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- PDB-4o6x: Crystal structure of human Ankyrin G death domain -

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Basic information

Entry
Database: PDB / ID: 4o6x
TitleCrystal structure of human Ankyrin G death domain
ComponentsAnkyrin-3
KeywordsPROTEIN BINDING / alpha helix bundle / death domain / alpha helix
Function / homology
Function and homology information


positive regulation of cell communication by electrical coupling / positive regulation of membrane depolarization during cardiac muscle cell action potential / maintenance of protein location in plasma membrane / membrane assembly / positive regulation of sodium ion transmembrane transporter activity / protein localization to axon / regulation of potassium ion transport / spectrin-associated cytoskeleton / magnesium ion homeostasis / positive regulation of membrane potential ...positive regulation of cell communication by electrical coupling / positive regulation of membrane depolarization during cardiac muscle cell action potential / maintenance of protein location in plasma membrane / membrane assembly / positive regulation of sodium ion transmembrane transporter activity / protein localization to axon / regulation of potassium ion transport / spectrin-associated cytoskeleton / magnesium ion homeostasis / positive regulation of membrane potential / plasma membrane organization / negative regulation of delayed rectifier potassium channel activity / positive regulation of homotypic cell-cell adhesion / positive regulation of cation channel activity / axon initial segment / Golgi to plasma membrane protein transport / cytoskeletal anchor activity / positive regulation of sodium ion transport / costamere / node of Ranvier / cellular response to magnesium ion / Interaction between L1 and Ankyrins / spectrin binding / neuromuscular junction development / neuronal action potential / mitotic cytokinesis / positive regulation of protein targeting to membrane / intercalated disc / lateral plasma membrane / endoplasmic reticulum to Golgi vesicle-mediated transport / COPI-mediated anterograde transport / T-tubule / cytoskeletal protein binding / axonogenesis / basal plasma membrane / sarcoplasmic reticulum / protein localization to plasma membrane / sarcolemma / neuromuscular junction / establishment of protein localization / structural constituent of cytoskeleton / Z disc / protein-macromolecule adaptor activity / postsynaptic membrane / basolateral plasma membrane / transmembrane transporter binding / lysosome / neuron projection / cadherin binding / dendrite / positive regulation of gene expression / Golgi apparatus / cell surface / endoplasmic reticulum / signal transduction / plasma membrane / cytosol
Similarity search - Function
Ankyrin-3, 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, Fas / Death Domain, Fas ...Ankyrin-3, 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, Fas / Death Domain, Fas / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.103 Å
AuthorsLiu, Y. / Zhang, Y. / Wang, J.H.
CitationJournal: Proteins / Year: 2014
Title: Crystal structure of human Ankyrin G death domain.
Authors: Liu, Y. / Zhang, Y. / Wang, J.H.
History
DepositionDec 24, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 29, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 17, 2014Group: Database references
Revision 1.2Feb 11, 2015Group: Other
Revision 1.3Sep 20, 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

Downloads & links

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Assembly

Deposited unit
A: Ankyrin-3
B: Ankyrin-3


Theoretical massNumber of molelcules
Total (without water)27,6432
Polymers27,6432
Non-polymers00
Water1,18966
1
A: Ankyrin-3


Theoretical massNumber of molelcules
Total (without water)13,8211
Polymers13,8211
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ankyrin-3


Theoretical massNumber of molelcules
Total (without water)13,8211
Polymers13,8211
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Ankyrin-3

B: Ankyrin-3


Theoretical massNumber of molelcules
Total (without water)27,6432
Polymers27,6432
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_664-x+3/2,-y+1,z-1/21
Buried area1170 Å2
ΔGint-6 kcal/mol
Surface area9680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.452, 56.817, 81.949
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-3 / / ANK-3 / Ankyrin-G


Mass: 13821.483 Da / Num. of mol.: 2 / Fragment: unp residues 4088-4200
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ANK3, Ankyrin G / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q12955
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 1.87 Å3/Da / Density % sol: 34.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG4000, NaAc, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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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: Mar 25, 2013
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 28939 / Num. obs: 12601 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 7.9 % / Rmerge(I) obs: 0.075 / Χ2: 1.037 / Net I/σ(I): 10.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.1-2.148.10.6735941.003199.5
2.14-2.188.10.586161.007198.2
2.18-2.228.10.4876131.06198.2
2.22-2.268.10.4116081.019199.3
2.26-2.318.10.3945961.009198.7
2.31-2.378.10.3856191.043198.9
2.37-2.428.10.3246091.009198.9
2.42-2.4980.2966161.009198.9
2.49-2.568.10.2266161.016199
2.56-2.6580.2046001.005199
2.65-2.7480.1786261.011199.4
2.74-2.8580.1446211.033199.5
2.85-2.9880.1126261.021199.5
2.98-3.1480.0846311.009199.7
3.14-3.337.90.0646251.07199.4
3.33-3.597.90.0576311.124199.4
3.59-3.957.80.0636361.025199.7
3.95-4.527.70.0576531.033199.8
4.52-5.77.30.0426421.093197.9
5.7-507.10.0327101.144198.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
PHENIX1.5_2refinement
PDB_EXTRACT3.14data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 4D8O

4d8o


Resolution: 2.103→39.074 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8202 / SU ML: 0.21 / σ(F): 0.14 / Phase error: 24.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2314 587 4.92 %
Rwork0.1822 --
obs0.1846 11928 94.77 %
all-28939 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.895 Å2 / ksol: 0.343 e/Å3
Displacement parametersBiso max: 111.05 Å2 / Biso mean: 48.7308 Å2 / Biso min: 24.8 Å2
Baniso -1Baniso -2Baniso -3
1--1.716 Å20 Å2-0 Å2
2--11.2222 Å20 Å2
3----9.5062 Å2
Refinement stepCycle: LAST / Resolution: 2.103→39.074 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1540 0 0 66 1606
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061560
X-RAY DIFFRACTIONf_angle_d0.8972110
X-RAY DIFFRACTIONf_chiral_restr0.056254
X-RAY DIFFRACTIONf_plane_restr0.003266
X-RAY DIFFRACTIONf_dihedral_angle_d18.836574
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.103-2.31470.28251330.22022570270388
2.3147-2.64950.3081420.20222779292194
2.6495-3.33780.2551680.19262887305597
3.3378-39.08040.19371440.16663105324999
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)
11.5747-0.1271-0.43490.707-0.25632.4655-0.0281-0.2736-0.2130.2536-0.018-0.010.0652-0.04160.05560.3489-0.02290.01120.29450.00440.286523.217631.756755.5138
21.25040.84940.03341.27580.51950.6988-0.2210.4243-0.0036-0.20120.23620.11090.0721-0.20020.00380.3294-0.1234-0.02050.50920.0060.278823.412932.929428.6764
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B'B2 - 101
4X-RAY DIFFRACTION2chain 'A'A2 - 101

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