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- PDB-6xag: Apo BRAF dimer bound to 14-3-3 -

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Basic information

Entry
Database: PDB / ID: 6xag
TitleApo BRAF dimer bound to 14-3-3
Components
  • 14-3-3 protein zeta/delta
  • Serine/threonine-protein kinase B-raf
KeywordsSIGNALING PROTEIN/Transferase / Kinase / SIGNALING PROTEIN / SIGNALING PROTEIN-Transferase complex
Function / homology
Function and homology information


Golgi reassembly / synaptic target recognition / respiratory system process / NOTCH4 Activation and Transmission of Signal to the Nucleus / regulation of synapse maturation / CD4-positive, alpha-beta T cell differentiation / trehalose metabolism in response to stress / CD4-positive or CD8-positive, alpha-beta T cell lineage commitment / establishment of Golgi localization / negative regulation of synaptic vesicle exocytosis ...Golgi reassembly / synaptic target recognition / respiratory system process / NOTCH4 Activation and Transmission of Signal to the Nucleus / regulation of synapse maturation / CD4-positive, alpha-beta T cell differentiation / trehalose metabolism in response to stress / CD4-positive or CD8-positive, alpha-beta T cell lineage commitment / establishment of Golgi localization / negative regulation of synaptic vesicle exocytosis / Signalling to p38 via RIT and RIN / head morphogenesis / myeloid progenitor cell differentiation / tube formation / ARMS-mediated activation / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / endothelial cell apoptotic process / Rap1 signalling / negative regulation of fibroblast migration / positive regulation of glucose transmembrane transport / establishment of protein localization to membrane / negative regulation of protein localization to nucleus / mitogen-activated protein kinase kinase binding / regulation of T cell differentiation / Negative feedback regulation of MAPK pathway / KSRP (KHSRP) binds and destabilizes mRNA / positive regulation of axonogenesis / Frs2-mediated activation / GP1b-IX-V activation signalling / stress fiber assembly / positive regulation of axon regeneration / face development / synaptic vesicle exocytosis / somatic stem cell population maintenance / MAP kinase kinase activity / thyroid gland development / Regulation of localization of FOXO transcription factors / Interleukin-3, Interleukin-5 and GM-CSF signaling / phosphoserine residue binding / MAP kinase kinase kinase activity / Activation of BAD and translocation to mitochondria / protein targeting / 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 / negative regulation of endothelial cell apoptotic process / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / positive regulation of substrate adhesion-dependent cell spreading / RHO GTPases activate PKNs / positive regulation of stress fiber assembly / negative regulation of TORC1 signaling / response to cAMP / protein sequestering activity / cellular response to calcium ion / ERK1 and ERK2 cascade / negative regulation of innate immune response / hippocampal mossy fiber to CA3 synapse / substrate adhesion-dependent cell spreading / regulation of ERK1 and ERK2 cascade / cellular response to nerve growth factor stimulus / thymus development / Translocation of SLC2A4 (GLUT4) to the plasma membrane / Deactivation of the beta-catenin transactivating complex / long-term synaptic potentiation / TP53 Regulates Metabolic Genes / animal organ morphogenesis / Negative regulation of NOTCH4 signaling / RAF activation / Spry regulation of FGF signaling / lung development / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / visual learning / regulation of protein stability / epidermal growth factor receptor signaling pathway / response to peptide hormone / 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 / cellular response to xenobiotic stimulus / presynapse / positive regulation of peptidyl-serine phosphorylation / T cell receptor signaling pathway / regulation of cell population proliferation / cell body / T cell differentiation in thymus / scaffold protein binding / angiogenesis / DNA-binding transcription factor binding / vesicle / transmembrane transporter binding / negative regulation of neuron apoptotic process / Ras protein signal transduction / positive regulation of ERK1 and ERK2 cascade
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 / 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 ...Raf-like Ras-binding domain / Raf-like Ras-binding / Ras-binding domain (RBD) profile. / Raf-like Ras-binding domain / 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 / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Ubiquitin-like domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / 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
Similarity search - Domain/homology
Serine/threonine-protein kinase B-raf / 14-3-3 protein zeta/delta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsLiau, N.P.D. / Hymowitz, S.G. / Sudhamsu, J.
CitationJournal: Biochemistry / Year: 2020
Title: Dimerization Induced by C-Terminal 14-3-3 Binding Is Sufficient for BRAF Kinase Activation.
Authors: Liau, N.P.D. / Venkatanarayan, A. / Quinn, J.G. / Phung, W. / Malek, S. / Hymowitz, S.G. / Sudhamsu, J.
History
DepositionJun 4, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 4, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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
C: Serine/threonine-protein kinase B-raf
D: Serine/threonine-protein kinase B-raf
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,1585
Polymers119,0954
Non-polymers621
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8820 Å2
ΔGint-27 kcal/mol
Surface area47050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.504, 115.752, 153.092
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
11(chain A and (resid 1 through 202 or resid 210 through 229))
21(chain B and resid 1 through 229)
12(chain C and (resid 449 through 464 or resid 466 or resid 470 through 732))
22(chain D and (resid 449 through 464 or resid 469 through 607 or resid 615 through 732))

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111METMETGLUGLU(chain A and (resid 1 through 202 or resid 210 through 229))AA1 - 2023 - 204
121SERSERTHRTHR(chain A and (resid 1 through 202 or resid 210 through 229))AA210 - 229212 - 231
211METMETTHRTHR(chain B and resid 1 through 229)BB1 - 2293 - 231
112ASPASPGLYGLY(chain C and (resid 449 through 464 or resid 466 or resid 470 through 732))CC449 - 4644 - 19
122GLYGLYGLYGLY(chain C and (resid 449 through 464 or resid 466 or resid 470 through 732))CC46621
132THRTHRSERSER(chain C and (resid 449 through 464 or resid 466 or resid 470 through 732))CC470 - 73225 - 287
212ASPASPGLYGLY(chain D and (resid 449 through 464 or resid 469 through 607 or resid 615 through 732))DD449 - 4644 - 19
222GLYGLYSERSER(chain D and (resid 449 through 464 or resid 469 through 607 or resid 615 through 732))DD469 - 60724 - 162
232GLYGLYSERSER(chain D and (resid 449 through 464 or resid 469 through 607 or resid 615 through 732))DD615 - 732170 - 287

NCS ensembles :
ID
1
2

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Components

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


Mass: 26460.891 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) / References: UniProt: P63104
#2: Protein Serine/threonine-protein kinase B-raf / Proto-oncogene B-Raf / p94 / v-Raf murine sarcoma viral oncogene homolog B1


Mass: 33086.852 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRAF, BRAF1, RAFB1 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P15056, non-specific serine/threonine protein kinase
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
Has ligand of interestN

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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: 2.36 Å3/Da / Density % sol: 47.92 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100 mM HEPES pH 7.5, 200 mM ammonium sulfate, 23% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.3→92.33 Å / Num. obs: 16106 / % possible obs: 94.31 % / Redundancy: 2 % / CC1/2: 0.998 / Rrim(I) all: 0.181 / Net I/σ(I): 8.13
Reflection shellResolution: 3.3→3.418 Å / Mean I/σ(I) obs: 1.14 / Num. unique obs: 3218 / CC1/2: 0.526 / Rrim(I) all: 0.9917 / % possible all: 98.38

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Processing

Software
NameVersionClassification
PHENIX1.17.1-3660_finalrefinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6U2H

6u2h


Resolution: 3.3→92.33 Å / SU ML: 0.55 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 35.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2997 658 4.09 %
Rwork0.2497 15448 -
obs0.2518 16106 94.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 292.7 Å2 / Biso mean: 132.0348 Å2 / Biso min: 61.21 Å2
Refinement stepCycle: final / Resolution: 3.3→92.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8059 0 4 0 8063
Biso mean--75.91 --
Num. residues----1007
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2037X-RAY DIFFRACTION11.387TORSIONAL
12B2037X-RAY DIFFRACTION11.387TORSIONAL
21C2634X-RAY DIFFRACTION11.387TORSIONAL
22D2634X-RAY DIFFRACTION11.387TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.3-3.550.44351220.36412861298390
3.55-3.910.30711120.30442704281684
3.91-4.480.28351390.252632523391100
4.48-5.640.3181390.24163233337299
5.64-92.330.27091460.22043398354499
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.3585-0.17450.56342.8351.37354.99420.07040.2812-0.1018-0.18790.1134-0.02060.71020.435-0.05390.73310.096-0.0520.71610.04380.872811.5842-14.57221.2887
23.2373-0.81220.29552.3551-0.73563.0682-0.2163-0.11310.6249-0.13290.04560.546-0.9347-0.8132-0.06440.95330.2777-0.09071.059-0.29371.2552-11.200814.3527.7069
32.53390.0355-0.33661.5312-0.06553.6901-0.10060.2037-0.068-0.2650.04910.20080.3437-0.375-0.06470.99250.1627-0.04650.95430.07290.8333-5.1155-11.0804-29.697
42.33060.5594-0.20152.5327-0.59513.3183-0.10470.25590.6425-0.13180.21790.0563-0.77130.1918-0.01690.96570.10970.10560.8138-0.01210.897217.258912.2864-35.9389
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 1 through 230)A1 - 230
2X-RAY DIFFRACTION2(chain 'B' and resid 0 through 229)B0 - 229
3X-RAY DIFFRACTION3(chain 'C' and resid 449 through 732)C449 - 732
4X-RAY DIFFRACTION4(chain 'D' and resid 448 through 733)D448 - 733

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