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- PDB-5vyk: Crystal structure of the BRS domain of BRAF in complex with the C... -

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Basic information

Entry
Database: PDB / ID: 5vyk
TitleCrystal structure of the BRS domain of BRAF in complex with the CC-SAM domain of KSR1
ComponentsChimera protein of BRS domain of BRAF and CC-SAM domain of KSR1,Serine/threonine-protein kinase B-raf
KeywordsSIGNALING PROTEIN / BRAF / KSR1 / BRS / CC-SAM / Complex / Kinase / Pseudokinase / Signaling.
Function / homology
Function and homology information


regulation of MAP kinase activity / trehalose metabolism in response to stress / CD4-positive, alpha-beta T cell differentiation / CD4-positive or CD8-positive, alpha-beta T cell lineage commitment / negative regulation of synaptic vesicle exocytosis / head morphogenesis / MAP-kinase scaffold activity / Signalling to p38 via RIT and RIN / myeloid progenitor cell differentiation / ARMS-mediated activation ...regulation of MAP kinase activity / trehalose metabolism in response to stress / CD4-positive, alpha-beta T cell differentiation / CD4-positive or CD8-positive, alpha-beta T cell lineage commitment / negative regulation of synaptic vesicle exocytosis / head morphogenesis / MAP-kinase scaffold activity / Signalling to p38 via RIT and RIN / myeloid progenitor cell differentiation / ARMS-mediated activation / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / endothelial cell apoptotic process / negative regulation of fibroblast migration / positive regulation of glucose transmembrane transport / establishment of protein localization to membrane / mitogen-activated protein kinase kinase binding / regulation of T cell differentiation / Negative feedback regulation of MAPK pathway / positive regulation of axonogenesis / Frs2-mediated activation / 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 / MAP kinase kinase kinase activity / negative regulation of endothelial cell apoptotic process / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of stress fiber assembly / 14-3-3 protein binding / response to cAMP / cellular response to calcium ion / ERK1 and ERK2 cascade / cAMP-mediated signaling / substrate adhesion-dependent cell spreading / cellular response to nerve growth factor stimulus / thymus development / long-term synaptic potentiation / animal organ morphogenesis / Spry regulation of FGF signaling / RAF activation / Signaling by high-kinase activity BRAF mutants / visual learning / MAP2K and MAPK activation / epidermal growth factor receptor signaling pathway / response to peptide hormone / ruffle membrane / 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 / cellular response to xenobiotic stimulus / presynapse / positive regulation of peptidyl-serine phosphorylation / T cell differentiation in thymus / T cell receptor signaling pathway / regulation of cell population proliferation / cell body / scaffold protein binding / negative regulation of neuron apoptotic process / Ras protein signal transduction / positive regulation of MAPK cascade / positive regulation of ERK1 and ERK2 cascade / non-specific serine/threonine protein kinase / protein kinase activity / neuron projection / phosphorylation / protein phosphorylation / intracellular membrane-bounded organelle / protein serine kinase activity / protein serine/threonine kinase activity / calcium ion binding / protein-containing complex binding / endoplasmic reticulum membrane / positive regulation of gene expression / negative regulation of apoptotic process / endoplasmic reticulum / protein-containing complex / mitochondrion / ATP binding / membrane / identical protein binding / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
SAM like domain present in kinase suppressor RAS 1 / Kinase suppressor RAS 1, N-terminal helical hairpin / Kinase suppressor RAS 1, N-terminal helical hairpin superfamily / Kinase suppressor RAS 1 N-terminal helical hairpin / 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) ...SAM like domain present in kinase suppressor RAS 1 / Kinase suppressor RAS 1, N-terminal helical hairpin / Kinase suppressor RAS 1, N-terminal helical hairpin superfamily / Kinase suppressor RAS 1 N-terminal helical hairpin / 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 / Sterile alpha motif/pointed domain superfamily / 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 / Kinase suppressor of Ras 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.749 Å
AuthorsMaisonneuve, P. / Kurinov, I. / Marullo, S.A. / Lavoie, H. / Thevakumaran, N. / Sahmi, M. / Jin, T. / Therrien, M. / SIcheri, F.
CitationJournal: Nature / Year: 2018
Title: MEK drives BRAF activation through allosteric control of KSR proteins.
Authors: Lavoie, H. / Sahmi, M. / Maisonneuve, P. / Marullo, S.A. / Thevakumaran, N. / Jin, T. / Kurinov, I. / Sicheri, F. / Therrien, M.
History
DepositionMay 25, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2018Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Mar 7, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: Chimera protein of BRS domain of BRAF and CC-SAM domain of KSR1,Serine/threonine-protein kinase B-raf
C: Chimera protein of BRS domain of BRAF and CC-SAM domain of KSR1,Serine/threonine-protein kinase B-raf
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,3524
Polymers51,1682
Non-polymers1842
Water1,78399
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6910 Å2
ΔGint-38 kcal/mol
Surface area17970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)179.796, 54.336, 51.864
Angle α, β, γ (deg.)90.000, 106.680, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 56 through 161 or (resid 162...
21(chain C and ((resid 56 and (name N or name...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGGLNGLN(chain A and (resid 56 through 161 or (resid 162...AA56 - 16133 - 138
12TYRTYRALAALA(chain A and (resid 56 through 161 or (resid 162...AA162 - 163139 - 140
13ALAALATHRTHR(chain A and (resid 56 through 161 or (resid 162...AA33 - 17110 - 148
14ALAALATHRTHR(chain A and (resid 56 through 161 or (resid 162...AA33 - 17110 - 148
15ALAALATHRTHR(chain A and (resid 56 through 161 or (resid 162...AA33 - 17110 - 148
16ALAALATHRTHR(chain A and (resid 56 through 161 or (resid 162...AA33 - 17110 - 148
21ARGARGARGARG(chain C and ((resid 56 and (name N or name...CB5633
22ALAALATHRTHR(chain C and ((resid 56 and (name N or name...CB33 - 17110 - 148
23ALAALATHRTHR(chain C and ((resid 56 and (name N or name...CB33 - 17110 - 148
24ALAALATHRTHR(chain C and ((resid 56 and (name N or name...CB33 - 17110 - 148
25ALAALATHRTHR(chain C and ((resid 56 and (name N or name...CB33 - 17110 - 148

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Components

#1: Protein Chimera protein of BRS domain of BRAF and CC-SAM domain of KSR1,Serine/threonine-protein kinase B-raf / / Proto-oncogene B-Raf / p94 / v-Raf murine sarcoma viral oncogene homolog B1


Mass: 25583.898 Da / Num. of mol.: 2
Fragment: UNP Q8IVT5 residues 27-172, UNP F7FV05 residues 39-108
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KSR1, KSR, BRAF, BRAF1, RAFB1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8IVT5, UniProt: P15056, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 2.59 Å3/Da / Density % sol: 52.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1M Tris pH 7.5, 3.0M sodium formate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.749→50 Å / Num. obs: 47556 / % possible obs: 97.9 % / Redundancy: 3.9 % / Biso Wilson estimate: 40.89 Å2 / Net I/σ(I): 14.5
Reflection shellResolution: 1.749→1.85 Å / Num. unique obs: 6677 / CC1/2: 0.403 / Rrim(I) all: 2.81

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.749→49.641 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2392 2517 5.34 %
Rwork0.2173 44646 -
obs0.2185 47163 97.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 165.84 Å2 / Biso mean: 72.0214 Å2 / Biso min: 33.94 Å2
Refinement stepCycle: final / Resolution: 1.749→49.641 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3038 0 12 99 3149
Biso mean--78.95 61.08 -
Num. residues----405
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063114
X-RAY DIFFRACTIONf_angle_d0.754226
X-RAY DIFFRACTIONf_chiral_restr0.044502
X-RAY DIFFRACTIONf_plane_restr0.005546
X-RAY DIFFRACTIONf_dihedral_angle_d17.3651918
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1040X-RAY DIFFRACTION9.359TORSIONAL
12C1040X-RAY DIFFRACTION9.359TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7494-1.78310.58811180.53112172229086
1.7831-1.81950.56081340.49182361249594
1.8195-1.8590.48161320.432471260396
1.859-1.90230.41791430.38262444258797
1.9023-1.94990.34441260.34282520264697
1.9499-2.00260.3621470.33632472261997
2.0026-2.06150.33051610.2912436259797
2.0615-2.1280.26771400.23572515265598
2.128-2.20410.29651250.21832513263898
2.2041-2.29240.22791630.21312503266699
2.2924-2.39670.22141330.21912485261899
2.3967-2.5230.25461480.22892503265198
2.523-2.68110.27671400.2312554269499
2.6811-2.88810.32631390.23512539267899
2.8881-3.17870.23291330.21912534266799
3.1787-3.63850.23721490.20212523267298
3.6385-4.58370.16441400.16822528266898
4.5837-49.66130.22131460.20762573271997
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)
14.170.06250.33735.7495-1.88647.07480.2984-0.4745-0.34330.207-0.2008-0.17380.3688-0.14830.0340.3137-0.0296-0.03390.46360.06710.29962.95230.6247.637
20.721-0.4351-0.48032.5872.78943.0084-0.2439-0.3326-0.34350.791-0.00640.011.15680.246-1.16661.4733-0.3138-0.52541.3751.54830.625663.49318.31228.56
35.06410.612.13985.4918-1.59477.32390.725-0.1219-1.73980.04960.4051-0.09921.95790.77871.50240.51970.1942-0.24920.64070.28950.695971.80224.31810.792
48.0808-1.15571.63883.3715-0.82332.0226-0.08970.5479-0.33980.19650.0625-1.10381.77980.9943-0.45640.561-0.0182-0.18011.45830.09720.763182.01827.81416.262
56.3362-1.58915.41774.8506-1.40444.7815-0.7653-0.24142.30440.19620.1985-0.1702-1.00641.08280.38040.6902-0.048-0.28581.00540.04661.244875.27336.59613.983
67.54184.0812-6.28473.9253-4.41269.94610.01880.5758-0.1251-1.00040.0594-0.29940.3633-0.1347-0.12580.6825-0.04020.03730.5236-0.0280.293357.7532.973-7.654
77.44232.7343-5.06764.432-1.54478.02890.40060.17170.2826-0.51870.15960.0279-0.1207-0.8509-0.47140.49-0.05230.05850.5022-0.01980.277651.67337.335-3.043
85.32151.3219-1.45995.6764-1.63277.460.1650.57130.8624-0.2281-0.2516-0.4364-0.63930.3671-0.10480.3011-0.02450.050.48550.15770.445366.03754.5421.415
93.24760.6805-2.38962.43771.02667.46270.4826-0.7523-0.13690.1966-0.2767-0.50980.11861.0088-0.36390.4218-0.1084-0.07281.01990.07770.809479.82552.5767.496
104.11360.5744-2.25667.3826-3.14663.50120.0623-0.31770.31441.39880.02760.3148-0.781-0.2952-0.3780.58530.03610.17410.5051-0.00880.34251.38850.03213.295
111.6051.4437-3.53171.3092-3.19497.83580.30492.05551.0249-0.3074-1.1541-1.1032-1.78560.74990.34020.74020.13610.15121.06440.32730.665450.53558.364-9.522
126.42020.777-2.01024.6765-1.57522.96660.20970.05680.07740.52540.04640.31540.6681-0.5262-0.18970.58640.00140.05850.54550.01870.274148.62543.1568.968
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 33:93 )A33 - 93
2X-RAY DIFFRACTION2( CHAIN A AND RESID 94:100 )A94 - 100
3X-RAY DIFFRACTION3( CHAIN A AND RESID 101:124 )A101 - 124
4X-RAY DIFFRACTION4( CHAIN A AND RESID 125:153 )A125 - 153
5X-RAY DIFFRACTION5( CHAIN A AND RESID 154:171 )A154 - 171
6X-RAY DIFFRACTION6( CHAIN C AND RESID 1042:1068 )C1042 - 1068
7X-RAY DIFFRACTION7( CHAIN C AND RESID 1069:1105 )C1069 - 1105
8X-RAY DIFFRACTION8( CHAIN C AND RESID 33:108 )C33 - 108
9X-RAY DIFFRACTION9( CHAIN C AND RESID 109:171 )C109 - 171
10X-RAY DIFFRACTION10( CHAIN A AND RESID 1042:1068 )A1042 - 1068
11X-RAY DIFFRACTION11( CHAIN A AND RESID 1069:1075 )A1069 - 1075
12X-RAY DIFFRACTION12( CHAIN A AND RESID 1076:1104 )A1076 - 1104

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