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- PDB-4rlv: Crystal Structure of AnkB 24 Ankyrin Repeats in Complex with AnkR... -

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Basic information

Entry
Database: PDB / ID: 4rlv
TitleCrystal Structure of AnkB 24 Ankyrin Repeats in Complex with AnkR Autoinhibition Segment
ComponentsAnkyrin-1, Ankyrin-2
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 / 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 / early endosome / lysosome / cytoskeleton / protein stabilization / neuron projection / 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 of unknown function DUF3447 / Domain present in ZO-1 and Unc5-like netrin receptors / ZU5 domain / ZU5 domain / ZU5 domain profile. / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain ...Ankyrin, UPA domain / UPA domain / Domain of unknown function DUF3447 / Domain present in ZO-1 and Unc5-like netrin receptors / ZU5 domain / ZU5 domain / ZU5 domain profile. / 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
Similarity search - Domain/homology
Ankyrin-1 / Ankyrin-2
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 3.4945 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 1.1May 20, 2015Group: Database references
Revision 1.2Aug 2, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)98,87610
Polymers98,0121
Non-polymers8659
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)179.685, 179.685, 304.856
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 / ANK-2 / Ankyrin-B / Brain ankyrin / Non-erythroid ankyrin


Mass: 98011.523 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: Ank1, ANK2 / Plasmid: pET32m / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: D3YTV8, UniProt: Q01484
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4

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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: 4.85 Å3/Da / Density % sol: 74.64 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.5 M ammonium sulfate, 1.0 M lithium sulfate, and 0.1 M sodium citrate, pH 5.6, 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
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 6, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.494→50 Å / Num. obs: 23268 / % possible obs: 96 % / Redundancy: 10.2 % / Biso Wilson estimate: 110.47 Å2 / Rmerge(I) obs: 0.121 / Χ2: 2.271 / Net I/σ(I): 9.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
3.494-3.5690.78311611.343197.2
3.56-3.6310.30.73511791.302197.3
3.63-3.699.80.66411311.721197.1
3.69-3.7710.30.59211671.365197.2
3.77-3.8510.20.39511721.503197
3.85-3.949.30.44411532.094197
3.94-4.0410.30.40111701.456196.7
4.04-4.1510.50.24311601.52197
4.15-4.2710.50.21911671.545196.6
4.27-4.4110.40.20411661.651196.4
4.41-4.579.90.21311542.724196.3
4.57-4.7510.20.20511582.232196.3
4.75-4.9710.50.15711712.024196.1
4.97-5.2310.50.15511562.112196.1
5.23-5.5510.60.15311572.142195.5
5.55-5.9810.50.14311702.354195.7
5.98-6.5810.40.11111582.378195.2
6.58-7.5310.10.07111613.196194.5
7.53-9.4810.50.05411754.042193.9
9.48-509.70.05511826.791191.3

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Phasing

PhasingMethod: SIRAS

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SIRAS / Resolution: 3.4945→38.59 Å / FOM work R set: 0.7283 / SU ML: 0.4 / σ(F): 1.33 / Phase error: 32.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2527 2641 6.01 %RANDOM
Rwork0.2201 ---
obs0.2221 43909 94.45 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 323.93 Å2 / Biso mean: 113.52 Å2 / Biso min: 20.94 Å2
Refinement stepCycle: LAST / Resolution: 3.4945→38.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6260 0 45 0 6305
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0136393
X-RAY DIFFRACTIONf_angle_d1.5458687
X-RAY DIFFRACTIONf_chiral_restr0.0741040
X-RAY DIFFRACTIONf_plane_restr0.011121
X-RAY DIFFRACTIONf_dihedral_angle_d12.4292302
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.4945-3.5580.38591420.36082161230394
3.558-3.62640.36041430.33972207235096
3.6264-3.70030.36381390.3422162230196
3.7003-3.78070.31071390.29962183232295
3.7807-3.86860.30641340.27622204233895
3.8686-3.96520.33461350.29462169230495
3.9652-4.07230.2711470.24772207235495
4.0723-4.1920.20181370.22882147228495
4.192-4.32720.2861360.21672183231994
4.3272-4.48160.24731360.22192137227393
4.4816-4.66070.30711400.27532130227093
4.6607-4.87250.20421420.18982206234895
4.8725-5.12880.26461380.1862184232295
5.1288-5.44930.23531400.19612171231195
5.4493-5.86870.30661360.21592204234095
5.8687-6.45680.22521360.20512171230795
6.4568-7.38550.221370.18942154229194
7.3855-9.28350.2051430.16122159230294
9.2835-38.59230.21761410.19372129227092
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)
10.75390.50020.01781.92680.29090.6906-0.0072-0.16550.6552-0.027-0.0344-0.3469-0.710.46570.13451.0703-0.37840.20950.62220.16542.016436.4735-43.294-64.4859
21.76720.58220.07811.019-0.01130.5710.17560.52430.6806-0.4028-0.01160.3843-0.3167-0.1164-0.15020.5269-0.02160.17250.4430.21380.1844-8.4155-78.2932-65.5568
31.8551-0.5176-0.49711.08470.77911.64630.0463-0.33630.36310.470.0820.5019-0.3561-0.3074-0.13051.30210.29750.28910.72790.09671.6968-52.5927-56.4733-32.6351
40.9894-0.5531-0.18532.03020.26190.04510.85280.31690.3756-0.9346-0.6332-0.1626-0.1383-0.0823-0.17572.61260.48850.371.7969-0.11081.4161-50.9206-63.44977.3057
51.15990.152.89241.2069-0.85518.48410.048-0.59910.51870.31240.1402-0.3958-0.09780.3508-0.18751.2543-0.3081-0.44131.25650.02821.3966-22.1082-74.3223-55.3283
61.399-0.83180.81080.9497-0.05750.86780.0703-0.0291-0.06720.2777-0.03940.54150.1701-0.0429-0.00691.45490.20590.20161.0548-0.1031.6986-4.9001-74.0073-58.7197
71.99966.4317-8.88246.4958-6.9992.00030.15440.11150.87550.2886-0.38330.5895-0.0152-0.30620.23560.56780.00840.20350.65680.10580.68999.3308-69.1152-59.9604
80.8538-0.89460.23671.26320.26670.884-0.24690.31840.6066-0.00390.21760.8912-0.2876-0.14030.00470.773-0.2181-0.16380.60220.181.550824.7378-39.7861-68.9909
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2026 through 2224 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 2225 through 2519 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 2520 through 2714 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 2715 through 2816 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 1584 through 1590 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 1591 through 1601 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 1602 through 1610 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 1611 through 1630 )A0

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