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- PDB-4cb9: Structure of full-length CTNNBL1 in P43212 space group -

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Basic information

Entry
Database: PDB / ID: 4cb9
TitleStructure of full-length CTNNBL1 in P43212 space group
ComponentsBETA-CATENIN-LIKE PROTEIN 1
KeywordsAPOPTOSIS / IMPORT / AID / DEAMINASE
Function / homology
Function and homology information


somatic diversification of immunoglobulins / Prp19 complex / mRNA Splicing - Major Pathway / spliceosomal complex / mRNA splicing, via spliceosome / adaptive immune response / positive regulation of apoptotic process / centrosome / enzyme binding / nucleoplasm ...somatic diversification of immunoglobulins / Prp19 complex / mRNA Splicing - Major Pathway / spliceosomal complex / mRNA splicing, via spliceosome / adaptive immune response / positive regulation of apoptotic process / centrosome / enzyme binding / nucleoplasm / membrane / nucleus / cytosol
Similarity search - Function
Beta-catenin-like protein 1, N-terminal / Beta-catenin-like protein 1 / Catenin-beta-like, Arm-motif containing nuclear / Eukaryotic domain of unknown function (DUF1716) / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Beta-catenin-like protein 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3 Å
AuthorsGanesh, K. / vanMaldegem, F. / Telerman, S.B. / Simpson, P. / Johnson, C.M. / Williams, R.L. / Neuberger, M.S. / Rada, C.
CitationJournal: FEBS Lett. / Year: 2014
Title: Structural and Mutational Analysis Reveals that Ctnnbl1 Binds Nlss in a Manner Distinct from that of its Closest Armadillo-Relative, Karyopherin Alpha
Authors: Ganesh, K. / Maldegem, F.V. / Telerman, S.B. / Simpson, P. / Johnson, C.M. / Williams, R.L. / Neuberger, M.S. / Rada, C.
History
DepositionOct 10, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 4, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2014Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BETA-CATENIN-LIKE PROTEIN 1


Theoretical massNumber of molelcules
Total (without water)66,2951
Polymers66,2951
Non-polymers00
Water362
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.727, 66.727, 325.883
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein BETA-CATENIN-LIKE PROTEIN 1 / NUCLEAR-ASSOCIATED PROTEIN / NAP / TESTIS DEVELOPMENT PROTEIN NYD-SP19 / CTNNBL1


Mass: 66295.492 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8WYA6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 2.86 Å3/Da / Density % sol: 57.07 %
Description: AN INITIAL MODEL WAS BUILT USING A 3-WAVELENGTH SE- MET MAD DATA SET. THIS INITIAL MODEL WAS USED AS IN MOLECULAR REPLACEMENT WITH THE HIGHEST RESOLUTION NATIVE DATA SET THAT IS ...Description: AN INITIAL MODEL WAS BUILT USING A 3-WAVELENGTH SE- MET MAD DATA SET. THIS INITIAL MODEL WAS USED AS IN MOLECULAR REPLACEMENT WITH THE HIGHEST RESOLUTION NATIVE DATA SET THAT IS DESCRIBED IN 4CB8. THE REFINED STRUCTURE OF 4CB8 WAS USED AS A MOLECULAR REPLACEMENT MODEL FOR THIS ENTRY. THE SE-MET DATA SET AND DERIVED SHARP DATA ARE INCLUDED WITH THIS ENTRY.
Crystal growpH: 8.5 / Details: 0.1M TRIS PH 8.5, 1.1M NAF

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD / Date: May 19, 2011 / Details: MIRRORS
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3→81.47 Å / Num. obs: 15841 / % possible obs: 100 % / Redundancy: 13.4 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 16.4
Reflection shellResolution: 3→3.2 Å / Redundancy: 13.6 % / Rmerge(I) obs: 0.92 / Mean I/σ(I) obs: 3.1 / % possible all: 100

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
PHASERphasing
SHARPphasing
REFMAC5.7.0032refinement
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 3→65.46 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.904 / SU B: 21.211 / SU ML: 0.38 / Cross valid method: THROUGHOUT / ESU R Free: 0.464 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. A 3-WAVELENGTH SE-MAD EXPERIMENT WAS CARRIED OUT TO GET AN INITIAL MODEL. THIS MODEL WAS USED AS A MOLECULAR REPLACEMENT MODEL FOR THE ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. A 3-WAVELENGTH SE-MAD EXPERIMENT WAS CARRIED OUT TO GET AN INITIAL MODEL. THIS MODEL WAS USED AS A MOLECULAR REPLACEMENT MODEL FOR THE HIGHER RESOLUTION STRUCTURE DESCRIBED IN THIS ENTRY. THE OBSERVED DATA AND SHARP REFINEMENT RESULTS FOR THE SE-MET DATA ARE INCLUDED IN THE STRUCTURE-FACTOR CIF FILES.
RfactorNum. reflection% reflectionSelection details
Rfree0.29867 787 5 %RANDOM
Rwork0.21824 ---
obs0.22216 14963 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 88.315 Å2
Baniso -1Baniso -2Baniso -3
1-0.97 Å20 Å20 Å2
2--0.97 Å20 Å2
3----1.93 Å2
Refinement stepCycle: LAST / Resolution: 3→65.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3874 0 0 2 3876
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0193924
X-RAY DIFFRACTIONr_bond_other_d0.0020.023863
X-RAY DIFFRACTIONr_angle_refined_deg1.3511.9815275
X-RAY DIFFRACTIONr_angle_other_deg0.77738893
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5255480
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.76825.124201
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.66615778
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4961529
X-RAY DIFFRACTIONr_chiral_restr0.0730.2601
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024411
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02860
X-RAY DIFFRACTIONr_nbd_refined0.250.21194
X-RAY DIFFRACTIONr_nbd_other0.1930.23970
X-RAY DIFFRACTIONr_nbtor_refined0.1860.22011
X-RAY DIFFRACTIONr_nbtor_other0.0920.22399
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2080.279
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1420.25
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2660.25
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1210.23
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1210.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.6438.4911925
X-RAY DIFFRACTIONr_mcbond_other5.6348.4911924
X-RAY DIFFRACTIONr_mcangle_it8.65712.7142402
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.8369.191999
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.8359.1912000
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.39 61 -
Rwork0.304 1067 -
obs--100 %

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