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- PDB-3bs5: Crystal Structure of hCNK2-SAM/dHYP-SAM Complex -

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Basic information

Entry
Database: PDB / ID: 3bs5
TitleCrystal Structure of hCNK2-SAM/dHYP-SAM Complex
Components
  • Connector enhancer of kinase suppressor of ras 2
  • Protein aveugle
KeywordsSignaling PROTEIN/membrane protein / Sterile alpha motif / SAM domain / SAM domain dimer / SAM domain complex / Cytoplasm / Membrane / Sensory transduction / Vision / Alternative splicing / Coiled coil / Phosphoprotein / Polymorphism / Signaling PROTEIN-membrane protein COMPLEX
Function / homology
Function and homology information


Phosphorylation of CI / compound eye cone cell differentiation / Phosphorylation of SMO / compound eye photoreceptor cell differentiation / Phosphorylation of PER and TIM / eye photoreceptor cell differentiation / extrinsic component of postsynaptic density membrane / postsynapse organization / positive regulation of Ras protein signal transduction / regulation of signal transduction ...Phosphorylation of CI / compound eye cone cell differentiation / Phosphorylation of SMO / compound eye photoreceptor cell differentiation / Phosphorylation of PER and TIM / eye photoreceptor cell differentiation / extrinsic component of postsynaptic density membrane / postsynapse organization / positive regulation of Ras protein signal transduction / regulation of signal transduction / visual perception / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / epidermal growth factor receptor signaling pathway / cytoplasmic side of plasma membrane / cell surface receptor protein tyrosine kinase signaling pathway / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / Signaling by BRAF and RAF1 fusions / scaffold protein binding / positive regulation of ERK1 and ERK2 cascade / intracellular signal transduction / neuronal cell body / glutamatergic synapse / protein kinase binding / extracellular exosome / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Connector enhancer of kinase suppressor of ras 2/3 domain / Connector enhancer of kinase suppressor of ras 2/3 domain / Aveugle-like, SAM domain / : / CRIC domain / Connector enhancer of kinase suppressor of ras / CRIC domain profile. / Transcription Factor, Ets-1 / SAM domain (Sterile alpha motif) / SAM domain (Sterile alpha motif) ...Connector enhancer of kinase suppressor of ras 2/3 domain / Connector enhancer of kinase suppressor of ras 2/3 domain / Aveugle-like, SAM domain / : / CRIC domain / Connector enhancer of kinase suppressor of ras / CRIC domain profile. / Transcription Factor, Ets-1 / SAM domain (Sterile alpha motif) / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / PH domain / Sterile alpha motif/pointed domain superfamily / PH domain profile. / Pleckstrin homology domain. / PDZ domain / Pleckstrin homology domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / DNA polymerase; domain 1 / PH-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Protein aveugle / Connector enhancer of kinase suppressor of ras 2
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsRajakulendran, T. / Ceccarelli, D.F. / Kurinov, I. / Sicheri, F.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2008
Title: CNK and HYP form a discrete dimer by their SAM domains to mediate RAF kinase signaling.
Authors: Rajakulendran, T. / Sahmi, M. / Kurinov, I. / Tyers, M. / Therrien, M. / Sicheri, F.
History
DepositionDec 22, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein aveugle
B: Connector enhancer of kinase suppressor of ras 2


Theoretical massNumber of molelcules
Total (without water)22,3242
Polymers22,3242
Non-polymers00
Water1,47782
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.477, 56.356, 84.040
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 Protein aveugle


Mass: 12991.161 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: ave / Production host: Escherichia coli (E. coli) / References: UniProt: Q8ML92
#2: Protein Connector enhancer of kinase suppressor of ras 2 / Connector enhancer of KSR2 / CNK2


Mass: 9333.226 Da / Num. of mol.: 1 / Fragment: SAM domain, UNP residues 5-84
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CNKSR2, CNK2, KIAA0902, KSR2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8WXI2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 2.57 Å3/Da / Density % sol: 52.16 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 18% PEG 2000 MME, 0.1M Tris, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 25, 2006
RadiationMonochromator: Two independent arrays of pairs of vertical and horizontal slit blade pairs
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 15908 / Num. obs: 15619 / % possible obs: 95 % / Observed criterion σ(F): 2.8 / Observed criterion σ(I): 10.1
Reflection shellResolution: 2→2.06 Å / % possible all: 97.6

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
SHELXphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.004data extraction
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 2→19.87 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.925 / SU B: 3.228 / SU ML: 0.093 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.167 / ESU R Free: 0.149
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24 786 4.9 %RANDOM
Rwork0.212 ---
all0.214 ---
obs0.214 15619 99.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.47 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å20 Å2
2--0.04 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2→19.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1299 0 0 82 1381
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0211304
X-RAY DIFFRACTIONr_angle_refined_deg1.5551.9461756
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8845152
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.48823.57170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.33115251
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.881514
X-RAY DIFFRACTIONr_chiral_restr0.1130.2192
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02974
X-RAY DIFFRACTIONr_nbd_refined0.240.2586
X-RAY DIFFRACTIONr_nbtor_refined0.3050.2903
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2490.2101
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2030.221
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1490.212
X-RAY DIFFRACTIONr_mcbond_it1.5661.5796
X-RAY DIFFRACTIONr_mcangle_it2.27321227
X-RAY DIFFRACTIONr_scbond_it3.6443599
X-RAY DIFFRACTIONr_scangle_it5.7454.5529
LS refinement shellResolution: 2→2.055 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.245 56 -
Rwork0.227 1036 -
all-1092 -
obs--97.59 %

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