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- PDB-4fj3: 14-3-3 isoform zeta in complex with a diphoyphorylated C-RAF peptide -

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Basic information

Entry
Database: PDB / ID: 4fj3
Title14-3-3 isoform zeta in complex with a diphoyphorylated C-RAF peptide
Components
  • 14-3-3 protein zeta/delta
  • RAF proto-oncogene serine/threonine-protein kinase
KeywordsPROTEIN BINDING/TRANSFERASE / 14-3-3 fold / all alpha-helical / adapter protein / PROTEIN BINDING-TRANSFERASE complex
Function / homology
Function and homology information


death-inducing signaling complex assembly / Golgi reassembly / intermediate filament cytoskeleton organization / regulation of synapse maturation / NOTCH4 Activation and Transmission of Signal to the Nucleus / establishment of Golgi localization / type B pancreatic cell proliferation / regulation of Rho protein signal transduction / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling ...death-inducing signaling complex assembly / Golgi reassembly / intermediate filament cytoskeleton organization / regulation of synapse maturation / NOTCH4 Activation and Transmission of Signal to the Nucleus / establishment of Golgi localization / type B pancreatic cell proliferation / regulation of Rho protein signal transduction / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / Rap1 signalling / regulation of cell motility / 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 / regulation of cell differentiation / face development / pseudopodium / somatic stem cell population maintenance / neurotrophin TRK receptor signaling pathway / thyroid gland development / Regulation of localization of FOXO transcription factors / Interleukin-3, Interleukin-5 and GM-CSF signaling / extrinsic apoptotic signaling pathway via death domain receptors / MAP kinase kinase kinase activity / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / negative regulation of protein-containing complex assembly / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / cellular response to glucose starvation / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / Schwann cell development / type II interferon-mediated signaling pathway / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / RHO GTPases activate PKNs / negative regulation of TORC1 signaling / activation of adenylate cyclase activity / response to muscle stretch / myelination / negative regulation of innate immune response / CD209 (DC-SIGN) signaling / regulation of ERK1 and ERK2 cascade / protein sequestering activity / insulin-like growth factor receptor signaling pathway / thymus development / Translocation of SLC2A4 (GLUT4) to the plasma membrane / Deactivation of the beta-catenin transactivating complex / TP53 Regulates Metabolic Genes / Negative regulation of NOTCH4 signaling / RAF activation / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / wound healing / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / Stimuli-sensing channels / Negative regulation of MAPK 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 / MAPK cascade / Signaling by BRAF and RAF1 fusions / melanosome / insulin receptor signaling pathway / positive regulation of peptidyl-serine phosphorylation / regulation of apoptotic process / DNA-binding transcription factor binding / blood microparticle / vesicle / mitochondrial outer membrane / transmembrane transporter binding / positive regulation of MAPK cascade / non-specific serine/threonine protein kinase / protein kinase activity / cadherin binding / negative regulation of cell population proliferation / protein phosphorylation / focal adhesion / protein serine kinase activity / protein serine/threonine kinase activity / glutamatergic synapse / apoptotic process / ubiquitin protein ligase binding / negative regulation of apoptotic process / protein kinase binding / Golgi apparatus / negative regulation of transcription by RNA polymerase II / enzyme binding / signal transduction / positive regulation of transcription by RNA polymerase II / mitochondrion / extracellular space / RNA binding / extracellular exosome / nucleoplasm
Similarity search - Function
14-3-3 domain / Raf-like Ras-binding domain / Raf-like Ras-binding / Ras-binding domain (RBD) profile. / Raf-like Ras-binding domain / Delta-Endotoxin; domain 1 / Diacylglycerol/phorbol-ester binding / Phorbol esters/diacylglycerol binding domain (C1 domain) / Zinc finger phorbol-ester/DAG-type signature. / Zinc finger phorbol-ester/DAG-type profile. ...14-3-3 domain / Raf-like Ras-binding domain / Raf-like Ras-binding / Ras-binding domain (RBD) profile. / Raf-like Ras-binding domain / Delta-Endotoxin; domain 1 / Diacylglycerol/phorbol-ester binding / Phorbol esters/diacylglycerol binding domain (C1 domain) / 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
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 / molecular replacement / Resolution: 1.95 Å
AuthorsOttmann, C. / Molzan, M.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: Synergistic binding of the phosphorylated S233- and S259-binding sites of C-RAF to one 14-3-3zeta dimer
Authors: Molzan, M. / Ottmann, C.
History
DepositionJun 11, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 14-3-3 protein zeta/delta
B: 14-3-3 protein zeta/delta
P: RAF proto-oncogene serine/threonine-protein kinase


Theoretical massNumber of molelcules
Total (without water)57,6253
Polymers57,6253
Non-polymers00
Water10,575587
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3760 Å2
ΔGint-25 kcal/mol
Surface area21950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.140, 102.430, 113.890
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1115A1 - 300
2115B1 - 300

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Components

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


Mass: 26720.217 Da / Num. of mol.: 2 / Fragment: UNP residues 1-230
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: YWHAZ / Production host: Escherichia coli (E. coli) / References: UniProt: P63104
#2: Protein/peptide RAF proto-oncogene serine/threonine-protein kinase / Proto-oncogene c-RAF / cRaf / Raf-1


Mass: 4184.204 Da / Num. of mol.: 1 / Fragment: UNP residues 229-264 / Source method: obtained synthetically / Details: synthetic peptide / Source: (synth.) Homo sapiens (human)
References: UniProt: P04049, non-specific serine/threonine protein kinase
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 587 / 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: 3.65 Å3/Da / Density % sol: 66.31 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M Na-acetate pH 7.0, 0.8 M NaH2PO4 and 1.2 M K2HPO4 , VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9778 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 14, 2011
RadiationMonochromator: Al2/Al2 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. all: 62201 / Num. obs: 61869 / % possible obs: 99.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Biso Wilson estimate: 36.724 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 19.57
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.95-20.4364.31238794451199.5
2-2.10.2886.24405937699199.4
2.1-2.20.1828.97318006376199.2
2.2-2.30.12812.47283755312199.5
2.3-2.50.09316.08448018295199.3
2.5-30.05922.736365312346199.6
3-40.04133.39513289912199.8
4-60.03837.05264905193199.5
6-100.03635.6582021762199.2
10-200.03438.042531523196.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMAC5.6.0093refinement
PDB_EXTRACT3.11data extraction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→46.73 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.947 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 5.167 / SU ML: 0.068 / Cross valid method: THROUGHOUT / σ(F): 4 / ESU R: 0.15 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.208 3094 5 %RANDOM
Rwork0.1586 ---
obs0.1611 61868 99.46 %-
all-62201 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 87.56 Å2 / Biso mean: 35.2967 Å2 / Biso min: 14.65 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å20 Å2
2--1.03 Å20 Å2
3----0.96 Å2
Refinement stepCycle: LAST / Resolution: 1.95→46.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3609 0 0 587 4196
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0223860
X-RAY DIFFRACTIONr_angle_refined_deg1.7241.975241
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9465503
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.33324.924197
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.04915.041737
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4851529
X-RAY DIFFRACTIONr_chiral_restr0.1260.2585
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022919
X-RAY DIFFRACTIONr_rigid_bond_restr4.498310953
X-RAY DIFFRACTIONr_sphericity_free18.4125588
X-RAY DIFFRACTIONr_sphericity_bonded13.82653784
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
849MEDIUM POSITIONAL0.20.5
786LOOSE POSITIONAL0.535
849MEDIUM THERMAL3.382
786LOOSE THERMAL4.9710
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.199 218 -
Rwork0.143 4009 -
all-4227 -
obs--99.39 %

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