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- PDB-9k1l: Complex structure of CNK2 and SAMD12 -

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Basic information

Entry
Database: PDB / ID: 9k1l
TitleComplex structure of CNK2 and SAMD12
Components
  • Connector enhancer of kinase suppressor of ras 2
  • Sterile alpha motif domain-containing protein 12
KeywordsSTRUCTURAL PROTEIN / Neurodevelopmental disorders / synapse formation
Function / homology
Function and homology information


postsynaptic specialization organization / MAP2K and MAPK activation / extrinsic component of postsynaptic density membrane / regulation of signal transduction / postsynaptic density / intracellular signal transduction / neuronal cell body / protein kinase binding / glutamatergic synapse / identical protein binding ...postsynaptic specialization organization / MAP2K and MAPK activation / extrinsic component of postsynaptic density membrane / regulation of signal transduction / postsynaptic density / intracellular signal transduction / neuronal cell body / protein kinase binding / glutamatergic synapse / identical protein binding / plasma membrane / 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. / : / 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. / : / 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 / PH-like domain superfamily
Similarity search - Domain/homology
Sterile alpha motif domain-containing protein 12 / Connector enhancer of kinase suppressor of ras 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsLin, Z. / Chen, K. / Zhang, M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: J.Mol.Biol. / Year: 2025
Title: SAMD12 as a Master Regulator of MAP4Ks by Decoupling Kinases From the CNKSR2 Scaffold.
Authors: Pan, W. / Lin, Z. / Chen, S. / Li, J. / Wang, Y. / Chen, K. / Zhang, M.
History
DepositionOct 16, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 12, 2025Provider: repository / Type: Initial release
Revision 1.1Mar 19, 2025Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Connector enhancer of kinase suppressor of ras 2
B: Sterile alpha motif domain-containing protein 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9363
Polymers46,8442
Non-polymers921
Water19811
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3330 Å2
ΔGint-16 kcal/mol
Surface area18520 Å2
MethodPISA
2
A: Connector enhancer of kinase suppressor of ras 2
B: Sterile alpha motif domain-containing protein 12
hetero molecules

A: Connector enhancer of kinase suppressor of ras 2
B: Sterile alpha motif domain-containing protein 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,8716
Polymers93,6874
Non-polymers1842
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_564x,x-y+1,-z-1/61
Buried area9800 Å2
ΔGint-43 kcal/mol
Surface area33890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.307, 109.307, 203.484
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6

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Components

#1: Protein Connector enhancer of kinase suppressor of ras 2 / Connector enhancer of KSR 2 / CNK homolog protein 2 / CNK2


Mass: 35486.648 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cnksr2, Kiaa0902 / Production host: Escherichia coli (E. coli) / References: UniProt: Q80YA9
#2: Protein Sterile alpha motif domain-containing protein 12 / SAM domain-containing protein 12


Mass: 11356.879 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Samd12 / Production host: Escherichia coli (E. coli) / References: UniProt: Q0VE29
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 3.75 Å3/Da / Density % sol: 67.16 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES pH 7.5 10% w/v Polyethylene glycol 8,000 8% v/v Ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.85→50 Å / Num. obs: 17568 / % possible obs: 100 % / Redundancy: 20 % / Biso Wilson estimate: 51.54 Å2 / CC1/2: 0.996 / Net I/σ(I): 14.25
Reflection shellResolution: 2.85→2.9 Å / Num. unique obs: 859 / CC1/2: 0.793

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.85→48.15 Å / SU ML: 0.3875 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.1743
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2992 819 4.9 %
Rwork0.2542 15901 -
obs0.2564 16720 95.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.83 Å2
Refinement stepCycle: LAST / Resolution: 2.85→48.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2884 0 6 11 2901
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00882930
X-RAY DIFFRACTIONf_angle_d1.05683972
X-RAY DIFFRACTIONf_chiral_restr0.0514475
X-RAY DIFFRACTIONf_plane_restr0.0081508
X-RAY DIFFRACTIONf_dihedral_angle_d6.7112396
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-3.030.33081360.28372564X-RAY DIFFRACTION95.07
3.03-3.260.40191320.30662608X-RAY DIFFRACTION96.28
3.26-3.590.37471400.28252617X-RAY DIFFRACTION96.6
3.59-4.110.33291370.32152425X-RAY DIFFRACTION88.31
4.11-5.170.22291520.19192760X-RAY DIFFRACTION99.15
5.17-48.150.25961220.2232927X-RAY DIFFRACTION97.19
Refinement TLS params.Method: refined / Origin x: -49.6161487994 Å / Origin y: 37.6509381158 Å / Origin z: -1.76142305716 Å
111213212223313233
T0.318979454955 Å2-0.0129859375447 Å2-0.0297945931592 Å2-0.349321023749 Å2-0.00099595336405 Å2--0.273824230871 Å2
L1.41002955381 °2-0.116428003767 °2-0.405981453748 °2-1.12258552987 °20.0551651918737 °2--1.11944288562 °2
S-0.0749701190817 Å °-0.289528309546 Å °-0.0513095556687 Å °0.161839467486 Å °0.0401145461407 Å °-0.0833912630277 Å °-0.112025983002 Å °0.0222942318763 Å °0.0398936368944 Å °
Refinement TLS groupSelection details: all

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