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- PDB-4lg6: Crystal structure of ANKRA2-CCDC8 complex -

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Basic information

Entry
Database: PDB / ID: 4lg6
TitleCrystal structure of ANKRA2-CCDC8 complex
Components
  • Ankyrin repeat family A protein 2
  • Coiled-coil domain-containing protein 8
KeywordsSTRUCTURAL PROTEIN / Structural Genomics Consortium / SGC / ankyrin repeat
Function / homology
Function and homology information


3M complex / negative regulation of phosphatase activity / low-density lipoprotein particle receptor binding / regulation of mitotic nuclear division / regulation of protein-containing complex assembly / post-translational protein modification / microtubule cytoskeleton organization / histone deacetylase binding / Neddylation / regulation of gene expression ...3M complex / negative regulation of phosphatase activity / low-density lipoprotein particle receptor binding / regulation of mitotic nuclear division / regulation of protein-containing complex assembly / post-translational protein modification / microtubule cytoskeleton organization / histone deacetylase binding / Neddylation / regulation of gene expression / cytoskeleton / centrosome / ubiquitin protein ligase binding / protein kinase binding / protein-containing complex / nucleoplasm / membrane / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
: / Paraneoplastic antigen Ma / PNMA / Ankyrin repeat-containing domain / Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat ...: / Paraneoplastic antigen Ma / PNMA / Ankyrin repeat-containing domain / 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 / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
Coiled-coil domain-containing protein 8 / Ankyrin repeat family A protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsXu, C. / Bian, C. / Tempel, W. / Mackenzie, F. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: Structure / Year: 2015
Title: Ankyrin Repeats of ANKRA2 Recognize a PxLPxL Motif on the 3M Syndrome Protein CCDC8.
Authors: Nie, J. / Xu, C. / Jin, J. / Aka, J.A. / Tempel, W. / Nguyen, V. / You, L. / Weist, R. / Min, J. / Pawson, T. / Yang, X.J.
History
DepositionJun 27, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 18, 2015Group: Database references
Revision 1.2Apr 29, 2015Group: Database references
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 / diffrn_source / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.type / _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 repeat family A protein 2
B: Coiled-coil domain-containing protein 8


Theoretical massNumber of molelcules
Total (without water)20,8625
Polymers20,8622
Non-polymers03
Water95553
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1320 Å2
ΔGint-14 kcal/mol
Surface area8890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.726, 49.791, 41.243
Angle α, β, γ (deg.)90.000, 98.230, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Ankyrin repeat family A protein 2 / RFXANK-like protein 2


Mass: 18784.270 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ANKRA2, ANKRA / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-V2R-pRARE2 / References: UniProt: Q9H9E1
#2: Protein/peptide Coiled-coil domain-containing protein 8


Mass: 2077.498 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic peptide / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9H0W5
#3: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 3 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 2 Å3/Da / Density % sol: 39.5 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7.5
Details: 25% PEG3350, 0.2 M sodium chloride, 0.1 M HEPES, pH 7.5, vapor diffusion, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Nov 9, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→40.818 Å / Num. all: 14082 / Num. obs: 14082 / % possible obs: 97 % / Redundancy: 3.7 % / Rsym value: 0.047 / Net I/σ(I): 16.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.8-1.93.70.651.2732819880.6594.8
1.9-2.013.70.322.4709919170.3295.7
2.01-2.153.70.174.6670818090.1796.1
2.15-2.323.70.1186.6626816820.11897.1
2.32-2.553.70.0799.8583415650.07997.2
2.55-2.853.70.05513.8533214290.05598
2.85-3.293.70.03520477612900.03599
3.29-4.023.70.02723.1396510800.02798.8
4.02-5.693.60.02426.230578450.02499.1
5.69-26.1353.50.0224.816884770.0298.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
PHASERphasing
REFMAC5.7.0032refinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3SO8

3so8


Resolution: 1.8→26.149 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.956 / WRfactor Rfree: 0.202 / WRfactor Rwork: 0.186 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 3.465 / SU ML: 0.106 / Cross valid method: THROUGHOUT / ESU R: 0.153 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE program coot and the molprobity server were also used during refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.2085 712 5.057 %RANDOM
Rwork0.196 ---
obs0.197 14080 97.023 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso max: 73.83 Å2 / Biso mean: 29.629 Å2 / Biso min: 13.25 Å2
Baniso -1Baniso -2Baniso -3
1-1.716 Å20 Å2-1.099 Å2
2---0.291 Å20 Å2
3----1.215 Å2
Refinement stepCycle: LAST / Resolution: 1.8→26.149 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1300 0 3 53 1356
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0191363
X-RAY DIFFRACTIONr_bond_other_d0.0010.021278
X-RAY DIFFRACTIONr_angle_refined_deg1.3521.971869
X-RAY DIFFRACTIONr_angle_other_deg0.78832948
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0415186
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.45626.36455
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.64115219
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.074152
X-RAY DIFFRACTIONr_chiral_restr0.0740.2223
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211575
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02284
X-RAY DIFFRACTIONr_mcbond_it2.0432.897712
X-RAY DIFFRACTIONr_mcbond_other2.0422.902713
X-RAY DIFFRACTIONr_mcangle_it3.1864.324890
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.8470.339460.299966107294.403
1.847-1.8970.3460.259927102295.205
1.897-1.9520.264480.244919101095.743
1.952-2.0120.297530.2288497795.906
2.012-2.0770.252410.20486594895.57
2.077-2.150.247410.21585892796.98
2.15-2.2310.188360.2280787396.564
2.231-2.3210.284380.21279785697.547
2.321-2.4240.243320.2178784497.038
2.424-2.5410.232400.20870276297.375
2.541-2.6770.255410.22269074897.727
2.677-2.8380.312360.20566571398.317
2.838-3.0330.164390.20161666398.793
3.033-3.2730.217280.18159663099.048
3.273-3.5810.194310.17853857998.273
3.581-3.9960.174270.15848952099.231
3.996-4.6010.125330.14342946798.929
4.601-5.6020.184280.16336139398.982
5.602-7.7880.139140.22429931499.682
7.788-300.227140.19617318998.942

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