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- PDB-3nkx: Impaired binding of 14-3-3 to Raf1 is linked to Noonan and LEOPAR... -

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Basic information

Entry
Database: PDB / ID: 3nkx
TitleImpaired binding of 14-3-3 to Raf1 is linked to Noonan and LEOPARD syndrome
Components
  • 14-3-3 protein zeta/delta
  • Peptide of RAF proto-oncogene serine/threonine-protein kinase
KeywordsPROTEIN BINDING / SIGNALING PROTEIN
Function / homology
Function and homology information


death-inducing signaling complex assembly / synaptic target recognition / Golgi reassembly / intermediate filament cytoskeleton organization / NOTCH4 Activation and Transmission of Signal to the Nucleus / establishment of Golgi localization / type B pancreatic cell proliferation / regulation of Rho protein signal transduction / respiratory system process / regulation of synapse maturation ...death-inducing signaling complex assembly / synaptic target recognition / Golgi reassembly / intermediate filament cytoskeleton organization / NOTCH4 Activation and Transmission of Signal to the Nucleus / establishment of Golgi localization / type B pancreatic cell proliferation / regulation of Rho protein signal transduction / respiratory system process / regulation of synapse maturation / tube formation / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / Rap1 signalling / insulin secretion involved in cellular response to glucose stimulus / negative regulation of protein localization to nucleus / Negative feedback regulation of MAPK pathway / KSRP (KHSRP) binds and destabilizes mRNA / IFNG signaling activates MAPKs / GP1b-IX-V activation signalling / ERBB2-ERBB3 signaling pathway / face development / pseudopodium / neurotrophin TRK receptor signaling pathway / regulation of cell differentiation / thyroid gland development / Regulation of localization of FOXO transcription factors / somatic stem cell population maintenance / Interleukin-3, Interleukin-5 and GM-CSF signaling / extrinsic apoptotic signaling pathway via death domain receptors / phosphoserine residue binding / MAP kinase kinase kinase activity / Activation of BAD and translocation to mitochondria / type II interferon-mediated signaling pathway / negative regulation of protein-containing complex assembly / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / protein targeting / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Schwann cell development / regulation of ERK1 and ERK2 cascade / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / cellular response to glucose starvation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / activation of adenylate cyclase activity / positive regulation of peptidyl-serine phosphorylation / negative regulation of TORC1 signaling / response to muscle stretch / myelination / Transcriptional and post-translational regulation of MITF-M expression and activity / ERK1 and ERK2 cascade / CD209 (DC-SIGN) signaling / protein sequestering activity / insulin-like growth factor receptor signaling pathway / negative regulation of innate immune response / hippocampal mossy fiber to CA3 synapse / thymus development / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / Deactivation of the beta-catenin transactivating complex / lung development / RAF activation / wound healing / Negative regulation of NOTCH4 signaling / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / regulation of protein stability / Stimuli-sensing channels / Signaling by RAF1 mutants / Negative regulation of MAPK pathway / 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 / MAPK cascade / intracellular protein localization / insulin receptor signaling pathway / melanosome / regulation of apoptotic process / angiogenesis / DNA-binding transcription factor binding / vesicle / blood microparticle / mitochondrial outer membrane / transmembrane transporter binding / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity
Similarity search - Function
Raf-like Ras-binding domain / Raf-like Ras-binding / Ras-binding domain (RBD) profile. / Raf-like Ras-binding domain / Diacylglycerol/phorbol-ester binding / 14-3-3 domain / : / Phorbol esters/diacylglycerol binding domain (C1 domain) / Delta-Endotoxin; domain 1 / Zinc finger phorbol-ester/DAG-type signature. ...Raf-like Ras-binding domain / Raf-like Ras-binding / Ras-binding domain (RBD) profile. / Raf-like Ras-binding domain / Diacylglycerol/phorbol-ester binding / 14-3-3 domain / : / Phorbol esters/diacylglycerol binding domain (C1 domain) / Delta-Endotoxin; domain 1 / Zinc finger phorbol-ester/DAG-type signature. / Zinc finger phorbol-ester/DAG-type profile. / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) / Protein kinase C-like, phorbol ester/diacylglycerol-binding domain / C1-like domain superfamily / 14-3-3 proteins signature 2. / 14-3-3 protein, conserved site / 14-3-3 proteins signature 1. / 14-3-3 protein / 14-3-3 homologues / 14-3-3 domain / 14-3-3 domain superfamily / 14-3-3 protein / Ubiquitin-like domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
PROPANOIC ACID / RAF proto-oncogene serine/threonine-protein kinase / 14-3-3 protein zeta/delta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsSchumacher, B. / Weyand, M. / Ottmann, C.
CitationJournal: Mol.Cell.Biol. / Year: 2010
Title: Impaired binding of 14-3-3 to C-RAF in Noonan syndrome suggests new approaches in diseases with increased Ras signaling
Authors: Molzan, M. / Schumacher, B. / Ottmann, C. / Baljuls, A. / Polzien, L. / Weyand, M. / Thiel, P. / Rose, R. / Rose, M. / Kuhenne, P. / Kaiser, M. / Rapp, U.R. / Kuhlmann, J. / Ottmann, C.
History
DepositionJun 21, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2014Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 14-3-3 protein zeta/delta
B: 14-3-3 protein zeta/delta
P: Peptide of RAF proto-oncogene serine/threonine-protein kinase
Q: Peptide of RAF proto-oncogene serine/threonine-protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,0455
Polymers57,9714
Non-polymers741
Water3,297183
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4470 Å2
ΔGint-24 kcal/mol
Surface area22530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.410, 83.850, 111.670
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein 14-3-3 protein zeta/delta / Protein kinase C inhibitor protein 1 / KCIP-1


Mass: 27777.092 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: YWHAZ / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 / References: UniProt: P63104
#2: Protein/peptide Peptide of RAF proto-oncogene serine/threonine-protein kinase / Proto-oncogene c-RAF / cRaf / Raf-1


Mass: 1208.175 Da / Num. of mol.: 2
Fragment: phosphorylated C-Raf peptide, UNP residues 255-264
Source method: obtained synthetically / Details: This sequence occurs naturally in humans.
References: UniProt: P04049, non-specific serine/threonine protein kinase
#3: Chemical ChemComp-PPI / PROPANOIC ACID


Mass: 74.079 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.92 Å3/Da / Density % sol: 57.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M (Sodium propionate, sodium cacodylate, BIS-TRIS propane), 27% PEG 1500, 2mM DTT, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97809 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 25, 2007
RadiationMonochromator: LN2 cooled fixed-exit Si(111) monochromator, Sagittal-horizontal; Dynamically bendable mirror, Meridional-vertical
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97809 Å / Relative weight: 1
ReflectionResolution: 2.4→60.76 Å / Num. all: 27180 / Num. obs: 27180 / % possible obs: 99.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.052 / Rsym value: 0.0495
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 5 % / Rmerge(I) obs: 0.416 / Mean I/σ(I) obs: 4.02 / Num. unique all: 3084 / % possible all: 100

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.5.0102refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1QJB

1qjb


Resolution: 2.4→60.76 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.924 / SU B: 6.827 / SU ML: 0.161 / Cross valid method: THROUGHOUT / ESU R Free: 0.236 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24733 1359 5 %RANDOM
Rwork0.20408 ---
obs0.20622 25804 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.024 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å20 Å20 Å2
2--2.1 Å20 Å2
3----1.9 Å2
Refinement stepCycle: LAST / Resolution: 2.4→60.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3730 0 5 183 3918
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0223797
X-RAY DIFFRACTIONr_angle_refined_deg1.991.9725126
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6975473
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.03525.246183
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.02915.043699
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1391523
X-RAY DIFFRACTIONr_chiral_restr0.1610.2579
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022829
X-RAY DIFFRACTIONr_mcbond_it1.1481.52368
X-RAY DIFFRACTIONr_mcangle_it2.22723788
X-RAY DIFFRACTIONr_scbond_it3.55331429
X-RAY DIFFRACTIONr_scangle_it5.8814.51336
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.375 100 -
Rwork0.266 1889 -
obs--100 %

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