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- PDB-6kzj: Crystal structure of Ankyrin B/NdeL1 complex -

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Basic information

Entry
Database: PDB / ID: 6kzj
TitleCrystal structure of Ankyrin B/NdeL1 complex
Components
  • Ankyrin-2
  • Nuclear distribution protein nudE-like 1
KeywordsPROTEIN BINDING / PROTEIN TRANSPORT / STRUCTURAL PROTEIN
Function / homology
Function and homology information


neurofilament cytoskeleton / 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 / cerebral cortex radially oriented cell migration / establishment of chromosome localization / protein localization to M-band / central nervous system neuron axonogenesis ...neurofilament cytoskeleton / 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 / cerebral cortex radially oriented cell migration / establishment of chromosome localization / protein localization to M-band / central nervous system neuron axonogenesis / protein localization to endoplasmic reticulum / positive regulation of potassium ion transmembrane transporter activity / T-tubule organization / oligopeptidase activity / SA node cell action potential / radial glia-guided pyramidal neuron migration / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / membrane depolarization during SA node cell action potential / protein localization to organelle / paranodal junction assembly / central region of growth cone / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / phosphorylation-dependent protein binding / Resolution of Sister Chromatid Cohesion / regulation of SA node cell action potential / regulation of atrial cardiac muscle cell action potential / RHO GTPases Activate Formins / nuclear membrane disassembly / Separation of Sister Chromatids / positive regulation of cation channel activity / atrial cardiac muscle cell action potential / vesicle transport along microtubule / sarcoplasmic reticulum calcium ion transport / cytoskeletal anchor activity / neurofilament cytoskeleton organization / microtubule nucleation / lysosome localization / atrial septum development / positive regulation of potassium ion transport / axon hillock / ventricular cardiac muscle cell action potential / costamere / positive regulation of calcium ion transport / regulation of cardiac muscle cell contraction / retrograde axonal transport / response to methylmercury / regulation of cardiac muscle contraction by calcium ion signaling / regulation of release of sequestered calcium ion into cytosol / regulation of ventricular cardiac muscle cell membrane repolarization / activation of GTPase activity / M band / protein localization to cell surface / positive regulation of ruffle assembly / Interaction between L1 and Ankyrins / mitotic centrosome separation / A band / microtubule associated complex / microtubule organizing center / centrosome localization / inner cell mass cell proliferation / kinesin complex / neuron projection extension / spectrin binding / beta-tubulin binding / regulation of neuron projection development / positive regulation of axon regeneration / regulation of intracellular protein transport / cell leading edge / regulation of heart rate by cardiac conduction / establishment of mitotic spindle orientation / regulation of calcium ion transport / alpha-tubulin binding / intercalated disc / regulation of cardiac muscle contraction / positive regulation of axon extension / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / COPI-mediated anterograde transport / axon cytoplasm / T-tubule / regulation of heart rate / chromosome segregation / protein localization to plasma membrane / neuron migration / sarcolemma / regulation of protein stability / protein localization / structural constituent of cytoskeleton / spindle / kinetochore / recycling endosome / microtubule cytoskeleton organization / intracellular calcium ion homeostasis / positive regulation of GTPase activity / Z disc / endocytosis / neuron projection development / cell migration / protein-macromolecule adaptor activity / synaptic vesicle
Similarity search - Function
NUDE domain / NUDE family / NUDE protein, C-terminal conserved region / Ankyrin, UPA domain / UPA domain / Domain present in ZO-1 and Unc5-like netrin receptors / ZU5 domain / ZU5 domain / ZU5 domain profile. / Death domain profile. ...NUDE domain / NUDE family / NUDE protein, C-terminal conserved region / Ankyrin, UPA domain / UPA domain / 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-2 / Nuclear distribution protein nudE-like 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.5 Å
AuthorsYe, J. / Li, J. / Ye, F. / Zhang, M. / Zhang, Y. / Wang, C.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31670734 China
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Mechanistic insights into the interactions of dynein regulator Ndel1 with neuronal ankyrins and implications in polarity maintenance.
Authors: Ye, J. / Li, J. / Ye, F. / Zhang, Y. / Zhang, M. / Wang, C.
History
DepositionSep 24, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ankyrin-2
B: Nuclear distribution protein nudE-like 1
C: Nuclear distribution protein nudE-like 1


Theoretical massNumber of molelcules
Total (without water)18,7093
Polymers18,7093
Non-polymers00
Water1,04558
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5660 Å2
ΔGint-59 kcal/mol
Surface area8960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.446, 44.690, 77.880
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21C

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: 0 / Auth seq-ID: 235 - 272 / Label seq-ID: 5 - 42

Dom-IDAuth asym-IDLabel asym-ID
1BB
2CC

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Components

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


Mass: 8237.317 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ANK2, ANKB / Production host: Escherichia coli (E. coli) / References: UniProt: Q01484
#2: Protein Nuclear distribution protein nudE-like 1 / Protein mNudE-like / mNudE-L


Mass: 5236.021 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ndel1, Nudel / Production host: Escherichia coli (E. coli) / References: UniProt: Q9ERR1
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 1.88 Å3/Da / Density % sol: 34.61 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 5.6
Details: 1.9M ammonium sulfate, 0.16M potassium sodium tartrate tetrahydrate, 0.1M sodium citrate tribasic dehydrate pH 5.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97852 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 22182 / % possible obs: 95 % / Redundancy: 10.7 % / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.019 / Rrim(I) all: 0.062 / Χ2: 0.583 / Net I/σ(I): 5.7 / Num. measured all: 238129
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.5-1.53110.43511350.9660.1360.4560.52599.9
1.53-1.5510.70.39811490.9630.1260.4180.50799.3
1.55-1.589.80.33111270.9650.110.3490.51799.7
1.58-1.6211.40.32811610.9770.1010.3430.48100
1.62-1.6511.60.26611310.9830.0810.2780.49199.8
1.65-1.6911.40.23911550.9860.0730.250.51699.7
1.69-1.7311.40.19811470.9910.0610.2080.5199.9
1.73-1.7811.40.17411490.9920.0530.1820.5299.8
1.78-1.8311.30.15111340.9930.0460.1580.53599.8
1.83-1.8911.20.13511690.9950.0420.1410.563100
1.89-1.966.10.1339690.9560.0610.1480.97483.9
1.96-2.04110.09511550.9960.030.10.597100
2.04-2.1311.80.07511640.9980.0230.0790.595100
2.13-2.2410.90.0659730.9980.020.0680.58882.7
2.24-2.3810.50.0568230.9980.0180.0590.59471.2
2.38-2.5611.40.0511660.9990.0150.0520.57799.9
2.56-2.82100.0511820.9980.0160.0530.6599.7
2.82-3.2311.50.04311900.9990.0130.0450.641100
3.23-4.079.10.048100.9980.0140.0430.7166.3
4.07-5010.10.04212930.9980.0140.0440.85799.8

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.8.0253refinement
PDB_EXTRACT3.25data extraction
Arcimboldophasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.5→10 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.842 / SU ML: 0.048 / SU R Cruickshank DPI: 0.0836 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.084 / ESU R Free: 0.077
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2108 1063 4.8 %RANDOM
Rwork0.1605 ---
obs0.1628 20976 94.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 63.12 Å2 / Biso mean: 22.795 Å2 / Biso min: 10.31 Å2
Baniso -1Baniso -2Baniso -3
1-0.68 Å20 Å2-0 Å2
2---0.56 Å20 Å2
3----0.12 Å2
Refinement stepCycle: final / Resolution: 1.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1100 0 0 58 1158
Biso mean---29.57 -
Num. residues----150
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0131126
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171116
X-RAY DIFFRACTIONr_angle_refined_deg1.6331.6371525
X-RAY DIFFRACTIONr_angle_other_deg1.5991.5832594
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7965154
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.59222.97947
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.16115204
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.359157
X-RAY DIFFRACTIONr_chiral_restr0.0920.2160
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021246
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02203
X-RAY DIFFRACTIONr_rigid_bond_restr1.69132242
Refine LS restraints NCS

Ens-ID: 1 / Number: 933 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.21 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1B
2C
LS refinement shellResolution: 1.5→1.537 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.207 71 -
Rwork0.159 1560 -
obs--98.73 %
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)
10.2625-0.2421-0.15151.96310.38131.5427-0.0086-0.03320.01740.02090.01620.05960.0951-0.0552-0.00760.0066-0.0062-0.00550.05810.00160.043714.0551-1.080516.2779
21.1370.39281.57530.47571.07273.57270.0256-0.04130.08540.0454-0.05440.01110.123-0.08330.02880.008-0.0051-0.01070.0437-0.00940.047112.3485-2.510814.8156
31.2951-0.77781.83470.6252-0.95423.23250.0242-0.0105-0.03480.03640.01540.02470.0727-0.0618-0.03950.02070.0079-0.01050.038-0.0030.036217.1257-8.442912.8175
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1500 - 1570
2X-RAY DIFFRACTION2B235 - 273
3X-RAY DIFFRACTION3C235 - 276

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