. / Chen, K. / Ye, F. / Yu, C. / Bennett, V. / Zhang, M.
History
DepositionOct 18, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 26, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 14, 2015Group: Refinement description
Revision 1.2May 20, 2015Group: Database references
Revision 1.3Aug 2, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Nov 22, 2017Group: Refinement description / Category: software
Revision 1.5Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nav1.2 - AnkB chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4838
Polymers34,8101
Non-polymers6727
Water1,33374
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Nav1.2 - AnkB chimera
hetero molecules

A: Nav1.2 - AnkB chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,96516
Polymers69,6202
Non-polymers1,34514
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_556x,-y,-z+11
Buried area2460 Å2
ΔGint-7 kcal/mol
Surface area26500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.295, 102.295, 106.008
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number93
Space group name H-MP4222
Components on special symmetry positions
IDModelComponents
11A-2403-

SO4

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Components

#1: Protein Nav1.2 - AnkB chimera


Mass: 34810.133 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Homo sapiens (human)
Gene: ANK2, Scn2a, Scn2a1
Plasmid details: The Nav1.2 Ankyrin binding domain is fused to the N-terminus of AnkB Ankyrin re peats
Plasmid: pET32m / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A9JQD3, UniProt: Q01484, UniProt: Q99250*PLUS
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O

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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: 3.98 Å3/Da / Density % sol: 69.12 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.8 M ammonium sulfate, 6-8% dioxane, and 0.1 M MES , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 1, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 19914 / % possible obs: 99.4 % / Redundancy: 9.5 % / Biso Wilson estimate: 53.21 Å2 / Rmerge(I) obs: 0.077 / Χ2: 1.209 / Net I/σ(I): 11.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.5-2.549.70.7489771.0551100
2.54-2.599.80.6159821.056199.8
2.59-2.649.70.5369601.086199.8
2.64-2.699.60.4529771.098199.9
2.69-2.759.80.3819781.1441100
2.75-2.829.70.3439851.104199.9
2.82-2.899.70.2869971.199199.8
2.89-2.969.60.249721.209199.9
2.96-3.059.70.199781.279199.9
3.05-3.159.70.15110041.308199.9
3.15-3.269.70.1219891.2781100
3.26-3.399.60.0969851.2971100
3.39-3.559.50.07810101.2241100
3.55-3.739.50.0649831.31100
3.73-3.979.40.05510051.161199.8
3.97-4.279.20.05710181.329199.7
4.27-4.79.10.05310011.309199.3
4.7-5.388.90.05610241.277199
5.38-6.788.80.04710311.175198.5
6.78-508.80.03910581.297193.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5032→34.229 Å / FOM work R set: 0.823 / SU ML: 0.65 / σ(F): 1.34 / Phase error: 23.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2384 1009 5.09 %
Rwork0.1875 --
obs0.19 19832 99.16 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 57.211 Å2 / ksol: 0.341 e/Å3
Displacement parametersBiso max: 163.12 Å2 / Biso mean: 69.27 Å2 / Biso min: 31.77 Å2
Baniso -1Baniso -2Baniso -3
1-10.595 Å20 Å2-0 Å2
2--10.595 Å2-0 Å2
3----21.19 Å2
Refinement stepCycle: LAST / Resolution: 2.5032→34.229 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2262 0 35 74 2371
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0152318
X-RAY DIFFRACTIONf_angle_d1.5433151
X-RAY DIFFRACTIONf_chiral_restr0.098380
X-RAY DIFFRACTIONf_plane_restr0.006410
X-RAY DIFFRACTIONf_dihedral_angle_d17.041811
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5032-2.63510.24531490.227226292778100
2.6351-2.80010.29741570.228726372794100
2.8001-3.01620.29781420.230226652807100
3.0162-3.31950.26711560.199726592815100
3.3195-3.79930.24241340.184927122846100
3.7993-4.78460.20211370.15322717285499
4.7846-34.23260.22261340.18772804293896
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)
12.2584-0.98240.76961.5564-0.28110.65230.0283-0.6322-0.3590.69070.02620.29610.1587-0.15440.04990.4383-0.03050.00640.30590.040.445340.9904-23.526358.6885
20.3395-0.37270.44680.5096-0.32230.46190.00760.29310.0042-0.27230.01250.00480.3585-0.146-0.00020.34270.0031-0.01160.4506-0.06230.457737.4855-12.940943.2483
30.2332-0.18790.65441.59511.18053.66710.4860.17170.30650.0757-0.62650.50430.288-1.1529-0.04770.30850.05440.02220.52350.0260.477834.4303-0.606736.9452
40.44260.21990.09640.53280.02720.02040.33270.5707-0.0248-0.1411-0.13510.24241.33440.426-0.01460.84820.2515-0.01210.63810.03790.433134.66171.896225.3009
50.8728-0.00940.79570.3579-1.03524.4035-0.0682-0.24230.30220.6543-0.1773-0.0859-1.0005-0.1046-0.15220.4230.093-0.03350.61240.03550.409929.334415.132530.8628
60.4877-0.30610.23760.6346-0.32840.30820.23220.1950.1092-0.4589-0.1260.17710.13120.467-0.0010.63870.18490.06120.49060.02350.295226.178610.392319.7096
70.0238-0.0655-0.03880.0252-0.0040.08540.21350.5616-0.4993-0.8505-0.26520.41611.261-0.25740.00130.79710.1551-0.07890.6192-0.02410.362617.6745.72415.4184
80.4193-0.18090.370.62670.07350.58860.30970.1730.6768-1.13510.0144-0.3025-0.6460.84510.26491.04780.23880.01450.81820.02070.487619.46514.03757.3215
90.31010.1776-0.23611.1644-0.33780.23280.82450.4076-0.0819-0.372-0.2140.55970.692-0.05981.03071.51770.1229-0.20360.913-0.2350.357713.23233.64356.8579
102.0331-0.0088-0.14311.8716-1.20582.7395-0.326-0.23160.04620.8038-0.0654-0.3871-0.4753-0.3354-0.11170.57240.02410.05720.4609-0.02780.424434.9676-4.633657.1305
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 2029:2086)A2029 - 2086
2X-RAY DIFFRACTION2chain 'A' and (resseq 2087:2152)A2087 - 2152
3X-RAY DIFFRACTION3chain 'A' and (resseq 2153:2183)A2153 - 2183
4X-RAY DIFFRACTION4chain 'A' and (resseq 2184:2204)A2184 - 2204
5X-RAY DIFFRACTION5chain 'A' and (resseq 2205:2227)A2205 - 2227
6X-RAY DIFFRACTION6chain 'A' and (resseq 2228:2268)A2228 - 2268
7X-RAY DIFFRACTION7chain 'A' and (resseq 2269:2287)A2269 - 2287
8X-RAY DIFFRACTION8chain 'A' and (resseq 2288:2301)A2288 - 2301
9X-RAY DIFFRACTION9chain 'A' and (resseq 2302:2322)A2302 - 2322
10X-RAY DIFFRACTION10chain 'A' and (resseq 1113:1132)A1113 - 1132

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